Starting phenix.real_space_refine on Tue Jan 14 00:18:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vae_43089/01_2025/8vae_43089.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vae_43089/01_2025/8vae_43089.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vae_43089/01_2025/8vae_43089.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vae_43089/01_2025/8vae_43089.map" model { file = "/net/cci-nas-00/data/ceres_data/8vae_43089/01_2025/8vae_43089.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vae_43089/01_2025/8vae_43089.cif" } resolution = 3.7 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= 0.006 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 41 5.16 5 C 2939 2.51 5 N 782 2.21 5 O 891 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 4653 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: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 30 Unusual residues: {'SAL': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 4.77, per 1000 atoms: 1.03 Number of scatterers: 4653 At special positions: 0 Unit cell: (66.788, 91.692, 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 41 16.00 O 891 8.00 N 782 7.00 C 2939 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=2.03 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=2.02 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=2.04 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 289 " distance=2.04 Simple disulfide: pdb=" SG CYS A 316 " - pdb=" SG CYS A 361 " distance=2.04 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=1.86 Simple disulfide: pdb=" SG CYS A 558 " - pdb=" SG CYS A 567 " distance=2.01 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 1.21 Conformation dependent library (CDL) restraints added in 571.3 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: 32 helices and 0 sheets defined 82.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 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 79 removed outlier: 3.949A pdb=" N THR A 76 " --> pdb=" O ASP A 72 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N VAL A 77 " --> pdb=" O LYS A 73 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALA A 78 " --> pdb=" O LEU A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 93 Processing helix chain 'A' and resid 96 through 105 Processing helix chain 'A' and resid 119 through 130 Processing helix chain 'A' and resid 131 through 146 Processing helix chain 'A' and resid 150 through 168 Processing helix chain 'A' and resid 174 through 223 removed outlier: 3.761A pdb=" N LEU A 178 " --> pdb=" O LYS A 174 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LEU A 179 " --> pdb=" O ALA A 175 " (cutoff:3.500A) Proline residue: A 180 - end of helix removed outlier: 7.432A pdb=" N GLU A 208 " --> pdb=" O GLN A 204 " (cutoff:3.500A) removed outlier: 9.321A pdb=" N ARG A 209 " --> pdb=" O LYS A 205 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA A 210 " --> pdb=" O PHE A 206 " (cutoff:3.500A) removed outlier: 4.056A 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 266 Processing helix chain 'A' and resid 267 through 272 removed outlier: 3.607A pdb=" N ILE A 271 " --> pdb=" O ASN A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 279 removed outlier: 3.594A pdb=" N LYS A 276 " --> pdb=" O SER A 273 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLU A 277 " --> pdb=" O LYS A 274 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N CYS A 279 " --> pdb=" O LYS A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 292 removed outlier: 3.526A pdb=" N GLU A 292 " --> pdb=" O HIS A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 310 removed outlier: 3.672A pdb=" N PHE A 309 " --> pdb=" O LEU A 305 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL A 310 " --> pdb=" O ALA A 306 " (cutoff:3.500A) No H-bonds generated for '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: 3.565A pdb=" N ARG A 337 " --> pdb=" O GLU A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 360 Processing helix chain 'A' and resid 365 through 371 removed outlier: 3.636A pdb=" N CYS A 369 " --> pdb=" O ASP A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 375 removed outlier: 3.887A pdb=" N ASP A 375 " --> pdb=" O LYS A 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 372 through 375' Processing helix chain 'A' and resid 376 through 399 removed outlier: 4.191A pdb=" N LEU A 380 " --> pdb=" O GLU A 376 " (cutoff:3.500A) Proline residue: A 384 - end of helix removed outlier: 3.533A pdb=" N GLN A 397 " --> pdb=" O GLU A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 415 Processing helix chain 'A' and resid 419 through 438 removed outlier: 3.880A pdb=" N GLY A 434 " --> pdb=" O LEU A 430 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER A 435 " --> pdb=" O GLY A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 466 removed outlier: 4.163A pdb=" N MET A 446 " --> pdb=" O GLU A 442 " (cutoff:3.500A) Proline residue: A 447 - end of helix removed outlier: 3.928A pdb=" N LYS A 466 " --> pdb=" O VAL A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 479 Processing helix chain 'A' and resid 483 through 491 Processing helix chain 'A' and resid 503 through 508 removed outlier: 3.609A pdb=" N THR A 506 " --> pdb=" O ASN A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 516 Processing helix chain 'A' and resid 517 through 536 Processing helix chain 'A' and resid 540 through 560 Processing helix chain 'A' and resid 563 through 582 removed outlier: 3.634A pdb=" N CYS A 567 " --> pdb=" O ASP A 563 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) 320 hydrogen bonds defined for protein. 