Starting phenix.real_space_refine on Thu Jun 5 00:29:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qqd_53298/06_2025/9qqd_53298.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qqd_53298/06_2025/9qqd_53298.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9qqd_53298/06_2025/9qqd_53298.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qqd_53298/06_2025/9qqd_53298.map" model { file = "/net/cci-nas-00/data/ceres_data/9qqd_53298/06_2025/9qqd_53298.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qqd_53298/06_2025/9qqd_53298.cif" } resolution = 3.1 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= 0.016 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 39 5.16 5 C 2891 2.51 5 N 775 2.21 5 O 887 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 4592 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 4592 Classifications: {'peptide': 579} Link IDs: {'PTRANS': 27, 'TRANS': 551} Time building chain proxies: 3.55, per 1000 atoms: 0.77 Number of scatterers: 4592 At special positions: 0 Unit cell: (67.525, 98.975, 91.575, 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 39 16.00 O 887 8.00 N 775 7.00 C 2891 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=2.04 Simple disulfide: pdb=" SG CYS A 90 " - pdb=" SG CYS A 101 " distance=2.32 Simple disulfide: pdb=" SG CYS A 123 " - pdb=" SG CYS A 168 " distance=2.06 Simple disulfide: pdb=" SG CYS A 167 " - pdb=" SG CYS A 176 " distance=2.04 Simple disulfide: pdb=" SG CYS A 199 " - pdb=" SG CYS A 245 " distance=2.07 Simple disulfide: pdb=" SG CYS A 244 " - pdb=" SG CYS A 252 " distance=2.03 Simple disulfide: pdb=" SG CYS A 264 " - pdb=" SG CYS A 278 " distance=2.02 Simple disulfide: pdb=" SG CYS A 277 " - pdb=" SG CYS A 288 " distance=2.37 Simple disulfide: pdb=" SG CYS A 315 " - pdb=" SG CYS A 360 " distance=2.04 Simple disulfide: pdb=" SG CYS A 359 " - pdb=" SG CYS A 368 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 437 " distance=2.02 Simple disulfide: pdb=" SG CYS A 436 " - pdb=" SG CYS A 447 " distance=2.21 Simple disulfide: pdb=" SG CYS A 460 " - pdb=" SG CYS A 476 " distance=2.02 Simple disulfide: pdb=" SG CYS A 475 " - pdb=" SG CYS A 486 " distance=2.43 Simple disulfide: pdb=" SG CYS A 513 " - pdb=" SG CYS A 558 " distance=2.04 Simple disulfide: pdb=" SG CYS A 557 " - pdb=" SG CYS A 566 " distance=2.28 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: 1.18 Conformation dependent library (CDL) restraints added in 585.4 milliseconds 1154 Ramachandran restraints generated. 577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1124 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 0 sheets defined 83.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 5 through 15 Processing helix chain 'A' and resid 15 through 31 Processing helix chain 'A' and resid 35 through 56 Processing helix chain 'A' and resid 65 through 76 Processing helix chain 'A' and resid 85 through 93 Processing helix chain 'A' and resid 94 through 105 removed outlier: 4.131A pdb=" N ASN A 99 " --> pdb=" O GLU A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 129 removed outlier: 3.785A pdb=" N ASP A 129 " --> pdb=" O GLU A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 145 Processing helix chain 'A' and resid 149 through 169 removed outlier: 4.060A pdb=" N GLN A 169 " --> pdb=" O GLN A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 205 removed outlier: 3.921A pdb=" N CYS A 176 " --> pdb=" O ASP A 172 " (cutoff:3.500A) Proline residue: A 179 - end of helix Processing helix chain 'A' and resid 206 through 222 removed outlier: 3.663A pdb=" N LEU A 210 " --> pdb=" O GLY A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 246 Processing helix chain 'A' and resid 248 through 266 Processing helix chain 'A' and resid 266 through 271 Processing helix chain 'A' and resid 276 through 280 removed outlier: 3.602A pdb=" N LYS A 280 " --> pdb=" O CYS A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 291 Processing helix chain 'A' and resid 304 through 309 Processing helix chain 'A' and resid 313 through 321 Processing helix chain 'A' and resid 321 through 337 Processing helix chain 'A' and resid 341 through 362 Processing helix chain 'A' and resid 364 through 371 removed outlier: 3.739A pdb=" N CYS A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N THR A 371 " --> pdb=" O ALA A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 414 removed outlier: 4.072A pdb=" N HIS A 378 " --> pdb=" O ASP A 374 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N LEU A 379 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL A 380 " --> pdb=" O LEU A 376 " (cutoff:3.500A) Proline residue: A 383 - end of helix removed outlier: 7.679A pdb=" N GLU A 399 " --> pdb=" O GLU A 395 " (cutoff:3.500A) removed outlier: 9.256A pdb=" N TYR A 400 " --> pdb=" O LYS A 396 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY A 401 " --> pdb=" O LEU A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 437 removed outlier: 4.052A pdb=" N GLY A 433 " --> pdb=" O LEU A 429 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N THR A 434 " --> pdb=" O GLY