Starting phenix.real_space_refine on Fri Aug 22 15:04:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qqd_53298/08_2025/9qqd_53298.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qqd_53298/08_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_53298/08_2025/9qqd_53298.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qqd_53298/08_2025/9qqd_53298.map" model { file = "/net/cci-nas-00/data/ceres_data/9qqd_53298/08_2025/9qqd_53298.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qqd_53298/08_2025/9qqd_53298.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 1.31, per 1000 atoms: 0.29 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: 0.37 Conformation dependent library (CDL) restraints added in 182.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.11 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: 0.67 Time building geometry restraints manager: 0.53 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: 1.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.890 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.170 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.068 0.013 ARG A 81 TYR 0.036 0.006 TYR A 160 PHE 0.027 0.005 PHE A 308 TRP 0.031 0.010 TRP A 134 HIS 0.008 0.003 HIS A 59 Details of bonding type rmsd covalent geometry : bond 0.00998 ( 4683) covalent geometry : angle 1.94408 ( 6322) SS BOND : bond 0.16225 ( 17) SS BOND : angle 3.80038 ( 34) hydrogen bonds : bond 0.22052 ( 329) hydrogen bonds : angle 7.03568 ( 963) *********************** 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 : 0.115 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: 0.9479 (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: 0.0703 time to fit residues: 8.4894 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 : 0.119 ------------------------------------------------------------------------------- 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 54 optimal weight: 0.6980 chunk 24 optimal weight: 0.0030 chunk 48 optimal weight: 0.0970 chunk 56 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 overall best weight: 0.5188 ------------------------------------------------------------------------------- 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 = 0.3316 r_free = 0.3316 target = 0.063652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.045268 restraints weight = 14254.716| |-----------------------------------------------------------------------------| r_work (start): 0.2769 rms_B_bonded: 4.09 r_work: 0.2557 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.2557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 4700 Z= 0.155 Angle : 0.700 8.509 6356 Z= 0.362 Chirality : 0.041 0.144 703 Planarity : 0.005 0.055 822 Dihedral : 9.721 76.939 675 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 5.07 % Allowed : 22.22 % Favored : 72.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.11 (0.33), residues: 577 helix: 0.67 (0.24), residues: 439 sheet: None (None), residues: 0 loop : -1.69 (0.49), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 143 TYR 0.022 0.002 TYR A 369 PHE 0.014 0.002 PHE A 567 TRP 0.026 0.004 TRP A 134 HIS 0.003 0.001 HIS A 59 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 4683) covalent geometry : angle 0.69259 ( 6322) SS BOND : bond 0.00395 ( 17) SS BOND : angle 1.51970 ( 34) hydrogen bonds : bond 0.04154 ( 329) hydrogen bonds : angle 4.43679 ( 963) *********************** 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 45 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 19 time to evaluate : 0.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 HIS cc_start: 0.9284 (t-90) cc_final: 0.8990 (t-90) REVERT: A 275 LYS cc_start: 0.9394 (ttmt) cc_final: 0.9043 (tptp) REVERT: A 304 LEU cc_start: 0.7454 (tp) cc_final: 0.7235 (tp) REVERT: A 312 LYS cc_start: 0.9694 (OUTLIER) cc_final: 0.9490 (mmmm) REVERT: A 385 ASN cc_start: 0.9419 (OUTLIER) cc_final: 0.9111 (t0) REVERT: A 511 ASP cc_start: 0.9321 (OUTLIER) cc_final: 0.8998 (p0) REVERT: A 564 GLU cc_start: 0.9369 (OUTLIER) cc_final: 0.9076 (pm20) outliers start: 26 outliers final: 12 residues processed: 43 average time/residue: 0.0638 time to fit residues: 3.6720 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 : 0.120 ------------------------------------------------------------------------------- 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 51 optimal weight: 6.9990 chunk 28 optimal weight: 0.0970 chunk 21 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 29 optimal weight: 0.0370 chunk 8 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 chunk 14 optimal weight: 0.7980 chunk 31 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 overall best weight: 0.5056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS A 161 ASN A 366 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.062234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.043413 restraints weight = 14409.559| |-----------------------------------------------------------------------------| r_work (start): 0.2759 rms_B_bonded: 4.14 r_work: 