Starting phenix.real_space_refine on Sat May 10 02:20:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vae_43089/05_2025/8vae_43089.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vae_43089/05_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_43089/05_2025/8vae_43089.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vae_43089/05_2025/8vae_43089.map" model { file = "/net/cci-nas-00/data/ceres_data/8vae_43089/05_2025/8vae_43089.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vae_43089/05_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-5687/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: 4.43, 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: 1.12 Conformation dependent library (CDL) restraints added in 577.1 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: 0.43 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: 1.22 Time building geometry restraints manager: 1.33 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: 4.850 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: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.600 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.720 ------------------------------------------------------------------------------- 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 : 0.479 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: 0.1659 time to fit residues: 12.2425 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 : 0.565 ------------------------------------------------------------------------------- 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 = 0.083916 restraints weight = 11885.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.086277 restraints weight = 7062.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.087937 restraints weight = 4970.369| |-----------------------------------------------------------------------------| 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 : 0.569 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 47 average time/residue: 0.1670 time to fit residues: 10.5401 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 : 0.557 ------------------------------------------------------------------------------- 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: 0.2980 chunk 13 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 = 0.3622 r_free = 0.3622 target = 0.101727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.082230 restraints weight = 12118.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.084609 restraints weight = 7125.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.086277 restraints weight = 5001.981| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4760 Z= 0.145 Angle : 0.629 11.750 6430 Z= 0.314 Chirality : 0.042 0.235 706 Planarity : 0.003 0.026 834 Dihedral : 5.265 57.075 625 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.38 % Allowed : 10.83 % Favored : 87.80 % 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: 1.71 (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 0.003 0.001 TRP A 214 HIS 0.003 0.001 HIS A 338 PHE 0.012 0.001 PHE A 127 TYR 0.015 0.002 TYR A 370 ARG 0.004 0.001 ARG A 197 Details of bonding type rmsd hydrogen bonds : bond 0.03616 ( 320) hydrogen bonds : angle 4.29862 ( 945) SS BOND : bond 0.00517 ( 17) SS BOND : angle 1.45220 ( 34) covalent geometry : bond 0.00335 ( 4743) covalent geometry : angle 0.62180 ( 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 : 0.501 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 45 average time/residue: 0.1198 time to fit residues: 7.8334 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 : 0.496 ------------------------------------------------------------------------------- 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: 0.6980 chunk 46 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 53 optimal weight: 0.4980 chunk 33 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3629 r_free = 0.3629 target = 0.101598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.082461 restraints weight = 12255.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.084778 restraints weight = 7308.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.086401 restraints weight = 5144.640| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4760 Z= 0.125 Angle : 0.627 12.778 6430 Z= 0.307 Chirality : 0.040 0.225 706 Planarity : 0.003 0.027 834 Dihedral : 5.057 50.690 625 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.17 % Allowed : 11.42 % 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: 1.88 (0.36), residues: 579 helix: 1.78 (0.25), residues: 419 sheet: None (None), residues: 0 loop : -0.10 (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 0.016 0.001 TYR A 370 ARG 0.003 0.000 ARG A 197 Details of bonding type rmsd hydrogen bonds : bond 0.03432 ( 320) hydrogen bonds : angle 4.19359 ( 945) SS BOND : bond 0.00378 ( 