A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 466 removed outlier: 4.198A pdb=" N MET A 445 " --> pdb=" O GLU A 441 " (cutoff:3.500A) Proline residue: A 446 - end of helix removed outlier: 3.619A pdb=" N LYS A 465 " --> pdb=" O VAL A 461 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N THR A 466 " --> pdb=" O LEU A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 479 removed outlier: 4.417A pdb=" N SER A 479 " --> pdb=" O CYS A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 489 Processing helix chain 'A' and resid 502 through 507 removed outlier: 3.660A pdb=" N PHE A 506 " --> pdb=" O ASP A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 515 removed outlier: 3.559A pdb=" N ALA A 515 " --> pdb=" O ILE A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 535 Processing helix chain 'A' and resid 539 through 560 Processing helix chain 'A' and resid 564 through 569 Processing helix chain 'A' and resid 571 through 580 removed outlier: 3.521A pdb=" N THR A 580 " --> pdb=" O VAL A 576 " (cutoff:3.500A) 329 hydrogen bonds defined for protein. 963 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: 1.20 Time building geometry restraints manager: 1.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1022 1.33 - 1.45: 1198 1.45 - 1.57: 2420 1.57 - 1.70: 0 1.70 - 1.82: 43 Bond restraints: 4683 Sorted by residual: bond pdb=" CA ALA A 150 " pdb=" CB ALA A 150 " ideal model delta sigma weight residual 1.534 1.490 0.045 1.18e-02 7.18e+03 1.44e+01 bond pdb=" CA SER A 479 " pdb=" CB SER A 479 " ideal model delta sigma weight residual 1.533 1.474 0.059 1.65e-02 3.67e+03 1.27e+01 bond pdb=" CA SER A 426 " pdb=" CB SER A 426 " ideal model delta sigma weight residual 1.528 1.475 0.054 1.56e-02 4.11e+03 1.19e+01 bond pdb=" CA SER A 442 " pdb=" CB SER A 442 " ideal model delta sigma weight residual 1.531 1.479 0.052 1.59e-02 3.96e+03 1.07e+01 bond pdb=" CA SER A 219 " pdb=" CB SER A 219 " ideal model delta sigma weight residual 1.529 1.477 0.053 1.63e-02 3.76e+03 1.05e+01 ... (remaining 4678 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.53: 5882 3.53 - 7.07: 392 7.07 - 10.60: 41 10.60 - 14.14: 6 14.14 - 17.67: 1 Bond angle restraints: 6322 Sorted by residual: angle pdb=" C CYS A 101 " pdb=" CA CYS A 101 " pdb=" CB CYS A 101 " ideal model delta sigma weight residual 110.85 93.18 17.67 1.70e+00 3.46e-01 1.08e+02 angle pdb=" CA THR A 238 " pdb=" CB THR A 238 " pdb=" OG1 THR A 238 " ideal model delta sigma weight residual 109.60 98.09 11.51 1.50e+00 4.44e-01 5.89e+01 angle pdb=" N CYS A 101 " pdb=" CA CYS A 101 " pdb=" CB CYS A 101 " ideal model delta sigma weight residual 110.16 121.18 -11.02 1.48e+00 4.57e-01 5.55e+01 angle pdb=" CA THR A 231 " pdb=" CB THR A 231 " pdb=" OG1 THR A 231 " ideal model delta sigma weight residual 109.60 99.38 10.22 1.50e+00 4.44e-01 4.64e+01 angle pdb=" N ASP A 562 " pdb=" CA ASP A 562 " pdb=" C ASP A 562 " ideal model delta sigma weight residual 107.73 118.62 -10.89 1.61e+00 3.86e-01 4.57e+01 ... (remaining 6317 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 2439 17.96 - 35.92: 322 35.92 - 53.88: 151 53.88 - 71.84: 28 71.84 - 89.80: 17 Dihedral angle restraints: 2957 sinusoidal: 1236 harmonic: 1721 Sorted by residual: dihedral pdb=" CB CYS A 315 " pdb=" SG CYS A 315 " pdb=" SG CYS A 360 " pdb=" CB CYS A 360 " ideal model delta sinusoidal sigma weight residual 93.00 179.37 -86.37 1 1.00e+01 1.00e-02 8.99e+01 dihedral pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " pdb=" SG CYS A 437 " pdb=" CB CYS A 437 " ideal model delta sinusoidal sigma weight residual -86.00 -163.67 77.67 1 1.00e+01 1.00e-02 7.55e+01 dihedral pdb=" CD ARG A 81 " pdb=" NE ARG A 81 " pdb=" CZ ARG A 81 " pdb=" NH1 ARG A 81 " ideal model delta sinusoidal sigma weight residual 0.00 -61.33 61.33 1 1.00e+01 1.00e-02 4.99e+01 ... (remaining 2954 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 439 0.080 - 0.160: 206 0.160 - 0.240: 46 0.240 - 0.320: 10 0.320 - 0.400: 2 Chirality restraints: 703 Sorted by residual: chirality pdb=" CA ASP A 323 " pdb=" N ASP A 323 " pdb=" C ASP A 323 " pdb=" CB ASP A 323 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.01e+00 chirality pdb=" CA GLU A 351 " pdb=" N GLU A 351 " pdb=" C GLU A 351 " pdb=" CB GLU A 351 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.76e+00 chirality pdb=" CA TYR A 369 " pdb=" N TYR A 369 " pdb=" C TYR A 369 " pdb=" CB TYR A 369 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.44e+00 ... (remaining 700 not shown) Planarity restraints: 822 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 81 " 1.084 9.50e-02 1.11e+02 4.87e-01 1.58e+02 pdb=" NE ARG A 81 " -0.042 2.00e-02 2.50e+03 pdb=" CZ ARG A 81 " -0.080 2.00e-02 2.50e+03 pdb=" NH1 ARG A 81 " 0.029 2.00e-02 2.50e+03 pdb=" NH2 ARG A 81 " 0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 484 " -0.880 9.50e-02 1.11e+02 3.95e-01 1.00e+02 pdb=" NE ARG A 484 " 0.067 2.00e-02 2.50e+03 pdb=" CZ ARG A 484 " -0.031 2.00e-02 2.50e+03 pdb=" NH1 ARG A 484 " 0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG A 484 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 435 " -0.809 