Starting phenix.real_space_refine on Sat May 10 01:28:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j7n_61208/05_2025/9j7n_61208.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j7n_61208/05_2025/9j7n_61208.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9j7n_61208/05_2025/9j7n_61208.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j7n_61208/05_2025/9j7n_61208.map" model { file = "/net/cci-nas-00/data/ceres_data/9j7n_61208/05_2025/9j7n_61208.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j7n_61208/05_2025/9j7n_61208.cif" } resolution = 3.14 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= 0.048 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: 5 Type Number sf(0) Gaussians S 32 5.16 5 Cl 1 4.86 5 C 3081 2.51 5 N 659 2.21 5 O 744 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 4517 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 543, 4321 Classifications: {'peptide': 543} Link IDs: {'PTRANS': 29, 'TRANS': 513} Chain breaks: 2 Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 6 Unusual residues: {'BAL': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 190 Unusual residues: {' CL': 1, 'CLR': 2, 'R16': 8} Classifications: {'undetermined': 11, 'water': 5} Link IDs: {None: 15} Time building chain proxies: 3.49, per 1000 atoms: 0.77 Number of scatterers: 4517 At special positions: 0 Unit cell: (73.95, 69.7, 94.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 1 17.00 S 32 16.00 O 744 8.00 N 659 7.00 C 3081 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 162 " - pdb=" SG CYS A 171 " distance=2.04 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: 1.23 Conformation dependent library (CDL) restraints added in 520.8 milliseconds 1074 Ramachandran restraints generated. 537 Oldfield, 0 Emsley, 537 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB BAL A 701 " Number of C-beta restraints generated: 988 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 1 sheets defined 78.7% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 46 through 59 removed outlier: 3.808A pdb=" N PHE A 50 " --> pdb=" O SER A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 65 removed outlier: 3.985A pdb=" N VAL A 64 " --> pdb=" O GLY A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 74 removed outlier: 4.113A pdb=" N TYR A 69 " --> pdb=" O TRP A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 91 removed outlier: 3.579A pdb=" N GLY A 91 " --> pdb=" O LEU A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 106 removed outlier: 3.563A pdb=" N PHE A 95 " --> pdb=" O GLY A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 116 Processing helix chain 'A' and resid 117 through 120 Processing helix chain 'A' and resid 121 through 138 removed outlier: 4.310A pdb=" N TYR A 125 " --> pdb=" O SER A 121 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL A 136 " --> pdb=" O SER A 132 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N TYR A 137 " --> pdb=" O LEU A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 152 Processing helix chain 'A' and resid 157 through 161 removed outlier: 3.576A pdb=" N ALA A 160 " --> pdb=" O LEU A 157 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N HIS A 161 " --> pdb=" O PRO A 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 157 through 161' Processing helix chain 'A' and resid 173 through 181 removed outlier: 4.519A pdb=" N LYS A 178 " --> pdb=" O ASP A 174 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N ASN A 179 " --> pdb=" O THR A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 202 Processing helix chain 'A' and resid 217 through 237 removed outlier: 3.572A pdb=" N LYS A 237 " --> pdb=" O PHE A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 250 removed outlier: 3.731A pdb=" N ALA A 250 " --> pdb=" O VAL A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 267 Processing helix chain 'A' and resid 269 through 279 removed outlier: 3.813A pdb=" N GLY A 273 " --> pdb=" O GLY A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 285 removed outlier: 3.694A pdb=" N LEU A 285 " --> pdb=" O ILE A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 302 removed outlier: 4.235A pdb=" N TRP A 291 " --> pdb=" O ASP A 287 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N THR A 296 " --> pdb=" O ILE A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 315 removed outlier: 3.596A pdb=" N SER A 311 " --> pdb=" O GLY A 307 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N TYR A 315 " --> pdb=" O SER A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 