17) SS BOND : angle 1.28068 ( 34) covalent geometry : bond 0.00283 ( 4743) covalent geometry : angle 0.62162 ( 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 47 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 36 time to evaluate : 0.549 Fit side-chains revert: symmetry clash REVERT: A 548 MET cc_start: 0.8288 (mmm) cc_final: 0.8020 (mmt) outliers start: 11 outliers final: 4 residues processed: 46 average time/residue: 0.1301 time to fit residues: 8.6553 Evaluate side-chains 35 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 31 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 48 optimal weight: 0.9980 chunk 2 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 10 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 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 = 0.3622 r_free = 0.3622 target = 0.101121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.081757 restraints weight = 12318.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.084095 restraints weight = 7394.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.085690 restraints weight = 5215.719| |-----------------------------------------------------------------------------| r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4760 Z= 0.133 Angle : 0.628 13.343 6430 Z= 0.308 Chirality : 0.041 0.245 706 Planarity : 0.003 0.028 834 Dihedral : 4.899 46.164 625 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.97 % Allowed : 13.98 % 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: 1.85 (0.36), residues: 579 helix: 1.76 (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 464 PHE 0.008 0.001 PHE A 127 TYR 0.016 0.002 TYR A 370 ARG 0.002 0.000 ARG A 197 Details of bonding type rmsd hydrogen bonds : bond 0.03410 ( 320) hydrogen bonds : angle 4.19729 ( 945) SS BOND : bond 0.00361 ( 17) SS BOND : angle 1.24799 ( 34) covalent geometry : bond 0.00304 ( 4743) covalent geometry : angle 0.62262 ( 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 45 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 35 time to evaluate : 0.565 Fit side-chains revert: symmetry clash REVERT: A 298 MET cc_start: 0.7375 (tpt) cc_final: 0.7111 (tpt) REVERT: A 554 PHE cc_start: 0.7503 (OUTLIER) cc_final: 0.6849 (t80) outliers start: 10 outliers final: 7 residues processed: 44 average time/residue: 0.1213 time to fit residues: 7.9874 Evaluate side-chains 38 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 30 time to evaluate : 0.536 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 50 optimal weight: 4.9990 chunk 1 optimal weight: 0.6980 chunk 30 optimal weight: 0.0030 chunk 35 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 overall best weight: 0.6192 ------------------------------------------------------------------------------- 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 = 0.3629 r_free = 0.3629 target = 0.101481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.082193 restraints weight = 12249.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.084488 restraints weight = 7318.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.086087 restraints weight = 5144.412| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4760 Z= 0.122 Angle : 0.625 13.946 6430 Z= 0.308 Chirality : 0.041 0.290 706 Planarity : 0.003 0.031 834 Dihedral : 4.767 44.994 625 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.56 % Allowed : 14.76 % Favored : 82.68 % 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: 1.90 (0.26), residues: 417 sheet: None (None), residues: 0 loop : -0.09 (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 0.008 0.001 PHE A 568 TYR 0.017 0.001 TYR A 370 ARG 0.002 0.000 ARG A 197 Details of bonding type rmsd hydrogen bonds : bond 0.03340 ( 320) hydrogen bonds : angle 4.19129 ( 945) SS BOND : bond 0.00315 ( 17) SS BOND : angle 1.36166 ( 34) covalent geometry : bond 0.00274 ( 4743) covalent geometry : angle 0.61918 ( 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 48 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 35 time to evaluate : 0.582 Fit side-chains revert: symmetry clash REVERT: A 178 LEU cc_start: 0.7796 (OUTLIER) cc_final: 0.7367 (tp) REVERT: A 380 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8761 (mp) REVERT: A 554 PHE cc_start: 0.7480 (OUTLIER) cc_final: 0.6736 (t80) outliers start: 13 outliers final: 6 residues processed: 47 average time/residue: 0.1074 time to fit residues: 7.8987 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 : 0.548 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- 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: 5.9990 chunk 49 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 chunk 36 optimal weight: 5.9990 chunk 6 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3622 r_free = 0.3622 target = 0.101011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.081700 restraints weight = 12154.