9.50e-02 1.11e+02 3.64e-01 9.21e+01 pdb=" NE ARG A 435 " 0.029 2.00e-02 2.50e+03 pdb=" CZ ARG A 435 " 0.069 2.00e-02 2.50e+03 pdb=" NH1 ARG A 435 " -0.018 2.00e-02 2.50e+03 pdb=" NH2 ARG A 435 " -0.044 2.00e-02 2.50e+03 ... (remaining 819 not shown) Histogram of nonbonded interaction distances: 2.43 - 2.92: 1836 2.92 - 3.42: 5071 3.42 - 3.91: 7719 3.91 - 4.41: 8666 4.41 - 4.90: 13950 Nonbonded interactions: 37242 Sorted by model distance: nonbonded pdb=" O HIS A 59 " pdb=" C ALA A 60 " model vdw 2.429 3.270 nonbonded pdb=" N THR A 371 " pdb=" OG1 THR A 371 " model vdw 2.500 2.496 nonbonded pdb=" N THR A 580 " pdb=" OG1 THR A 580 " model vdw 2.516 2.496 nonbonded pdb=" N THR A 269 " pdb=" OG1 THR A 269 " model vdw 2.521 2.496 nonbonded pdb=" O PHE A 567 " pdb=" O GLU A 570 " model vdw 2.529 3.040 ... (remaining 37237 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.890 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: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 15.690 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: 19.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8882 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 : 0.014 0.394 4700 Z= 0.799 Angle : 1.959 17.669 6356 Z= 1.287 Chirality : 0.093 0.400 703 Planarity : 0.043 0.487 822 Dihedral : 20.808 89.798 1782 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.87 % Allowed : 4.68 % Favored : 94.45 % Rotamer: Outliers : 13.84 % Allowed : 17.54 % Favored : 68.62 % Cbeta Deviations : 1.60 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.10 (0.29), residues: 577 helix: -1.72 (0.20), residues: 436 sheet: None (None), residues: 0 loop : -2.53 (0.45), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.010 TRP A 134 HIS 0.008 0.003 HIS A 59 PHE 0.027 0.005 PHE A 308 TYR 0.036 0.006 TYR A 160 ARG 0.068 0.013 ARG A 81 Details of bonding type rmsd hydrogen bonds : bond 0.22052 ( 329) hydrogen bonds : angle 7.03568 ( 963) SS BOND : bond 0.16225 ( 17) SS BOND : angle 3.80038 ( 34) covalent geometry : bond 0.00998 ( 4683) covalent geometry : angle 1.94408 ( 6322) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1154 Ramachandran restraints generated. 577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1154 Ramachandran restraints generated. 577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 36 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 251 GLU cc_start: 0.9180 (OUTLIER) cc_final: 0.8912 (mp0) REVERT: A 275 LYS cc_start: 0.9616 (ttmt) cc_final: 0.9404 (tptp) REVERT: A 312 LYS cc_start: 0.9725 (OUTLIER) cc_final: 0.9476 (tppt) REVERT: A 369 TYR cc_start: 0.8973 (OUTLIER) cc_final: 0.8622 (p90) REVERT: A 382 GLU cc_start: 0.9230 (OUTLIER) cc_final: 0.8939 (tm-30) REVERT: A 385 ASN cc_start: 0.9613 (OUTLIER) cc_final: 0.9218 (t0) REVERT: A 547 MET cc_start: 0.9356 (mtp) cc_final: 0.8962 (tpt) REVERT: A 566 CYS cc_start: 0.7796 (OUTLIER) cc_final: 0.7245 (t) REVERT: A 573 LYS cc_start: 0.9675 (OUTLIER) cc_final: 0.9432 (mttm) outliers start: 71 outliers final: 19 residues processed: 96 average time/residue: 0.1854 time to fit residues: 22.1008 Evaluate side-chains 44 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 18 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain A residue 108 ASP Chi-restraints excluded: chain A residue 123 CYS Chi-restraints excluded: chain A residue 161 ASN Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 244 CYS Chi-restraints excluded: chain A residue 251 GLU Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 313 ASP Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 378 HIS Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 385 ASN Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 437 CYS Chi-restraints excluded: chain A residue 520 LYS Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 564 GLU Chi-restraints excluded: chain A residue 566 CYS Chi-restraints excluded: chain A residue 573 LYS Chi-restraints excluded: chain A residue 579 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 48 optimal weight: 0.0970 chunk 43 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 29 optimal weight: 0.0770 chunk 44 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 27 optimal weight: 0.5980 chunk 33 optimal weight: 0.7980 chunk 51 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.4536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 579 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.063744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.045192 restraints weight = 14202.141| |-----------------------------------------------------------------------------| r_work (start): 0.2780 rms_B_bonded: 4.10 r_work: 0.2574 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.2574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 4700 Z= 0.151 Angle : 0.692 8.366 6356 Z= 0.359 Chirality : 0.041 0.139 703 Planarity : 0.005 0.055 822 Dihedral : 9.887 78.214 675 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 5.07 % Allowed : 22.03 % Favored : 72.