Starting phenix.real_space_refine on Sun Apr 27 05:35:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vae_43089/04_2025/8vae_43089.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vae_43089/04_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_43089/04_2025/8vae_43089.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vae_43089/04_2025/8vae_43089.map" model { file = "/net/cci-nas-00/data/ceres_data/8vae_43089/04_2025/8vae_43089.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vae_43089/04_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-5669/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: 4.44, per 1000 atoms: 0.95 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: 1.08 Conformation dependent library (CDL) restraints added in 506.7 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: 0.49 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: 1.27 Time building geometry restraints manager: 1.29 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: 5.680 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: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 16.150 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:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.290 ------------------------------------------------------------------------------- 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 : 0.004 0.174 4760 Z= 0.216 Angle : 1.026 60.871 6430 Z= 0.517 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 Details of bonding type rmsd hydrogen bonds : bond 0.11423 ( 320) hydrogen bonds : angle 4.82163 ( 945) SS BOND : bond 0.04290 ( 17) SS BOND : angle 10.64186 ( 34) covalent geometry : bond 0.00347 ( 4743) covalent geometry : angle 0.67540 ( 6396) *********************** 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 : 0.507 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: 0.1643 time to fit residues: 12.1726 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 : 0.531 ------------------------------------------------------------------------------- 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: 4.9990 chunk 15 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 chunk 23 optimal weight: 0.7980 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: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3643 r_free = 0.3643 target = 0.103034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.083919 restraints weight = 11885.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.086289 restraints weight = 7058.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.087916 restraints weight = 4974.634| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.1367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4760 Z= 0.144 Angle : 0.641 11.341 6430 Z= 0.325 Chirality : 0.042 0.225 706 Planarity : 0.004 0.028 834 Dihedral : 5.538 64.210 625 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.18 % Allowed : 6.69 % Favored : 92.13 % 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: 1.82 (0.36), residues: 579 helix: 1.76 (0.26), residues: 417 sheet: None (None), residues: 0 loop : -0.13 (0.51), 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 0.016 0.002 TYR A 370 ARG 0.003 0.001 ARG A 81 Details of bonding type rmsd hydrogen bonds : bond 0.03648 ( 320) hydrogen bonds : angle 4.24834 ( 945) SS BOND : bond 0.00370 ( 17) SS BOND : angle 1.48430 ( 34) covalent geometry : bond 0.00333 ( 4743) covalent geometry : angle 0.63318 ( 6396) *********************** 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 : 0.605 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 47 average time/residue: 0.1714 time to fit residues: 10.8291 Evaluate side-chains 34 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 32 time to evaluate : 0.501 ------------------------------------------------------------------------------- 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: 0.6980 chunk 13 optimal weight: 1.9990 chunk 47 optimal weight: 0.2980 chunk 6 optimal weight: 3.9990 chunk 42 optimal weight: 0.1980 chunk 54 optimal weight: 0.9990 chunk 56 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- 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 = 0.3649 r_free = 0.3649 target = 0.103314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.083939 restraints weight = 12003.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.086292 restraints weight = 7135.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.087958 restraints weight = 5040.442| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4760 Z= 0.123 Angle : 0.610 11.976 6430 Z= 0.303 Chirality : 0.041 0.239 706 Planarity : 0.003 0.025 834 Dihedral : 5.222 58.390 625 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.38 % Allowed : 10.04 % Favored : 88.58 % 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: 1.86 (0.36), residues: 579 helix: 1.80 (0.26), residues: 418 sheet: None (None), residues: 0 loop : -0.19 (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 338 PHE 0.013 0.001 PHE A 127 TYR 0.017 0.002 TYR A 370 ARG 0.004 0.000 ARG A 197 Details of bonding type rmsd hydrogen bonds : bond 0.03448 ( 320) hydrogen bonds : angle 4.22988 ( 945) SS BOND : bond 0.00515 ( 17) SS BOND : angle 1.33045 ( 34) covalent geometry : bond 0.00277 ( 4743) covalent geometry : angle 0.60375 ( 6396) *********************** 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 : 0.572 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 45 average time/residue: 0.1271 time to fit residues: 8.3204 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 : 0.507 ------------------------------------------------------------------------------- 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: 0.7980 chunk 46 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 7 optimal weight: 0.0980 chunk 21 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 53 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 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 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 = 0.3632 r_free = 0.3632 target = 0.101728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.082613 restraints weight = 12209.