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.083953 restraints weight = 7329.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.085466 restraints weight = 5211.113| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4760 Z= 0.129 Angle : 0.632 14.347 6430 Z= 0.309 Chirality : 0.042 0.249 706 Planarity : 0.003 0.031 834 Dihedral : 4.772 44.091 625 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.95 % Allowed : 16.34 % 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: 2.02 (0.36), residues: 579 helix: 1.94 (0.25), residues: 415 sheet: None (None), residues: 0 loop : -0.16 (0.52), residues: 164 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 0.007 0.001 PHE A 488 TYR 0.016 0.001 TYR A 370 ARG 0.002 0.000 ARG A 197 Details of bonding type rmsd hydrogen bonds : bond 0.03361 ( 320) hydrogen bonds : angle 4.17987 ( 945) SS BOND : bond 0.00333 ( 17) SS BOND : angle 1.40382 ( 34) covalent geometry : bond 0.00292 ( 4743) covalent geometry : angle 0.62553 ( 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 48 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 33 time to evaluate : 0.601 Fit side-chains revert: symmetry clash REVERT: A 178 LEU cc_start: 0.7770 (OUTLIER) cc_final: 0.7396 (tt) REVERT: A 380 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8758 (mp) REVERT: A 554 PHE cc_start: 0.7429 (OUTLIER) cc_final: 0.6652 (t80) outliers start: 15 outliers final: 8 residues processed: 47 average time/residue: 0.1024 time to fit residues: 7.4471 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 : 0.567 ------------------------------------------------------------------------------- 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 315 VAL Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 433 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: 0.7980 chunk 18 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 29 optimal weight: 0.2980 chunk 20 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 31 optimal weight: 0.0040 chunk 2 optimal weight: 0.6980 chunk 52 optimal weight: 0.7980 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 458 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.101799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.082473 restraints weight = 12288.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.084753 restraints weight = 7336.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.086355 restraints weight = 5176.919| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4760 Z= 0.117 Angle : 0.629 15.057 6430 Z= 0.305 Chirality : 0.041 0.231 706 Planarity : 0.003 0.032 834 Dihedral : 4.818 44.179 625 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.36 % Allowed : 17.52 % Favored : 80.12 % 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: 2.09 (0.36), residues: 579 helix: 1.98 (0.25), 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 0.003 0.001 HIS A 288 PHE 0.007 0.001 PHE A 488 TYR 0.017 0.001 TYR A 370 ARG 0.002 0.000 ARG A 197 Details of bonding type rmsd hydrogen bonds : bond 0.03260 ( 320) hydrogen bonds : angle 4.15797 ( 945) SS BOND : bond 0.00305 ( 17) SS BOND : angle 1.33032 ( 34) covalent geometry : bond 0.00259 ( 4743) covalent geometry : angle 0.62293 ( 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 49 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 37 time to evaluate : 0.639 Fit side-chains REVERT: A 178 LEU cc_start: 0.7757 (OUTLIER) cc_final: 0.7413 (tt) REVERT: A 298 MET cc_start: 0.6713 (tpt) cc_final: 0.6431 (tpt) REVERT: A 554 PHE cc_start: 0.7421 (OUTLIER) cc_final: 0.6505 (t80) outliers start: 12 outliers final: 6 residues processed: 48 average time/residue: 0.1096 time to fit residues: 8.3141 Evaluate side-chains 42 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 34 time to evaluate : 0.551 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 37 optimal weight: 0.7980 chunk 55 optimal weight: 0.6980 chunk 10 optimal weight: 4.9990 chunk 8 optimal weight: 0.0270 chunk 50 optimal weight: 0.0270 chunk 54 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 43 optimal weight: 0.9980 chunk 11 optimal weight: 0.3980 chunk 15 optimal weight: 0.6980 chunk 26 optimal weight: 0.4980 overall best weight: 0.3296 ------------------------------------------------------------------------------- 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 = 0.3650 r_free = 0.3650 target = 0.102746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.083752 restraints weight = 12407.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.086113 restraints weight = 7286.