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.34), residues: 577 helix: 0.68 (0.24), residues: 439 sheet: None (None), residues: 0 loop : -1.70 (0.49), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.004 TRP A 134 HIS 0.005 0.001 HIS A 59 PHE 0.017 0.002 PHE A 567 TYR 0.023 0.002 TYR A 369 ARG 0.007 0.001 ARG A 143 Details of bonding type rmsd hydrogen bonds : bond 0.04233 ( 329) hydrogen bonds : angle 4.44563 ( 963) SS BOND : bond 0.00362 ( 17) SS BOND : angle 1.51801 ( 34) covalent geometry : bond 0.00352 ( 4683) covalent geometry : angle 0.68524 ( 6322) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1154 Ramachandran restraints generated. 577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1154 Ramachandran restraints generated. 577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 20 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 HIS cc_start: 0.9278 (t-90) cc_final: 0.8991 (t-90) REVERT: A 275 LYS cc_start: 0.9377 (ttmt) cc_final: 0.9022 (tptp) REVERT: A 304 LEU cc_start: 0.7438 (tp) cc_final: 0.7237 (tp) REVERT: A 312 LYS cc_start: 0.9699 (OUTLIER) cc_final: 0.9498 (mmmm) REVERT: A 385 ASN cc_start: 0.9419 (OUTLIER) cc_final: 0.9102 (t0) REVERT: A 511 ASP cc_start: 0.9314 (OUTLIER) cc_final: 0.9019 (p0) REVERT: A 520 LYS cc_start: 0.9200 (OUTLIER) cc_final: 0.8578 (mttm) REVERT: A 564 GLU cc_start: 0.9385 (OUTLIER) cc_final: 0.9069 (pm20) outliers start: 26 outliers final: 11 residues processed: 43 average time/residue: 0.1737 time to fit residues: 10.0699 Evaluate side-chains 29 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 13 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 CYS Chi-restraints excluded: chain A residue 108 ASP Chi-restraints excluded: chain A residue 161 ASN Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 244 CYS Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 385 ASN Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 447 CYS Chi-restraints excluded: chain A residue 509 HIS Chi-restraints excluded: chain A residue 511 ASP Chi-restraints excluded: chain A residue 520 LYS Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 564 GLU Chi-restraints excluded: chain A residue 579 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 3 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 55 optimal weight: 0.6980 chunk 50 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 51 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS ** A 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.061997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.043110 restraints weight = 14548.781| |-----------------------------------------------------------------------------| r_work (start): 0.2728 rms_B_bonded: 4.13 r_work: 0.2537 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.2537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.3429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4700 Z= 0.140 Angle : 0.594 8.031 6356 Z= 0.303 Chirality : 0.039 0.123 703 Planarity : 0.004 0.055 822 Dihedral : 7.045 64.582 644 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.12 % Allowed : 22.81 % Favored : 74.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.35), residues: 577 helix: 1.61 (0.24), residues: 442 sheet: None (None), residues: 0 loop : -1.08 (0.52), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP A 134 HIS 0.002 0.001 HIS A 378 PHE 0.028 0.001 PHE A 553 TYR 0.017 0.002 TYR A 369 ARG 0.005 0.001 ARG A 81 Details of bonding type rmsd hydrogen bonds : bond 0.03616 ( 329) hydrogen bonds : angle 4.02247 ( 963) SS BOND : bond 0.00260 ( 17) SS BOND : angle 1.08534 ( 34) covalent geometry : bond 0.00326 ( 4683) covalent geometry : angle 0.59059 ( 6322) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1154 Ramachandran restraints generated. 577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1154 Ramachandran restraints generated. 577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 10 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 HIS cc_start: 0.9351 (t-90) cc_final: 0.9068 (t-90) REVERT: A 275 LYS cc_start: 0.9426 (ttmt) cc_final: 0.9110 (tptp) REVERT: A 385 ASN cc_start: 0.9438 (OUTLIER) cc_final: 0.9093 (t0) REVERT: A 520 LYS cc_start: 0.9169 (OUTLIER) cc_final: 0.8469 (mttm) outliers start: 16 outliers final: 8 residues processed: 26 average time/residue: 0.1545 time to fit residues: 5.9288 Evaluate side-chains 19 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 9 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 101 CYS Chi-restraints excluded: chain A residue 161 ASN Chi-restraints excluded: chain A residue 244 CYS Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 385 ASN Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 447 CYS Chi-restraints excluded: chain A residue 509 HIS Chi-restraints excluded: chain A residue 520 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 40 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 20 optimal weight: 0.1980 chunk 41 optimal weight: 0.8980 chunk 4 optimal weight: 6.9990 chunk 48 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3234 r_free = 0.3234 target = 0.061468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.042671 restraints weight = 14628.412| |-----------------------------------------------------------------------------| r_work (start): 0.2738 rms_B_bonded: 4.14 r_work: 0.2547 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.2547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.3779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4700 Z= 0.123 Angle : 0.556 7.638 6356 Z= 0.285 Chirality : 0.038 0.122 703 Planarity : 0.004 0.056 822 Dihedral : 5.553 59.126 629 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.53 % Allowed : 21.64 % Favored : 75.