945 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: 1.25 Time building geometry restraints manager: 1.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1538 1.34 - 1.46: 1008 1.46 - 1.58: 2150 1.58 - 1.70: 0 1.70 - 1.82: 47 Bond restraints: 4743 Sorted by residual: bond pdb=" C1 SAL A 603 " pdb=" C2 SAL A 603 " ideal model delta sigma weight residual 1.409 1.485 -0.076 2.00e-02 2.50e+03 1.44e+01 bond pdb=" C1 SAL A 602 " pdb=" C2 SAL A 602 " ideal model delta sigma weight residual 1.409 1.480 -0.071 2.00e-02 2.50e+03 1.25e+01 bond pdb=" C2 SAL A 601 " pdb=" O2 SAL A 601 " ideal model delta sigma weight residual 1.331 1.398 -0.067 2.00e-02 2.50e+03 1.13e+01 bond pdb=" N CYS A 558 " pdb=" CA CYS A 558 " ideal model delta sigma weight residual 1.456 1.487 -0.030 1.22e-02 6.72e+03 6.18e+00 bond pdb=" N CYS A 559 " pdb=" CA CYS A 559 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.27e-02 6.20e+03 5.75e+00 ... (remaining 4738 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 6180 1.64 - 3.29: 167 3.29 - 4.93: 38 4.93 - 6.58: 6 6.58 - 8.22: 5 Bond angle restraints: 6396 Sorted by residual: angle pdb=" N CYS A 559 " pdb=" CA CYS A 559 " pdb=" C CYS A 559 " ideal model delta sigma weight residual 113.41 106.51 6.90 1.22e+00 6.72e-01 3.20e+01 angle pdb=" C LYS A 557 " pdb=" N CYS A 558 " pdb=" CA CYS A 558 " ideal model delta sigma weight residual 122.60 114.38 8.22 1.56e+00 4.11e-01 2.78e+01 angle pdb=" N VAL A 469 " pdb=" CA VAL A 469 " pdb=" C VAL A 469 " ideal model delta sigma weight residual 113.71 109.69 4.02 9.50e-01 1.11e+00 1.79e+01 angle pdb=" C VAL A 315 " pdb=" N CYS A 316 " pdb=" CA CYS A 316 " ideal model delta sigma weight residual 122.06 116.46 5.60 1.86e+00 2.89e-01 9.06e+00 angle pdb=" C ALA A 569 " pdb=" N GLU A 570 " pdb=" CA GLU A 570 " ideal model delta sigma weight residual 121.52 116.39 5.13 1.84e+00 2.95e-01 7.77e+00 ... (remaining 6391 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 2608 17.56 - 35.12: 293 35.12 - 52.68: 58 52.68 - 70.24: 10 70.24 - 87.79: 13 Dihedral angle restraints: 2982 sinusoidal: 1244 harmonic: 1738 Sorted by residual: dihedral pdb=" CB CYS A 514 " pdb=" SG CYS A 514 " pdb=" SG CYS A 559 " pdb=" CB CYS A 559 " ideal model delta sinusoidal sigma weight residual -86.00 -1.59 -84.41 1 1.00e+01 1.00e-02 8.66e+01 dihedral pdb=" CB CYS A 558 " pdb=" SG CYS A 558 " pdb=" SG CYS A 567 " pdb=" CB CYS A 567 " ideal model delta sinusoidal sigma weight residual 93.00 174.19 -81.19 1 1.00e+01 1.00e-02 8.13e+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 -166.30 80.30 1 1.00e+01 1.00e-02 7.98e+01 ... (remaining 2979 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 516 0.040 - 0.079: 142 0.079 - 0.119: 40 0.119 - 0.158: 6 0.158 - 0.198: 2 Chirality restraints: 706 Sorted by residual: chirality pdb=" CB THR A 467 " pdb=" CA THR A 467 " pdb=" OG1 THR A 467 " pdb=" CG2 THR A 467 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 9.78e-01 chirality pdb=" CA GLU A 570 " pdb=" N GLU A 570 " pdb=" C GLU A 570 " pdb=" CB GLU A 570 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.15e-01 chirality pdb=" CG LEU A 408 " pdb=" CB LEU A 408 " pdb=" CD1 LEU A 408 " pdb=" CD2 LEU A 408 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.16e-01 ... (remaining 703 not shown) Planarity restraints: 834 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 568 " -0.009 2.00e-02 2.50e+03 1.71e-02 2.92e+00 pdb=" C PHE A 568 " 0.030 2.00e-02 2.50e+03 pdb=" O PHE A 568 " -0.011 2.00e-02 2.50e+03 pdb=" N ALA A 569 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 567 " -0.007 2.00e-02 2.50e+03 1.37e-02 1.89e+00 pdb=" C CYS A 567 " 0.024 2.00e-02 2.50e+03 pdb=" O CYS A 567 " -0.009 2.00e-02 2.50e+03 pdb=" N PHE A 568 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 370 " -0.008 2.00e-02 2.50e+03 7.84e-03 1.23e+00 pdb=" CG TYR A 370 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR A 370 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR A 370 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR A 370 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR A 370 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR A 370 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 370 " 0.001 2.00e-02 2.50e+03 ... (remaining 831 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1027 2.78 - 3.31: 4832 3.31 - 3.84: 7879 3.84 - 4.37: 8460 4.37 - 4.90: 14909 Nonbonded interactions: 37107 Sorted by model distance: nonbonded pdb=" OH TYR A 319 " pdb=" OE2 GLU A 358 " model vdw 2.251 3.040 nonbonded pdb=" NH1 ARG A 81 " pdb=" O GLY A 85 " model vdw 2.282 3.120 nonbonded pdb=" NE2 GLN A 221 " pdb=" O PRO A 339 " model vdw 2.312 3.120 nonbonded pdb=" NH2 ARG A 160 " pdb=" OE1 GLU A 188 " model vdw 2.379 3.120 nonbonded pdb=" ND2 ASN A 391 " pdb=" C6 SAL A 601 " model vdw 2.398 3.420 ... (remaining 37102 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: 5.