0.2566 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.2566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.3610 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= 0.121 Angle : 0.582 8.173 6356 Z= 0.295 Chirality : 0.038 0.125 703 Planarity : 0.004 0.056 822 Dihedral : 6.748 61.860 644 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.31 % Allowed : 21.64 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.58 (0.35), residues: 577 helix: 1.71 (0.24), residues: 440 sheet: None (None), residues: 0 loop : -1.11 (0.54), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 81 TYR 0.018 0.001 TYR A 369 PHE 0.031 0.001 PHE A 553 TRP 0.018 0.003 TRP A 134 HIS 0.002 0.001 HIS A 378 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 4683) covalent geometry : angle 0.57792 ( 6322) SS BOND : bond 0.00217 ( 17) SS BOND : angle 1.07670 ( 34) hydrogen bonds : bond 0.03480 ( 329) hydrogen bonds : angle 3.96785 ( 963) *********************** 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 28 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 11 time to evaluate : 0.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 HIS cc_start: 0.9373 (t-90) cc_final: 0.9100 (t-90) REVERT: A 275 LYS cc_start: 0.9407 (ttmt) cc_final: 0.9116 (tptp) REVERT: A 304 LEU cc_start: 0.7605 (tp) cc_final: 0.7401 (tp) REVERT: A 385 ASN cc_start: 0.9444 (OUTLIER) cc_final: 0.9082 (t0) REVERT: A 547 MET cc_start: 0.9579 (mtp) cc_final: 0.8831 (mmm) outliers start: 17 outliers final: 9 residues processed: 28 average time/residue: 0.0478 time to fit residues: 1.9102 Evaluate side-chains 21 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 11 time to evaluate : 0.112 ------------------------------------------------------------------------------- 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 312 LYS 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 520 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 33 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 36 optimal weight: 6.9990 chunk 45 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 32 optimal weight: 0.6980 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 337 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.061282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.042533 restraints weight = 14449.389| |-----------------------------------------------------------------------------| r_work (start): 0.2728 rms_B_bonded: 4.12 r_work: 0.2535 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.2535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.3802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4700 Z= 0.138 Angle : 0.563 7.658 6356 Z= 0.289 Chirality : 0.038 0.140 703 Planarity : 0.004 0.056 822 Dihedral : 5.539 52.149 633 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.34 % Allowed : 21.25 % Favored : 76.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.10 (0.35), residues: 577 helix: 2.00 (0.25), residues: 439 sheet: None (None), residues: 0 loop : -0.57 (0.54), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 81 TYR 0.016 0.001 TYR A 369 PHE 0.022 0.001 PHE A 553 TRP 0.017 0.002 TRP A 134 HIS 0.003 0.001 HIS A 59 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 4683) covalent geometry : angle 0.55999 ( 6322) SS BOND : bond 0.00324 ( 17) SS BOND : angle 1.01235 ( 34) hydrogen bonds : bond 0.03346 ( 329) hydrogen bonds : angle 3.87846 ( 963) *********************** 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: 12 poor density : 13 time to evaluate : 0.139 Fit side-chains revert: symmetry clash REVERT: A 59 HIS cc_start: 0.9411 (t-90) cc_final: 0.9114 (t-90) REVERT: A 103 LEU cc_start: 0.9150 (tt) cc_final: 0.8880 (mm) REVERT: A 275 LYS cc_start: 0.9434 (ttmt) cc_final: 0.9146 (tptp) REVERT: A 520 LYS cc_start: 0.9222 (OUTLIER) cc_final: 0.8600 (mttm) REVERT: A 573 LYS cc_start: 0.9686 (tptp) cc_final: 0.9433 (pttt) outliers start: 12 outliers final: 10 residues processed: 25 average time/residue: 0.0612 time to fit residues: 2.1687 Evaluate side-chains 24 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 13 time to evaluate : 0.106 ------------------------------------------------------------------------------- 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 520 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 25 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 23 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3253 r_free = 0.3253 target = 0.061814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.043228 restraints weight = 14528.549| |-----------------------------------------------------------------------------| r_work (start): 0.2737 rms_B_bonded: 4.11 r_work: 0.2542 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.2542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.4109 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= 0.123 Angle : 0.525 7.368 6356 Z= 0.267 Chirality : 0.037 0.146 703 Planarity : 0.004 0.056 822 Dihedral : 5.033 47.580 627 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 : 3.12 % Allowed : 21.25 % Favored : 75.