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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 (0.35), residues: 577 helix: 1.96 (0.24), residues: 439 sheet: None (None), residues: 0 loop : -0.49 (0.54), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 134 HIS 0.002 0.001 HIS A 59 PHE 0.024 0.001 PHE A 553 TYR 0.016 0.001 TYR A 369 ARG 0.003 0.000 ARG A 81 Details of bonding type rmsd hydrogen bonds : bond 0.03276 ( 329) hydrogen bonds : angle 3.88481 ( 963) SS BOND : bond 0.00284 ( 17) SS BOND : angle 0.89248 ( 34) covalent geometry : bond 0.00283 ( 4683) covalent geometry : angle 0.55409 ( 6322) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1154 Ramachandran restraints generated. 577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1154 Ramachandran restraints generated. 577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 12 time to evaluate : 0.646 Fit side-chains revert: symmetry clash REVERT: A 59 HIS cc_start: 0.9405 (t-90) cc_final: 0.9110 (t-90) REVERT: A 103 LEU cc_start: 0.9091 (tt) cc_final: 0.8699 (mp) REVERT: A 275 LYS cc_start: 0.9435 (ttmt) cc_final: 0.9149 (tptp) REVERT: A 520 LYS cc_start: 0.9218 (OUTLIER) cc_final: 0.8606 (mttm) REVERT: A 547 MET cc_start: 0.9402 (mtp) cc_final: 0.8951 (mmm) REVERT: A 573 LYS cc_start: 0.9682 (tptp) cc_final: 0.9419 (pttt) outliers start: 13 outliers final: 11 residues processed: 25 average time/residue: 0.1414 time to fit residues: 5.3732 Evaluate side-chains 24 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 12 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 101 CYS Chi-restraints excluded: chain A residue 161 ASN Chi-restraints excluded: chain A residue 244 CYS Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 437 CYS Chi-restraints excluded: chain A residue 447 CYS Chi-restraints excluded: chain A residue 509 HIS Chi-restraints excluded: chain A residue 520 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 55 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 HIS A 404 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.061107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.042043 restraints weight = 14717.163| |-----------------------------------------------------------------------------| r_work (start): 0.2720 rms_B_bonded: 4.18 r_work: 0.2524 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.2524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.3990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4700 Z= 0.132 Angle : 0.533 7.194 6356 Z= 0.271 Chirality : 0.038 0.137 703 Planarity : 0.004 0.057 822 Dihedral : 5.257 58.280 627 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.73 % Allowed : 22.22 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: 2.36 (0.35), residues: 577 helix: 2.14 (0.25), residues: 440 sheet: None (None), residues: 0 loop : -0.33 (0.54), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 134 HIS 0.002 0.001 HIS A 337 PHE 0.019 0.001 PHE A 553 TYR 0.015 0.001 TYR A 369 ARG 0.003 0.000 ARG A 185 Details of bonding type rmsd hydrogen bonds : bond 0.03226 ( 329) hydrogen bonds : angle 3.80194 ( 963) SS BOND : bond 0.00265 ( 17) SS BOND : angle 0.91814 ( 34) covalent geometry : bond 0.00311 ( 4683) covalent geometry : angle 0.53001 ( 6322) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1154 Ramachandran restraints generated. 577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1154 Ramachandran restraints generated. 577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 14 time to evaluate : 0.540 Fit side-chains revert: symmetry clash REVERT: A 59 HIS cc_start: 0.9434 (t-90) cc_final: 0.9110 (t-90) REVERT: A 103 LEU cc_start: 0.9111 (tt) cc_final: 0.8733 (mp) REVERT: A 275 LYS cc_start: 0.9437 (ttmt) cc_final: 0.9158 (tptp) REVERT: A 520 LYS cc_start: 0.9207 (OUTLIER) cc_final: 0.8703 (mttt) REVERT: A 547 MET cc_start: 0.9446 (mtp) cc_final: 0.9026 (mmm) REVERT: A 553 PHE cc_start: 0.9326 (t80) cc_final: 0.7662 (t80) REVERT: A 573 LYS cc_start: 0.9702 (tptp) cc_final: 0.9430 (pttt) outliers start: 14 outliers final: 10 residues processed: 28 average time/residue: 0.1421 time to fit residues: 5.9095 Evaluate side-chains 23 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 12 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 CYS Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 101 CYS Chi-restraints excluded: chain A residue 161 ASN Chi-restraints excluded: chain A residue 244 CYS Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 437 CYS Chi-restraints excluded: chain A residue 447 CYS Chi-restraints excluded: chain A