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 16.440 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 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 0.076 4743 Z= 0.235 Angle : 0.675 8.222 6396 Z= 0.364 Chirality : 0.041 0.198 706 Planarity : 0.003 0.027 834 Dihedral : 15.274 87.795 1791 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % 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 (0.35), residues: 579 helix: 1.68 (0.26), residues: 411 sheet: None (None), residues: 0 loop : -0.03 (0.50), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 214 HIS 0.002 0.001 HIS A 242 PHE 0.017 0.001 PHE A 134 TYR 0.020 0.002 TYR A 370 ARG 0.002 0.001 ARG A 197 *********************** 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 56 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.597 Fit side-chains REVERT: A 174 LYS cc_start: 0.8194 (mmtm) cc_final: 0.7981 (mmtt) REVERT: A 467 THR cc_start: 0.8772 (t) cc_final: 0.8524 (p) REVERT: A 501 GLU cc_start: 0.7690 (tp30) cc_final: 0.7386 (tp30) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.1726 time to fit residues: 12.8253 Evaluate side-chains 37 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.511 ------------------------------------------------------------------------------- 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: 0.9980 chunk 43 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 15 optimal weight: 0.4980 chunk 29 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 33 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.103298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.084223 restraints weight = 11876.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.086612 restraints weight = 7054.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.088238 restraints weight = 4958.793| |-----------------------------------------------------------------------------| r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4743 Z= 0.203 Angle : 0.630 11.424 6396 Z= 0.320 Chirality : 0.042 0.230 706 Planarity : 0.004 0.027 834 Dihedral : 5.518 63.741 625 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.18 % Allowed : 6.50 % Favored : 92.32 % 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: 1.84 (0.36), residues: 579 helix: 1.77 (0.26), residues: 417 sheet: None (None), residues: 0 loop : -0.12 (0.52), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 214 HIS 0.004 0.001 HIS A 338 PHE 0.022 0.001 PHE A 127 TYR 0.017 0.002 TYR A 370 ARG 0.003 0.001 ARG A 197 *********************** 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 50 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.550 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 47 average time/residue: 0.1666 time to fit residues: 10.4765 Evaluate side-chains 35 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 33 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 550 ASP Chi-restraints excluded: chain A residue 575 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 1 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 47 optimal weight: 6.9990 chunk 6 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 54 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.102361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.082837 restraints weight = 12125.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.085191 restraints weight = 7252.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.086756 restraints weight = 5152.009| |-----------------------------------------------------------------------------| r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4743 Z= 0.204 Angle : 0.616 12.055 6396 Z= 0.308 Chirality : 0.042 0.234 706 Planarity : 0.003 0.026 834 Dihedral : 5.238 57.572 625 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.38 % Allowed : 10.24 % Favored : 88.39 % 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: 1.80 (0.35), residues: 579 helix: 1.75 (0.25), residues: 418 sheet: None (None), residues: 0 loop : -0.20 (0.51), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 214 HIS 0.003 0.001 HIS A 242 PHE 0.012 0.001 PHE A 127 TYR 0.015 0.002 TYR A 370 ARG 0.004 0.000 ARG A 197 *********************** 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 46 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 39 time to evaluate : 0.517 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 45 average time/residue: 0.1240 time to fit residues: 8.1000 Evaluate side-chains 34 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 31 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 550 ASP Chi-restraints excluded: chain A residue 575 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 1 optimal weight: 0.0370 chunk 46 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 7 optimal weight: 0.0010 chunk 21 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 53 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 overall best weight: 0.4064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.103253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.084192 restraints weight = 12240.