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.39 (0.36), residues: 577 helix: 2.20 (0.25), residues: 439 sheet: None (None), residues: 0 loop : -0.44 (0.55), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 81 TYR 0.015 0.001 TYR A 369 PHE 0.021 0.001 PHE A 553 TRP 0.016 0.002 TRP A 134 HIS 0.002 0.000 HIS A 59 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 4683) covalent geometry : angle 0.52170 ( 6322) SS BOND : bond 0.00275 ( 17) SS BOND : angle 0.92575 ( 34) hydrogen bonds : bond 0.03119 ( 329) hydrogen bonds : angle 3.77163 ( 963) *********************** 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 30 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 14 time to evaluate : 0.210 Fit side-chains revert: symmetry clash REVERT: A 59 HIS cc_start: 0.9438 (t-90) cc_final: 0.9096 (t-90) REVERT: A 103 LEU cc_start: 0.9153 (tt) cc_final: 0.8932 (mm) REVERT: A 275 LYS cc_start: 0.9440 (ttmt) cc_final: 0.9161 (tptp) REVERT: A 520 LYS cc_start: 0.9203 (OUTLIER) cc_final: 0.8632 (mttt) REVERT: A 547 MET cc_start: 0.9445 (mtp) cc_final: 0.9091 (mmm) outliers start: 16 outliers final: 10 residues processed: 29 average time/residue: 0.0427 time to fit residues: 1.8011 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 : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 CYS 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 244 CYS 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 509 HIS 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 27 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 34 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3241 r_free = 0.3241 target = 0.061651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.042647 restraints weight = 15299.198| |-----------------------------------------------------------------------------| r_work (start): 0.2725 rms_B_bonded: 4.25 r_work: 0.2527 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.2527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.4245 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= 0.128 Angle : 0.527 6.805 6356 Z= 0.270 Chirality : 0.038 0.156 703 Planarity : 0.004 0.063 822 Dihedral : 4.595 46.062 625 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.12 % Allowed : 21.05 % Favored : 75.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.61 (0.36), residues: 577 helix: 2.30 (0.25), residues: 441 sheet: None (None), residues: 0 loop : -0.21 (0.55), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 81 TYR 0.014 0.001 TYR A 369 PHE 0.022 0.001 PHE A 553 TRP 0.015 0.002 TRP A 134 HIS 0.002 0.001 HIS A 59 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 4683) covalent geometry : angle 0.52338 ( 6322) SS BOND : bond 0.00309 ( 17) SS BOND : angle 0.99934 ( 34) hydrogen bonds : bond 0.03121 ( 329) hydrogen bonds : angle 3.74518 ( 963) *********************** 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 28 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 12 time to evaluate : 0.200 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 HIS cc_start: 0.9430 (t-90) cc_final: 0.9053 (t-90) REVERT: A 103 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8966 (mm) REVERT: A 520 LYS cc_start: 0.9220 (OUTLIER) cc_final: 0.8672 (mttt) REVERT: A 547 MET cc_start: 0.9471 (mtp) cc_final: 0.9102 (mmm) outliers start: 16 outliers final: 12 residues processed: 27 average time/residue: 0.0520 time to fit residues: 2.0809 Evaluate side-chains 24 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 10 time to evaluate : 0.132 ------------------------------------------------------------------------------- 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 103 LEU 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 34 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 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 = 0.3254 r_free = 0.3254 target = 0.061920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.042834 restraints weight = 14861.185| |-----------------------------------------------------------------------------| r_work (start): 0.2730 rms_B_bonded: 4.19 r_work: 0.2534 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.2534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.4384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4700 Z= 0.124 Angle : 0.514 6.619 6356 Z= 0.263 Chirality : 0.038 0.135 703 Planarity : 0.004 0.064 822 Dihedral : 4.481 46.173 625 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.31 % Allowed : 21.05 % Favored : 75.