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.084964 restraints weight = 7279.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.086584 restraints weight = 5113.029| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4760 Z= 0.128 Angle : 0.625 12.569 6430 Z= 0.307 Chirality : 0.041 0.223 706 Planarity : 0.003 0.026 834 Dihedral : 4.991 50.430 625 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.77 % Allowed : 11.81 % 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: 1.92 (0.36), residues: 579 helix: 1.81 (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 242 PHE 0.009 0.001 PHE A 127 TYR 0.015 0.002 TYR A 370 ARG 0.002 0.000 ARG A 197 Details of bonding type rmsd hydrogen bonds : bond 0.03438 ( 320) hydrogen bonds : angle 4.17350 ( 945) SS BOND : bond 0.00374 ( 17) SS BOND : angle 1.26254 ( 34) covalent geometry : bond 0.00292 ( 4743) covalent geometry : angle 0.61971 ( 6396) *********************** 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 45 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 36 time to evaluate : 0.495 Fit side-chains revert: symmetry clash REVERT: A 548 MET cc_start: 0.8246 (mmm) cc_final: 0.7973 (mmt) outliers start: 9 outliers final: 3 residues processed: 44 average time/residue: 0.1170 time to fit residues: 7.5759 Evaluate side-chains 32 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 29 time to evaluate : 0.572 ------------------------------------------------------------------------------- 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: 1.9990 chunk 2 optimal weight: 0.5980 chunk 14 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 46 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 25 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3628 r_free = 0.3628 target = 0.101439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.082113 restraints weight = 12333.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.084475 restraints weight = 7332.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.086088 restraints weight = 5177.810| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4760 Z= 0.132 Angle : 0.624 13.384 6430 Z= 0.306 Chirality : 0.041 0.240 706 Planarity : 0.003 0.028 834 Dihedral : 4.873 46.599 625 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % 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: 1.89 (0.36), residues: 579 helix: 1.79 (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 0.003 0.001 TRP A 214 HIS 0.003 0.001 HIS A 288 PHE 0.007 0.001 PHE A 127 TYR 0.015 0.002 TYR A 370 ARG 0.002 0.000 ARG A 197 Details of bonding type rmsd hydrogen bonds : bond 0.03378 ( 320) hydrogen bonds : angle 4.17485 ( 945) SS BOND : bond 0.00357 ( 17) SS BOND : angle 1.26407 ( 34) covalent geometry : bond 0.00305 ( 4743) covalent geometry : angle 0.61923 ( 6396) *********************** 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 43 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 33 time to evaluate : 0.562 Fit side-chains REVERT: A 298 MET cc_start: 0.7381 (tpt) cc_final: 0.7095 (tpt) outliers start: 10 outliers final: 7 residues processed: 42 average time/residue: 0.1169 time to fit residues: 7.4523 Evaluate side-chains 36 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 29 time to evaluate : 0.621 ------------------------------------------------------------------------------- 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 575 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 50 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 chunk 35 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 54 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3617 r_free = 0.3617 target = 0.101069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.081544 restraints weight = 12073.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.083873 restraints weight = 7123.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.085500 restraints weight = 4979.336| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4760 Z= 0.128 Angle : 0.628 13.917 6430 Z= 0.309 Chirality : 0.040 0.238 706 Planarity : 0.003 0.030 834 Dihedral : 4.772 45.277 625 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.36 % Allowed : 15.35 % Favored : 82.28 % 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: 1.87 (0.26), residues: 417 sheet: None (None), residues: 0 loop : -0.14 (0.52), 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 0.007 0.001 PHE A 568 TYR 0.016 0.001 TYR A 370 ARG 0.002 0.000 ARG A 197 Details of bonding type rmsd hydrogen bonds : bond 0.03400 ( 320) hydrogen bonds : angle 4.20026 ( 945) SS BOND : bond 0.00321 ( 17) SS BOND : angle 1.40217 ( 34) covalent geometry : bond 0.00291 ( 4743) covalent geometry : angle 0.62098 ( 6396) *********************** 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: 12 poor density : 35 time to evaluate : 0.592 Fit side-chains REVERT: A 178 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7408 (tt) REVERT: A 554 PHE cc_start: 0.7499 (OUTLIER) cc_final: 0.6761 (t80) outliers start: 12 outliers final: 6 residues processed: 46 average time/residue: 0.1053 time to fit residues: 7.5843 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 : 0.595 ------------------------------------------------------------------------------- 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 178 LEU 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: 3.9990 chunk 23 optimal weight: 0.5980 chunk 7 optimal weight: 0.9980 chunk 49 optimal weight: 0.0030 chunk 31 optimal weight: 0.0870 chunk 36 optimal weight: 5.9990 chunk 6 optimal weight: 0.1980 chunk 4 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 overall best weight: 0.3168 ------------------------------------------------------------------------------- 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 = 0.3645 r_free = 0.3645 target = 0.103000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.083628 restraints weight = 11940.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.085938 restraints weight = 6999.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.087652 restraints weight = 4902.498| |-----------------------------------------------------------------------------| r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 4760 Z= 0.111 Angle : 0.618 14.676 6430 Z= 0.299 Chirality : 0.041 0.314 706 Planarity : 0.003 0.032 834 Dihedral : 4.652 44.107 625 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.36 % Allowed : 16.73 % Favored : 80.91 % 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: 2.08 (0.36), residues: 579 helix: 1.98 (0.25), residues: 416 sheet: None (None), residues: 0 loop : -0.16 (0.51), 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 127 TYR 0.018 0.001 TYR A 370 ARG 0.002 0.000 ARG A 197 Details of bonding type rmsd hydrogen bonds : bond 0.03173 ( 320) hydrogen bonds : angle 4.10811 ( 945) SS BOND : bond 0.00279 ( 17) SS BOND : angle 1.24175 ( 34) covalent geometry : bond 0.00236 ( 4743) covalent geometry : angle 0.61298 ( 6396) *********************** 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 46 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 34 time to evaluate : 0.560 Fit side-chains REVERT: A 298 MET cc_start: 0.6823 (tpt) cc_final: 0.6493 (tpt) REVERT: A 380 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8735 (mp) REVERT: A 554 PHE cc_start: 0.7458 (OUTLIER) cc_final: 0.6693 (t80) outliers start: 12 outliers final: 7 residues processed: 45 average time/residue: 0.1079 time to fit residues: 7.7215 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 : 0.503 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 25 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 31 optimal weight: 0.0570 chunk 2 optimal weight: 0.6980 chunk 52 optimal weight: 0.9990 overall best weight: 0.7298 ------------------------------------------------------------------------------- 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 = 0.101192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.081736 restraints weight = 12214.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.084075 restraints weight = 7200.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.085719 restraints weight = 5041.141| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4760 Z= 0.129 Angle : 0.642 14.170 6430 Z= 0.310 Chirality : 0.043 0.344 706 Planarity : 0.003 0.032 834 Dihedral : 4.723 43.592 625 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.56 % Allowed : 16.34 % 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: 2.04 (0.36), residues: 579 helix: 1.94 (0.26), residues: 417 sheet: None (None), residues: 0 loop : -0.14 (0.52), 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 0.007 0.001 PHE A 488 TYR 0.016 0.001 TYR A 370 ARG 0.001 0.000 ARG A 197 Details of bonding type rmsd hydrogen bonds : bond 0.03364 ( 320) hydrogen bonds : angle 4.16142 ( 945) SS BOND : bond 0.00319 ( 17) SS BOND : angle 1.30614 ( 34) covalent geometry : bond 0.00293 ( 4743) covalent geometry : angle 0.63683 ( 6396) *********************** 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 45 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 32 time to evaluate : 0.574 Fit side-chains revert: symmetry clash REVERT: A 380 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8730 (mp) REVERT: A 554 PHE cc_start: 0.7436 (OUTLIER) cc_final: 0.6503 (t80) outliers start: 13 outliers final: 8 residues processed: 44 average time/residue: 0.1038 time to fit residues: 7.1951 Evaluate side-chains 41 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 31 time to evaluate : 0.565 ------------------------------------------------------------------------------- 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 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: 0.9980 chunk 10 optimal weight: 0.7980 chunk 8 optimal weight: 5.9990 chunk 50 optimal weight: 0.2980 chunk 54 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 11 optimal weight: 6.9990 chunk 15 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 overall best weight: 0.5118 ------------------------------------------------------------------------------- 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 = 0.3624 r_free = 0.3624 target = 0.101785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.082213 restraints weight = 12445.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.084577 restraints weight = 7225.