residue 520 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 23 optimal weight: 0.0870 chunk 45 optimal weight: 0.7980 chunk 48 optimal weight: 6.9990 chunk 3 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 54 optimal weight: 0.8980 chunk 8 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 29 optimal weight: 0.0050 overall best weight: 0.4972 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.062130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.042946 restraints weight = 14785.319| |-----------------------------------------------------------------------------| r_work (start): 0.2741 rms_B_bonded: 4.22 r_work: 0.2545 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.2545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.4223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 4700 Z= 0.104 Angle : 0.517 6.898 6356 Z= 0.261 Chirality : 0.037 0.157 703 Planarity : 0.004 0.058 822 Dihedral : 5.079 55.773 627 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.12 % Allowed : 22.03 % Favored : 74.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.56 (0.36), residues: 577 helix: 2.23 (0.25), residues: 446 sheet: None (None), residues: 0 loop : -0.14 (0.56), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 134 HIS 0.002 0.000 HIS A 378 PHE 0.021 0.001 PHE A 553 TYR 0.014 0.001 TYR A 369 ARG 0.002 0.000 ARG A 81 Details of bonding type rmsd hydrogen bonds : bond 0.02961 ( 329) hydrogen bonds : angle 3.68945 ( 963) SS BOND : bond 0.00193 ( 17) SS BOND : angle 0.79405 ( 34) covalent geometry : bond 0.00234 ( 4683) covalent geometry : angle 0.51494 ( 6322) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1154 Ramachandran restraints generated. 577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1154 Ramachandran restraints generated. 577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 14 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 HIS cc_start: 0.9436 (t-90) cc_final: 0.9046 (t-90) REVERT: A 103 LEU cc_start: 0.9121 (tt) cc_final: 0.8772 (mp) REVERT: A 520 LYS cc_start: 0.9220 (OUTLIER) cc_final: 0.8727 (mttt) REVERT: A 547 MET cc_start: 0.9442 (mtp) cc_final: 0.9028 (mmm) REVERT: A 553 PHE cc_start: 0.9335 (t80) cc_final: 0.7775 (t80) REVERT: A 573 LYS cc_start: 0.9686 (tptp) cc_final: 0.9457 (pttt) outliers start: 16 outliers final: 12 residues processed: 29 average time/residue: 0.1474 time to fit residues: 6.3224 Evaluate side-chains 27 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 14 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 CYS Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 101 CYS Chi-restraints excluded: chain A residue 161 ASN Chi-restraints excluded: chain A residue 244 CYS Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 437 CYS Chi-restraints excluded: chain A residue 447 CYS Chi-restraints excluded: chain A residue 520 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 23 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 44 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.060291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.041004 restraints weight = 14551.503| |-----------------------------------------------------------------------------| r_work (start): 0.2647 rms_B_bonded: 4.08 r_work: 0.2448 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.2448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.4141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 4700 Z= 0.174 Angle : 0.549 6.576 6356 Z= 0.280 Chirality : 0.039 0.131 703 Planarity : 0.004 0.057 822 Dihedral : 5.095 54.003 627 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.92 % Allowed : 22.03 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.67 (0.36), residues: 577 helix: 2.34 (0.25), residues: 441 sheet: None (None), residues: 0 loop : -0.16 (0.55), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 134 HIS 0.003 0.001 HIS A 59 PHE 0.020 0.001 PHE A 567 TYR 0.014 0.001 TYR A 369 ARG 0.002 0.000 ARG A 81 Details of bonding type rmsd hydrogen bonds : bond 0.03316 ( 329) hydrogen bonds : angle 3.81440 ( 963) SS BOND : bond 0.00252 ( 17) SS BOND : angle 0.84095 ( 34) covalent geometry : bond 0.00408 ( 4683) covalent geometry : angle 0.54663 ( 6322) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1154 Ramachandran restraints generated. 577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1154 Ramachandran restraints generated. 577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 11 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 HIS cc_start: 0.9444 (t-90) cc_final: 0.9072 (t-90) REVERT: A 103 LEU cc_start: 0.9192 (tt) cc_final: 0.8825 (mp) REVERT: A 275 LYS cc_start: 0.9453 (ttmt) cc_final: 0.9147 (tptp) REVERT: A 520 LYS cc_start: 0.9194 (OUTLIER) cc_final: 0.8665 (mttt) REVERT: A 547 MET cc_start: 0.9436 (mtp) cc_final: 0.9046 (mmm) outliers start: 15 outliers final: 13 residues processed: 26 average time/residue: 0.1421 time to fit residues: 5.5109 Evaluate side-chains 25 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 11 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 CYS Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 101 CYS Chi-restraints excluded: chain A residue 161 ASN Chi-restraints excluded: chain A residue 244 CYS Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 437 CYS Chi-restraints excluded: chain A residue 447 CYS Chi-restraints excluded: chain A residue 520 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 29 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 54 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 43 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 49 optimal weight: 0.1980 chunk 31 optimal weight: 3.9990 chunk 11 optimal weight: 6.