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.086605 restraints weight = 7244.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.088226 restraints weight = 5066.765| |-----------------------------------------------------------------------------| r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 4743 Z= 0.156 Angle : 0.596 12.943 6396 Z= 0.293 Chirality : 0.040 0.232 706 Planarity : 0.003 0.028 834 Dihedral : 4.966 50.993 625 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.97 % Allowed : 11.61 % Favored : 86.42 % 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: 1.96 (0.36), residues: 579 helix: 1.84 (0.25), residues: 419 sheet: None (None), residues: 0 loop : -0.08 (0.52), residues: 160 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 0.010 0.001 PHE A 127 TYR 0.017 0.001 TYR A 370 ARG 0.003 0.000 ARG A 197 *********************** 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 47 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 37 time to evaluate : 0.585 Fit side-chains revert: symmetry clash REVERT: A 298 MET cc_start: 0.7368 (tpt) cc_final: 0.7072 (tpt) outliers start: 10 outliers final: 3 residues processed: 46 average time/residue: 0.1485 time to fit residues: 9.4471 Evaluate side-chains 33 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 30 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 550 ASP Chi-restraints excluded: chain A residue 575 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 48 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 25 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.101314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.081947 restraints weight = 12289.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.084274 restraints weight = 7363.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.085893 restraints weight = 5193.188| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4743 Z= 0.200 Angle : 0.628 13.333 6396 Z= 0.307 Chirality : 0.041 0.233 706 Planarity : 0.003 0.028 834 Dihedral : 4.864 46.488 625 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.17 % Allowed : 13.78 % Favored : 84.06 % 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: 1.92 (0.36), residues: 579 helix: 1.80 (0.25), residues: 419 sheet: None (None), residues: 0 loop : -0.05 (0.53), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 214 HIS 0.003 0.001 HIS A 288 PHE 0.007 0.001 PHE A 330 TYR 0.015 0.002 TYR A 370 ARG 0.003 0.000 ARG A 336 *********************** 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 46 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 35 time to evaluate : 0.575 Fit side-chains outliers start: 11 outliers final: 7 residues processed: 45 average time/residue: 0.1211 time to fit residues: 8.0178 Evaluate side-chains 37 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 30 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 CYS Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 169 CYS Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 550 ASP Chi-restraints excluded: chain A residue 575 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 50 optimal weight: 4.9990 chunk 1 optimal weight: 0.5980 chunk 30 optimal weight: 0.0870 chunk 35 optimal weight: 0.6980 chunk 4 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 chunk 40 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.101961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.082336 restraints weight = 12028.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.084700 restraints weight = 7001.