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.086293 restraints weight = 5037.777| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4760 Z= 0.118 Angle : 0.650 15.526 6430 Z= 0.311 Chirality : 0.042 0.303 706 Planarity : 0.003 0.033 834 Dihedral : 4.786 44.156 625 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.36 % Allowed : 16.73 % Favored : 80.91 % 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: 2.03 (0.36), residues: 579 helix: 1.95 (0.25), residues: 417 sheet: None (None), residues: 0 loop : -0.20 (0.52), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 214 HIS 0.005 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 197 Details of bonding type rmsd hydrogen bonds : bond 0.03313 ( 320) hydrogen bonds : angle 4.17696 ( 945) SS BOND : bond 0.00343 ( 17) SS BOND : angle 1.55300 ( 34) covalent geometry : bond 0.00261 ( 4743) covalent geometry : angle 0.64175 ( 6396) *********************** 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 47 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 35 time to evaluate : 0.572 Fit side-chains REVERT: A 178 LEU cc_start: 0.7782 (OUTLIER) cc_final: 0.7427 (tt) REVERT: A 298 MET cc_start: 0.6984 (tpt) cc_final: 0.6622 (tpt) REVERT: A 380 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8729 (mp) REVERT: A 554 PHE cc_start: 0.7470 (OUTLIER) cc_final: 0.6604 (t80) outliers start: 12 outliers final: 8 residues processed: 46 average time/residue: 0.1134 time to fit residues: 7.8942 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 : 0.570 ------------------------------------------------------------------------------- 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 178 LEU Chi-restraints excluded: chain A residue 297 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 15 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 29 optimal weight: 0.2980 chunk 50 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 31 optimal weight: 0.4980 chunk 34 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3619 r_free = 0.3619 target = 0.101452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.081770 restraints weight = 12270.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.084152 restraints weight = 7146.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.085830 restraints weight = 4973.658| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4760 Z= 0.124 Angle : 0.652 15.500 6430 Z= 0.311 Chirality : 0.042 0.283 706 Planarity : 0.003 0.032 834 Dihedral : 4.866 43.721 625 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.17 % Allowed : 17.13 % 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: 2.00 (0.36), residues: 579 helix: 1.91 (0.25), residues: 419 sheet: None (None), residues: 0 loop : -0.19 (0.53), residues: 160 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 551 TYR 0.019 0.001 TYR A 370 ARG 0.002 0.000 ARG A 197 Details of bonding type rmsd hydrogen bonds : bond 0.03407 ( 320) hydrogen bonds : angle 4.20880 ( 945) SS BOND : bond 0.00390 ( 17) SS BOND : angle 1.51446 ( 34) covalent geometry : bond 0.00280 ( 4743) covalent geometry : angle 0.64478 ( 6396) ********************** 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: 11 poor density : 33 time to evaluate : 0.449 Fit side-chains REVERT: A 298 MET cc_start: 0.7033 (tpt) cc_final: 0.6705 (tpt) REVERT: A 380 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8729 (mp) REVERT: A 554 PHE cc_start: 0.7496 (OUTLIER) cc_final: 0.6558 (t80) outliers start: 11 outliers final: 8 residues processed: 43 average time/residue: 0.1105 time to fit residues: 7.6138 Evaluate side-chains 43 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 33 time to evaluate : 0.550 ------------------------------------------------------------------------------- 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 169 CYS Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 297 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 53 optimal weight: 3.9990 chunk 45 optimal weight: 0.1980 chunk 51 optimal weight: 0.1980 chunk 48 optimal weight: 0.0040 chunk 9 optimal weight: 0.7980 chunk 14 optimal weight: 0.0970 chunk 20 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 44 optimal weight: 0.2980 chunk 13 optimal weight: 0.2980 chunk 34 optimal weight: 0.0870 overall best weight: 0.1168 ------------------------------------------------------------------------------- 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 = 0.3669 r_free = 0.3669 target = 0.104628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.085301 restraints weight = 12374.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.087724 restraints weight = 7209.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.089477 restraints weight = 5005.271| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 4760 Z= 0.108 Angle : 0.633 16.276 6430 Z= 0.299 Chirality : 0.040 0.259 706 Planarity : 0.003 0.032 834 Dihedral : 4.665 44.068 625 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.97 % Allowed : 17.52 % Favored : 80.51 % 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: 2.10 (0.36), residues: 579 helix: 2.00 (0.25), residues: 419 sheet: None (None), residues: 0 loop : -0.18 (0.54), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 214 HIS 0.004 0.001 HIS A 288 PHE 0.008 0.001 PHE A 127 TYR 0.021 0.001 TYR A 370 ARG 0.002 0.000 ARG A 197 Details of bonding type rmsd hydrogen bonds : bond 0.03163 ( 320) hydrogen bonds : angle 4.11841 ( 945) SS BOND : bond 0.00306 ( 17) SS BOND : angle 1.27180 ( 34) covalent geometry : bond 0.00224 ( 4743) covalent geometry : angle 0.62789 ( 6396) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1873.80 seconds wall clock time: 33 minutes 22.02 seconds (2002.02 seconds total)