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.68 (0.36), residues: 577 helix: 2.36 (0.25), residues: 441 sheet: None (None), residues: 0 loop : -0.21 (0.56), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 81 TYR 0.014 0.001 TYR A 369 PHE 0.019 0.001 PHE A 553 TRP 0.015 0.002 TRP A 134 HIS 0.002 0.000 HIS A 59 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 4683) covalent geometry : angle 0.51114 ( 6322) SS BOND : bond 0.00270 ( 17) SS BOND : angle 0.90450 ( 34) hydrogen bonds : bond 0.03057 ( 329) hydrogen bonds : angle 3.71759 ( 963) *********************** 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 28 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 11 time to evaluate : 0.207 Fit side-chains revert: symmetry clash REVERT: A 59 HIS cc_start: 0.9447 (t-90) cc_final: 0.9056 (t-90) REVERT: A 275 LYS cc_start: 0.9445 (ttmt) cc_final: 0.9176 (tptp) REVERT: A 520 LYS cc_start: 0.9204 (OUTLIER) cc_final: 0.8716 (mttt) REVERT: A 547 MET cc_start: 0.9524 (mtp) cc_final: 0.9106 (mmm) outliers start: 17 outliers final: 12 residues processed: 27 average time/residue: 0.0533 time to fit residues: 2.2646 Evaluate side-chains 22 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 9 time to evaluate : 0.166 ------------------------------------------------------------------------------- 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 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 9 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 11 optimal weight: 9.9990 chunk 44 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 = 0.3203 r_free = 0.3203 target = 0.060995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2689 r_free = 0.2689 target = 0.041401 restraints weight = 14810.300| |-----------------------------------------------------------------------------| r_work (start): 0.2714 rms_B_bonded: 4.13 r_work: 0.2514 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.2514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.4431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 4700 Z= 0.155 Angle : 0.530 6.207 6356 Z= 0.271 Chirality : 0.038 0.124 703 Planarity : 0.004 0.060 822 Dihedral : 4.503 47.449 625 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.12 % Allowed : 21.05 % Favored : 75.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.63 (0.36), residues: 577 helix: 2.28 (0.25), residues: 447 sheet: None (None), residues: 0 loop : -0.15 (0.57), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 81 TYR 0.014 0.001 TYR A 369 PHE 0.016 0.001 PHE A 553 TRP 0.016 0.002 TRP A 134 HIS 0.002 0.001 HIS A 59 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 4683) covalent geometry : angle 0.52779 ( 6322) SS BOND : bond 0.00270 ( 17) SS BOND : angle 0.87525 ( 34) hydrogen bonds : bond 0.03186 ( 329) hydrogen bonds : angle 3.77313 ( 963) *********************** 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 24 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 8 time to evaluate : 0.187 Fit side-chains revert: symmetry clash REVERT: A 59 HIS cc_start: 0.9419 (t-90) cc_final: 0.9032 (t-90) REVERT: A 275 LYS cc_start: 0.9468 (ttmt) cc_final: 0.9195 (tptp) REVERT: A 520 LYS cc_start: 0.9182 (OUTLIER) cc_final: 0.8697 (mttt) REVERT: A 547 MET cc_start: 0.9522 (mtp) cc_final: 0.9072 (mmm) outliers start: 16 outliers final: 13 residues processed: 24 average time/residue: 0.0471 time to fit residues: 1.7434 Evaluate side-chains 22 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 8 time to evaluate : 0.188 ------------------------------------------------------------------------------- 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 123 CYS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 24 optimal weight: 0.6980 chunk 53 optimal weight: 0.0570 chunk 5 optimal weight: 0.3980 chunk 44 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 0 optimal weight: 0.6980 chunk 50 optimal weight: 7.9990 chunk 30 optimal weight: 0.7980 overall best weight: 0.5098 ------------------------------------------------------------------------------- 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 = 0.3250 r_free = 0.3250 target = 0.062134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.042880 restraints weight = 14664.756| |-----------------------------------------------------------------------------| r_work (start): 0.2743 rms_B_bonded: 4.23 r_work: 0.2546 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.2546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.4648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 4700 Z= 0.104 Angle : 0.489 6.116 6356 Z= 0.251 Chirality : 0.037 0.123 703 Planarity : 0.004 0.062 822 Dihedral : 4.368 44.227 625 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.12 % Allowed : 21.25 % Favored : 75.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.68 (0.36), residues: 577 helix: 2.29 (0.25), residues: 452 sheet: None (None), residues: 0 loop : -0.10 (0.57), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 81 TYR 0.013 0.001 TYR A 369 PHE 0.009 0.001 PHE A 553 TRP 0.014 0.002 TRP A 134 HIS 0.002 0.000 HIS A 59 Details of bonding type rmsd covalent geometry : bond 0.00236 ( 4683) covalent geometry : angle 0.48750 ( 6322) SS BOND : bond 0.00212 ( 17) SS BOND : angle 0.77397 ( 34) hydrogen bonds : bond 0.02882 ( 329) hydrogen bonds : angle 3.63986 ( 963) *********************** 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 26 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 10 time to evaluate : 0.146 Fit side-chains revert: symmetry clash REVERT: A 59 HIS cc_start: 0.9463 (t-90) cc_final: 