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.086374 restraints weight = 4875.306| |-----------------------------------------------------------------------------| r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4743 Z= 0.168 Angle : 0.634 14.000 6396 Z= 0.307 Chirality : 0.040 0.231 706 Planarity : 0.003 0.032 834 Dihedral : 4.739 45.333 625 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.56 % Allowed : 15.75 % Favored : 81.69 % 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: 2.01 (0.36), residues: 579 helix: 1.89 (0.26), residues: 418 sheet: None (None), residues: 0 loop : -0.07 (0.52), residues: 161 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 0.007 0.001 PHE A 568 TYR 0.017 0.001 TYR A 370 ARG 0.002 0.000 ARG A 197 *********************** 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 47 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 34 time to evaluate : 0.533 Fit side-chains REVERT: A 554 PHE cc_start: 0.7473 (OUTLIER) cc_final: 0.6741 (t80) outliers start: 13 outliers final: 8 residues processed: 46 average time/residue: 0.1094 time to fit residues: 7.5902 Evaluate side-chains 38 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 29 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 CYS Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 169 CYS Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 550 ASP Chi-restraints excluded: chain A residue 554 PHE Chi-restraints excluded: chain A residue 575 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 28 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 chunk 7 optimal weight: 0.6980 chunk 49 optimal weight: 0.0470 chunk 31 optimal weight: 0.3980 chunk 36 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 386 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.102524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.082900 restraints weight = 12015.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.085267 restraints weight = 7106.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.086930 restraints weight = 4971.104| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4743 Z= 0.161 Angle : 0.631 14.566 6396 Z= 0.306 Chirality : 0.042 0.318 706 Planarity : 0.003 0.032 834 Dihedral : 4.680 44.223 625 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.17 % Allowed : 16.73 % Favored : 81.10 % 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: 2.07 (0.36), residues: 579 helix: 1.93 (0.25), residues: 418 sheet: None (None), residues: 0 loop : -0.04 (0.53), 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 288 PHE 0.006 0.001 PHE A 127 TYR 0.017 0.001 TYR A 370 ARG 0.002 0.000 ARG A 336 *********************** 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 43 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 32 time to evaluate : 0.526 Fit side-chains REVERT: A 298 MET cc_start: 0.6810 (tpt) cc_final: 0.6484 (tpt) REVERT: A 554 PHE cc_start: 0.7473 (OUTLIER) cc_final: 0.6618 (t80) outliers start: 11 outliers final: 7 residues processed: 42 average time/residue: 0.1023 time to fit residues: 6.6993 Evaluate side-chains 37 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 29 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 CYS Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 169 CYS Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 550 ASP Chi-restraints excluded: chain A residue 554 PHE Chi-restraints excluded: chain A residue 575 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 25 optimal weight: 0.5980 chunk 18 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 31 optimal weight: 0.1980 chunk 2 optimal weight: 0.5980 chunk 52 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.101751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.082571 restraints weight = 12321.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.084847 restraints weight = 7306.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.086464 restraints weight = 5147.563| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4743 Z= 0.175 Angle : 0.640 15.010 6396 Z= 0.311 Chirality : 0.042 0.275 706 Planarity : 0.003 0.031 834 Dihedral : 4.725 43.848 625 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.36 % Allowed : 16.34 % Favored : 81.30 % 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: 2.06 (0.36), residues: 579 helix: 1.94 (0.25), residues: 416 sheet: None (None), residues: 0 loop : -0.07 (0.52), residues: 163 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 0.006 0.001 PHE A 488 TYR 0.016 0.001 TYR A 370 ARG 0.002 0.000 ARG A 336 *********************** 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 40 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 28 time to evaluate : 0.547 Fit side-chains REVERT: A 380 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8753 (mp) REVERT: A 554 PHE cc_start: 0.7456 (OUTLIER) cc_final: 0.6628 (t80) outliers start: 12 outliers final: 7 residues processed: 39 average time/residue: 0.1052 time to fit residues: 6.5190 Evaluate side-chains 37 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 28 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 CYS Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 169 CYS Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 550 ASP Chi-restraints excluded: chain A residue 554 PHE Chi-restraints excluded: chain A residue 575 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 37 optimal weight: 0.0670 chunk 55 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 11 optimal weight: 4.9990 chunk 15 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 overall best weight: 0.7322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.100982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.081761 restraints weight = 12383.