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3234 r_free = 0.3234 target = 0.061498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.042386 restraints weight = 14535.503| |-----------------------------------------------------------------------------| r_work (start): 0.2732 rms_B_bonded: 4.20 r_work: 0.2535 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.2535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.4337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4700 Z= 0.113 Angle : 0.498 6.471 6356 Z= 0.254 Chirality : 0.037 0.121 703 Planarity : 0.004 0.058 822 Dihedral : 4.916 50.501 627 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.51 % Allowed : 21.64 % Favored : 74.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.76 (0.35), residues: 577 helix: 2.46 (0.25), residues: 440 sheet: None (None), residues: 0 loop : -0.29 (0.54), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 134 HIS 0.002 0.001 HIS A 59 PHE 0.017 0.001 PHE A 567 TYR 0.014 0.001 TYR A 369 ARG 0.001 0.000 ARG A 81 Details of bonding type rmsd hydrogen bonds : bond 0.02988 ( 329) hydrogen bonds : angle 3.68302 ( 963) SS BOND : bond 0.00192 ( 17) SS BOND : angle 0.74925 ( 34) covalent geometry : bond 0.00260 ( 4683) covalent geometry : angle 0.49674 ( 6322) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1154 Ramachandran restraints generated. 577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1154 Ramachandran restraints generated. 577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 14 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 HIS cc_start: 0.9462 (t-90) cc_final: 0.9064 (t-90) REVERT: A 103 LEU cc_start: 0.9126 (tt) cc_final: 0.8785 (mp) REVERT: A 275 LYS cc_start: 0.9450 (ttmt) cc_final: 0.9154 (tptp) REVERT: A 520 LYS cc_start: 0.9202 (OUTLIER) cc_final: 0.8725 (mttt) REVERT: A 547 MET cc_start: 0.9458 (mtp) cc_final: 0.9056 (mmm) outliers start: 18 outliers final: 14 residues processed: 32 average time/residue: 0.1407 time to fit residues: 6.7059 Evaluate side-chains 27 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 12 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 CYS Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 101 CYS Chi-restraints excluded: chain A residue 161 ASN Chi-restraints excluded: chain A residue 244 CYS Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 437 CYS Chi-restraints excluded: chain A residue 447 CYS Chi-restraints excluded: chain A residue 520 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 56 optimal weight: 10.0000 chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 0.3980 chunk 41 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 chunk 13 optimal weight: 0.8980 chunk 22 optimal weight: 0.3980 chunk 25 optimal weight: 1.9990 chunk 17 optimal weight: 0.4980 chunk 24 optimal weight: 0.6980 chunk 1 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.3248 r_free = 0.3248 target = 0.062010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.042880 restraints weight = 14662.403| |-----------------------------------------------------------------------------| r_work (start): 0.2744 rms_B_bonded: 4.22 r_work: 0.2552 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.2552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.4468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 4700 Z= 0.101 Angle : 0.495 6.227 6356 Z= 0.251 Chirality : 0.037 0.122 703 Planarity : 0.004 0.059 822 Dihedral : 4.813 47.272 627 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.12 % Allowed : 22.03 % Favored : 74.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.68 (0.36), residues: 577 helix: 2.31 (0.25), residues: 451 sheet: None (None), residues: 0 loop : -0.19 (0.56), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 134 HIS 0.002 0.000 HIS A 59 PHE 0.018 0.001 PHE A 567 TYR 0.013 0.001 TYR A 369 ARG 0.002 0.000 ARG A 81 Details of bonding type rmsd hydrogen bonds : bond 0.02902 ( 329) hydrogen bonds : angle 3.62128 ( 963) SS BOND : bond 0.00168 ( 17) SS BOND : angle 0.73113 ( 34) covalent geometry : bond 0.00225 ( 4683) covalent geometry : angle 0.49341 ( 6322) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1154 Ramachandran restraints generated. 577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1154 Ramachandran restraints generated. 