0.9070 (t-90) REVERT: A 275 LYS cc_start: 0.9456 (ttmt) cc_final: 0.9188 (tptp) REVERT: A 520 LYS cc_start: 0.9191 (OUTLIER) cc_final: 0.8738 (mttt) REVERT: A 547 MET cc_start: 0.9540 (mtp) cc_final: 0.9077 (mmm) outliers start: 16 outliers final: 13 residues processed: 25 average time/residue: 0.0382 time to fit residues: 1.4773 Evaluate side-chains 23 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 9 time to evaluate : 0.204 ------------------------------------------------------------------------------- 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 123 CYS 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 24 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 7 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 47 optimal weight: 0.0070 chunk 17 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 chunk 8 optimal weight: 7.9990 chunk 21 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 overall best weight: 0.5998 ------------------------------------------------------------------------------- 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 = 0.3262 r_free = 0.3262 target = 0.062502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.043201 restraints weight = 14864.383| |-----------------------------------------------------------------------------| r_work (start): 0.2744 rms_B_bonded: 4.13 r_work: 0.2543 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.2543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.4706 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 : 0.491 6.001 6356 Z= 0.250 Chirality : 0.037 0.122 703 Planarity : 0.004 0.063 822 Dihedral : 4.322 44.444 625 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.92 % Allowed : 21.25 % Favored : 75.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.76 (0.36), residues: 577 helix: 2.36 (0.25), residues: 451 sheet: None (None), residues: 0 loop : -0.14 (0.57), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 81 TYR 0.013 0.001 TYR A 369 PHE 0.008 0.001 PHE A 164 TRP 0.014 0.002 TRP A 134 HIS 0.002 0.000 HIS A 59 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 4683) covalent geometry : angle 0.48886 ( 6322) SS BOND : bond 0.00202 ( 17) SS BOND : angle 0.76302 ( 34) hydrogen bonds : bond 0.02879 ( 329) hydrogen bonds : angle 3.61646 ( 963) ********************** 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: 15 poor density : 11 time to evaluate : 0.169 Fit side-chains revert: symmetry clash REVERT: A 59 HIS cc_start: 0.9396 (t-90) cc_final: 0.8982 (t-90) REVERT: A 103 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8931 (mp) REVERT: A 184 MET cc_start: 0.8818 (tpp) cc_final: 0.8583 (ttt) REVERT: A 275 LYS cc_start: 0.9466 (ttmt) cc_final: 0.9191 (tptt) REVERT: A 520 LYS cc_start: 0.9205 (OUTLIER) cc_final: 0.8737 (mttt) REVERT: A 547 MET cc_start: 0.9527 (mtp) cc_final: 0.9059 (mmm) outliers start: 15 outliers final: 13 residues processed: 25 average time/residue: 0.0574 time to fit residues: 2.0727 Evaluate side-chains 25 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 10 time to evaluate : 0.114 ------------------------------------------------------------------------------- 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 103 LEU Chi-restraints excluded: chain A residue 123 CYS 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 40 optimal weight: 0.6980 chunk 10 optimal weight: 0.0670 chunk 18 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 20 optimal weight: 0.0170 chunk 55 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 overall best weight: 0.4956 ------------------------------------------------------------------------------- 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 = 0.3260 r_free = 0.3260 target = 0.062550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.043400 restraints weight = 14750.731| |-----------------------------------------------------------------------------| r_work (start): 0.2761 rms_B_bonded: 4.24 r_work: 0.2565 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.2565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.4843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 4700 Z= 0.098 Angle : 0.480 6.029 6356 Z= 0.244 Chirality : 0.036 0.126 703 Planarity : 0.004 0.063 822 Dihedral : 4.235 43.371 625 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.73 % Allowed : 21.44 % Favored : 75.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.84 (0.36), residues: 577 helix: 2.41 (0.25), residues: 451 sheet: None (None), residues: 0 loop : -0.06 (0.58), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 81 TYR 0.013 0.001 TYR A 369 PHE 0.007 0.001 PHE A 164 TRP 0.013 0.002 TRP A 134 HIS 0.002 0.000 HIS A 59 Details of bonding type rmsd covalent geometry : bond 0.00221 ( 4683) covalent geometry : angle 0.47856 ( 6322) SS BOND : bond 0.00177 ( 17) SS BOND : angle 0.71253 ( 34) hydrogen bonds : bond 0.02758 ( 329) hydrogen bonds : angle 3.56325 ( 963) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1051.06 seconds wall clock time: 18 minutes 38.75 seconds (1118.75 seconds total)