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.083940 restraints weight = 7354.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.085598 restraints weight = 5219.237| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4743 Z= 0.187 Angle : 0.643 15.202 6396 Z= 0.311 Chirality : 0.042 0.261 706 Planarity : 0.003 0.032 834 Dihedral : 4.884 43.955 625 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.17 % Allowed : 16.73 % Favored : 81.10 % 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: 1.99 (0.36), residues: 579 helix: 1.90 (0.25), residues: 417 sheet: None (None), residues: 0 loop : -0.12 (0.53), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 214 HIS 0.006 0.001 HIS A 288 PHE 0.007 0.001 PHE A 488 TYR 0.018 0.001 TYR A 370 ARG 0.002 0.000 ARG A 336 *********************** 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 44 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 33 time to evaluate : 0.516 Fit side-chains REVERT: A 554 PHE cc_start: 0.7490 (OUTLIER) cc_final: 0.6546 (t80) outliers start: 11 outliers final: 8 residues processed: 43 average time/residue: 0.1031 time to fit residues: 6.9831 Evaluate side-chains 42 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 33 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 CYS Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 169 CYS Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 550 ASP Chi-restraints excluded: chain A residue 554 PHE Chi-restraints excluded: chain A residue 575 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 15 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 23 optimal weight: 0.5980 chunk 51 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 31 optimal weight: 0.0770 chunk 34 optimal weight: 0.7980 overall best weight: 0.8140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.100693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.081398 restraints weight = 12315.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.083651 restraints weight = 7348.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.085153 restraints weight = 5201.012| |-----------------------------------------------------------------------------| r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4743 Z= 0.197 Angle : 0.653 14.868 6396 Z= 0.315 Chirality : 0.042 0.257 706 Planarity : 0.003 0.032 834 Dihedral : 4.940 43.755 625 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.97 % Allowed : 17.32 % Favored : 80.71 % 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: 1.98 (0.36), residues: 579 helix: 1.91 (0.25), residues: 416 sheet: None (None), residues: 0 loop : -0.19 (0.52), 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 288 PHE 0.007 0.001 PHE A 488 TYR 0.016 0.002 TYR A 370 ARG 0.002 0.000 ARG A 336 ********************** 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 44 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 34 time to evaluate : 0.517 Fit side-chains REVERT: A 84 TYR cc_start: 0.3061 (OUTLIER) cc_final: 0.2518 (m-10) REVERT: A 554 PHE cc_start: 0.7500 (OUTLIER) cc_final: 0.6501 (t80) outliers start: 10 outliers final: 7 residues processed: 43 average time/residue: 0.1104 time to fit residues: 7.3206 Evaluate side-chains 40 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 31 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 CYS Chi-restraints excluded: chain A residue 84 TYR Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 169 CYS Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 550 ASP Chi-restraints excluded: chain A residue 554 PHE Chi-restraints excluded: chain A residue 575 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 53 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 51 optimal weight: 0.0770 chunk 48 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 44 optimal weight: 0.2980 chunk 13 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.101509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.082220 restraints weight = 12329.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.084498 restraints weight = 7327.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.086066 restraints weight = 5184.794| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4743 Z= 0.177 Angle : 0.658 15.338 6396 Z= 0.315 Chirality : 0.042 0.250 706 Planarity : 0.003 0.033 834 Dihedral : 4.902 43.832 625 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.97 % Allowed : 17.72 % Favored : 80.31 % 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: 1.97 (0.36), residues: 579 helix: 1.92 (0.25), residues: 417 sheet: None (None), residues: 0 loop : -0.27 (0.52), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 214 HIS 0.004 0.001 HIS A 288 PHE 0.006 0.001 PHE A 488 TYR 0.018 0.001 TYR A 370 ARG 0.002 0.000 ARG A 336 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1701.55 seconds wall clock time: 31 minutes 20.35 seconds (1880.35 seconds total)