577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 12 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 HIS cc_start: 0.9465 (t-90) cc_final: 0.9058 (t-90) REVERT: A 275 LYS cc_start: 0.9453 (ttmt) cc_final: 0.9155 (tptp) REVERT: A 520 LYS cc_start: 0.9199 (OUTLIER) cc_final: 0.8692 (mttt) REVERT: A 547 MET cc_start: 0.9449 (mtp) cc_final: 0.9071 (mmm) outliers start: 16 outliers final: 14 residues processed: 28 average time/residue: 0.1441 time to fit residues: 5.9910 Evaluate side-chains 26 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 11 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 CYS Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 101 CYS Chi-restraints excluded: chain A residue 161 ASN Chi-restraints excluded: chain A residue 244 CYS Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 437 CYS Chi-restraints excluded: chain A residue 447 CYS Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain A residue 520 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 21 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 14 optimal weight: 0.0980 chunk 16 optimal weight: 0.5980 chunk 47 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.061941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.042798 restraints weight = 14760.430| |-----------------------------------------------------------------------------| r_work (start): 0.2740 rms_B_bonded: 4.24 r_work: 0.2546 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.2546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.4544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 4700 Z= 0.107 Angle : 0.492 6.128 6356 Z= 0.251 Chirality : 0.037 0.121 703 Planarity : 0.004 0.058 822 Dihedral : 4.732 44.720 627 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.73 % Allowed : 22.61 % Favored : 74.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.80 (0.36), residues: 577 helix: 2.38 (0.25), residues: 451 sheet: None (None), residues: 0 loop : -0.09 (0.57), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 134 HIS 0.002 0.000 HIS A 59 PHE 0.017 0.001 PHE A 567 TYR 0.013 0.001 TYR A 369 ARG 0.002 0.000 ARG A 81 Details of bonding type rmsd hydrogen bonds : bond 0.02881 ( 329) hydrogen bonds : angle 3.59586 ( 963) SS BOND : bond 0.00176 ( 17) SS BOND : angle 0.72333 ( 34) covalent geometry : bond 0.00246 ( 4683) covalent geometry : angle 0.49056 ( 6322) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1154 Ramachandran restraints generated. 577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1154 Ramachandran restraints generated. 577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 12 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 HIS cc_start: 0.9461 (t-90) cc_final: 0.9054 (t-90) REVERT: A 275 LYS cc_start: 0.9458 (ttmt) cc_final: 0.9138 (tptt) REVERT: A 520 LYS cc_start: 0.9201 (OUTLIER) cc_final: 0.8820 (mttt) REVERT: A 547 MET cc_start: 0.9453 (mtp) cc_final: 0.9127 (mmm) outliers start: 14 outliers final: 13 residues processed: 26 average time/residue: 0.1515 time to fit residues: 5.7998 Evaluate side-chains 25 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 11 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 CYS Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 101 CYS Chi-restraints excluded: chain A residue 161 ASN Chi-restraints excluded: chain A residue 244 CYS Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 437 CYS Chi-restraints excluded: chain A residue 447 CYS Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain A residue 520 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 9 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 21 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 54 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 11 optimal weight: 0.0070 overall best weight: 0.6800 ------------------------------------------------------------------------------- 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 = 0.3245 r_free = 0.3245 target = 0.061802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.042758 restraints weight = 15093.916| |-----------------------------------------------------------------------------| r_work (start): 0.2736 rms_B_bonded: 4.24 r_work: 0.2537 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.2537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.4601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4700 Z= 0.111 Angle : 0.493 6.064 6356 Z= 0.251 Chirality : 0.037 0.121 703 Planarity : 0.004 0.058 822 Dihedral : 4.647 44.882 627 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.12 % Allowed : 22.81 % Favored : 74.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.85 (0.36), residues: 577 helix: 2.39 (0.25), residues: 451 sheet: None (None), residues: 0 loop : 0.02 (0.57), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 134 HIS 0.002 0.000 HIS A 59 PHE 0.017 0.001 PHE A 567 TYR 0.013 0.001 TYR A 369 ARG 0.002 0.000 ARG A 81 Details of bonding type rmsd hydrogen bonds : bond 0.02906 ( 329) hydrogen bonds : angle 3.58645 ( 963) SS BOND : bond 0.00174 ( 17) SS BOND : angle 0.72272 ( 34) covalent geometry : bond 0.00256 ( 4683) covalent geometry : angle 0.49142 ( 6322) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2554.25 seconds wall clock time: 45 minutes 2.49 seconds (2702.49 seconds total)