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.087746 restraints weight = 5082.555| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 4760 Z= 0.111 Angle : 0.637 15.224 6430 Z= 0.307 Chirality : 0.041 0.216 706 Planarity : 0.003 0.033 834 Dihedral : 4.784 44.129 625 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.17 % Allowed : 17.91 % Favored : 79.92 % 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: 1.98 (0.25), residues: 418 sheet: None (None), residues: 0 loop : -0.19 (0.52), residues: 161 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 0.018 0.001 TYR A 370 ARG 0.002 0.000 ARG A 197 Details of bonding type rmsd hydrogen bonds : bond 0.03264 ( 320) hydrogen bonds : angle 4.17341 ( 945) SS BOND : bond 0.00259 ( 17) SS BOND : angle 1.44490 ( 34) covalent geometry : bond 0.00238 ( 4743) covalent geometry : angle 0.63014 ( 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 50 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 39 time to evaluate : 0.557 Fit side-chains REVERT: A 298 MET cc_start: 0.6596 (tpt) cc_final: 0.6342 (tpt) REVERT: A 554 PHE cc_start: 0.7440 (OUTLIER) cc_final: 0.6575 (t80) outliers start: 11 outliers final: 8 residues processed: 49 average time/residue: 0.1549 time to fit residues: 10.4011 Evaluate side-chains 44 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 35 time to evaluate : 0.556 ------------------------------------------------------------------------------- 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 178 LEU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 433 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: 0.7980 chunk 1 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 chunk 51 optimal weight: 0.1980 chunk 29 optimal weight: 6.9990 chunk 50 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 31 optimal weight: 0.5980 chunk 34 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.101823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.082030 restraints weight = 12301.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.084460 restraints weight = 7227.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.086127 restraints weight = 5047.957| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.2685 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 : 0.666 14.743 6430 Z= 0.318 Chirality : 0.042 0.292 706 Planarity : 0.003 0.032 834 Dihedral : 4.864 43.738 625 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.77 % Allowed : 18.70 % Favored : 79.53 % 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: 1.97 (0.25), residues: 416 sheet: None (None), residues: 0 loop : -0.22 (0.53), 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 0.017 0.001 TYR A 370 ARG 0.005 0.000 ARG A 336 Details of bonding type rmsd hydrogen bonds : bond 0.03383 ( 320) hydrogen bonds : angle 4.21794 ( 945) SS BOND : bond 0.00364 ( 17) SS BOND : angle 1.48259 ( 34) covalent geometry : bond 0.00275 ( 4743) covalent geometry : angle 0.65937 ( 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 42 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 33 time to evaluate : 0.591 Fit side-chains outliers start: 9 outliers final: 8 residues processed: 41 average time/residue: 0.1003 time to fit residues: 6.5719 Evaluate side-chains 40 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 32 time to evaluate : 0.496 ------------------------------------------------------------------------------- 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 178 LEU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 433 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: 0.0010 chunk 45 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 chunk 14 optimal weight: 0.2980 chunk 20 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 overall best weight: 0.4986 ------------------------------------------------------------------------------- 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 = 0.3637 r_free = 0.3637 target = 0.102495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.082649 restraints weight = 12270.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.085057 restraints weight = 7100.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.086742 restraints weight = 4961.368| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4760 Z= 0.116 Angle : 0.648 14.993 6430 Z= 0.309 Chirality : 0.042 0.307 706 Planarity : 0.003 0.033 834 Dihedral : 4.838 43.973 625 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.77 % Allowed : 19.29 % Favored : 78.94 % 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: 2.05 (0.36), residues: 579 helix: 1.97 (0.25), residues: 418 sheet: None (None), residues: 0 loop : -0.22 (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 0.007 0.001 PHE A 551 TYR 0.021 0.002 TYR A 370 ARG 0.004 0.000 ARG A 337 Details of bonding type rmsd hydrogen bonds : bond 0.03319 ( 320) hydrogen bonds : angle 4.16854 ( 945) SS BOND : bond 0.00344 ( 17) SS BOND : angle 1.36808 ( 34) covalent geometry : bond 0.00257 ( 4743) covalent geometry : angle 0.64229 ( 6396) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1780.85 seconds wall clock time: 31 minutes 55.78 seconds (1915.78 seconds total)