356 removed outlier: 4.389A pdb=" N ASP A 325 " --> pdb=" O ASN A 321 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLY A 341 " --> pdb=" O SER A 337 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA A 343 " --> pdb=" O VAL A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 381 removed outlier: 3.767A pdb=" N TYR A 374 " --> pdb=" O ALA A 370 " (cutoff:3.500A) Proline residue: A 375 - end of helix removed outlier: 3.839A pdb=" N MET A 380 " --> pdb=" O LYS A 376 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N MET A 381 " --> pdb=" O ALA A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 418 removed outlier: 3.676A pdb=" N TRP A 387 " --> pdb=" O LEU A 383 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER A 402 " --> pdb=" O LEU A 398 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TYR A 418 " --> pdb=" O LEU A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 444 removed outlier: 4.316A pdb=" N GLU A 429 " --> pdb=" O GLY A 425 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE A 430 " --> pdb=" O TYR A 426 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N PHE A 431 " --> pdb=" O ARG A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 447 No H-bonds generated for 'chain 'A' and resid 445 through 447' Processing helix chain 'A' and resid 450 through 462 removed outlier: 4.221A pdb=" N VAL A 454 " --> pdb=" O GLY A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 482 removed outlier: 3.894A pdb=" N LEU A 469 " --> pdb=" O GLY A 465 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL A 471 " --> pdb=" O CYS A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 497 Processing helix chain 'A' and resid 501 through 510 removed outlier: 4.670A pdb=" N LYS A 505 " --> pdb=" O GLY A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 526 removed outlier: 3.587A pdb=" N VAL A 514 " --> pdb=" O VAL A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 555 removed outlier: 3.814A pdb=" N SER A 553 " --> pdb=" O LEU A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 567 Processing helix chain 'A' and resid 571 through 579 Processing sheet with id=AA1, first strand: chain 'A' and resid 531 through 532 265 hydrogen bonds defined for protein. 777 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: 1.28 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: 805 1.33 - 1.45: 1227 1.45 - 1.57: 2571 1.57 - 1.69: 0 1.69 - 1.81: 46 Bond restraints: 4649 Sorted by residual: bond pdb=" N VAL A 339 " pdb=" CA VAL A 339 " ideal model delta sigma weight residual 1.461 1.496 -0.036 1.19e-02 7.06e+03 8.93e+00 bond pdb=" N GLU A 584 " pdb=" CA GLU A 584 " ideal model delta sigma weight residual 1.462 1.487 -0.025 8.50e-03 1.38e+04 8.61e+00 bond pdb=" C16 CLR A 711 " pdb=" C17 CLR A 711 " ideal model delta sigma weight residual 1.554 1.496 0.058 2.00e-02 2.50e+03 8.33e+00 bond pdb=" N HIS A 164 " pdb=" CA HIS A 164 " ideal model delta sigma weight residual 1.453 1.488 -0.035 1.22e-02 6.72e+03 8.21e+00 bond pdb=" N VAL A 195 " pdb=" CA VAL A 195 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.17e-02 7.31e+03 8.04e+00 ... (remaining 4644 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 5900 1.65 - 3.31: 328 3.31 - 4.96: 49 4.96 - 6.61: 14 6.61 - 8.27: 4 Bond angle restraints: 6295 Sorted by residual: angle pdb=" N PRO A 38 " pdb=" CA PRO A 38 " pdb=" C PRO A 38 " ideal model delta sigma weight residual 110.70 115.48 -4.78 1.22e+00 6.72e-01 1.54e+01 angle pdb=" CA LEU A 422 " pdb=" C LEU A 422 " pdb=" O LEU A 422 " ideal model delta sigma weight residual 122.63 117.66 4.97 1.29e+00 6.01e-01 1.49e+01 angle pdb=" CA ARG A 583 " pdb=" C ARG A 583 " pdb=" O ARG A 583 " ideal model delta sigma weight residual 122.64 118.24 4.40 1.25e+00 6.40e-01 1.24e+01 angle pdb=" N LEU A 580 " pdb=" CA LEU A 580 " pdb=" C LEU A 580 " ideal model delta sigma weight residual 113.38 109.09 4.29 1.23e+00 6.61e-01 1.22e+01 angle pdb=" CA PRO A 38 " pdb=" C PRO A 38 " pdb=" N PRO A 39 " ideal model delta sigma weight residual 117.93 122.01 -4.08 1.20e+00 6.94e-01 1.16e+01 ... (remaining 6290 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 2354 17.96 - 35.91: 314 35.91 - 53.87: 65 53.87 - 71.82: 23 71.82 - 89.78: 7 Dihedral angle restraints: 2763 sinusoidal: 1202 harmonic: 1561 Sorted by residual: dihedral pdb=" CB CYS A 162 " pdb=" SG CYS A 162 " pdb=" SG CYS A 171 " pdb=" CB CYS A 171 " ideal model delta sinusoidal sigma weight residual 93.00 62.94 30.06 1 1.00e+01 1.00e-02 1.29e+01 dihedral pdb=" CB GLU A 200 " pdb=" CG GLU A 200 " pdb=" CD GLU A 200 " pdb=" OE1 GLU A 200 " ideal model delta sinusoidal sigma weight residual 0.00 -84.66 84.66 1 3.00e+01 1.11e-03 9.67e+00 dihedral pdb=" N LYS A 577 " pdb=" CA LYS A 577 " pdb=" CB LYS A 577 " pdb=" CG LYS A 577 " ideal model delta sinusoidal sigma weight residual -180.00 -121.68 -58.32 3 1.50e+01 4.44e-03 9.46e+00 ... (remaining 2760 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 602 0.080 - 0.161: 69 0.161 - 0.241: 6 0.241 - 0.322: 3 0.322 - 0.402: 3 Chirality restraints: 683 Sorted by residual: chirality pdb=" C13 CLR A 710 " pdb=" C12 CLR A 710 " pdb=" C14 CLR A 710 " pdb=" C17 CLR A 710 " both_signs ideal model delta sigma weight residual False -2.93 -2.53 -0.40 2.00e-01 2.50e+01 4.04e+00 chirality pdb=" C13 CLR A 711 " pdb=" C12 CLR A 711 " pdb=" C14 CLR A 711 " pdb=" C17 CLR A 711 " both_signs ideal model delta sigma weight residual False -2.93 -2.55 -0.38 2.00e-01 2.50e+01 3.60e+00 chirality pdb=" C10 CLR A 710 " pdb=" C1 CLR A 710 " pdb=" C5 CLR A 710 " pdb=" C9 CLR A 710 " both_signs ideal model delta sigma weight residual False -2.85 -2.49 -0.36 2.00e-01 2.50e+01 3.27e+00 ... (remaining 680 not shown) Planarity restraints: 744 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 177 " 0.220 9.50e-02 1.11e+02 9.88e-02 5.99e+00 pdb=" NE ARG A 177 " -0.014 2.00e-02 2.50e+03 pdb=" CZ ARG A 177 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG A 177 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 177 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 237 " -0.011 2.00e-02 2.50e+03 2.26e-02 5.13e+00 pdb=" C LYS A 237 " 0.039 2.00e-02 2.50e+03 pdb=" O LYS A 237 " -0.015 2.00e-02 2.50e+03 pdb=" N GLY A 238 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 58 " -0.012 2.00e-02 2.50e+03 1.19e-02 2.49e+00 pdb=" CG PHE A 58 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 PHE A 58 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE A 58 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE A 58 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 58 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE A 58 " -0.001 2.00e-02 2.50e+03 ... (remaining 741 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 790 2.76 - 3.30: 4074 3.30 - 3.83: 7186 3.83 - 4.37: 8009 4.37 - 4.90: 14977 Nonbonded interactions: 35036 Sorted by model distance: nonbonded pdb=" OH TYR A 489 " pdb=" O GLY A 501 " model vdw 2.229 3.040 nonbonded pdb=" OH TYR A 320 " pdb=" OD2 ASP A 325 " model vdw 2.259 3.040 nonbonded pdb=" OE2 GLU A 364 " pdb=" OH TYR A 532 " model vdw 2.329 3.040 nonbonded pdb=" N ASP A 219 " pdb=" OD1 ASP A 219 " model vdw 2.400 3.120 nonbonded pdb=" O SER A 365 " pdb=" OG SER A 365 " model vdw 2.410 3.040 ... (remaining 35031 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: 0.710 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.060 Process input model: 15.060 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 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 : 0.006 0.058 4650 Z= 0.407 Angle : 0.829 8.268 6297 Z= 0.505 Chirality : 0.059 0.402 683 Planarity : 0.006 0.099 744 Dihedral : 17.157 89.778 1772 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.16 % Allowed : 21.77 % Favored : 76.08 % Cbeta Deviations : 0.20 % 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: 0.85 (0.38), residues: 537 helix: 1.65 (0.28), residues: 382 sheet: None (None), residues: 0 loop : -2.33 (0.46), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 470 HIS 0.003 0.001 HIS A 212 PHE 0.027 0.001 PHE A 58 TYR 0.010 0.001 TYR A 69 ARG 0.003 0.000 ARG A 583 Details of bonding type rmsd hydrogen bonds : bond 0.13490 ( 265) hydrogen bonds : angle 4.83397 ( 777) SS BOND : bond 0.00744 ( 1) SS BOND : angle 0.97581 ( 2) covalent geometry : bond 0.00636 ( 4649) covalent geometry : angle 0.82922 ( 6295) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1074 Ramachandran restraints generated. 537 Oldfield, 0 Emsley, 537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1074 Ramachandran restraints generated. 537 Oldfield, 0 Emsley, 537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 52 time to evaluate : 0.491 Fit side-chains REVERT: A 45 SER cc_start: 0.8150 (m) cc_final: 0.7847 (p) REVERT: A 114 GLU cc_start: 0.6627 (OUTLIER) cc_final: 0.6411 (tt0) REVERT: A 586 ASN cc_start: 0.2313 (OUTLIER) cc_final: 0.1822 (p0) outliers start: 10 outliers final: 8 residues processed: 60 average time/residue: 0.1495 time to fit residues: 11.9744 Evaluate side-chains 52 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 42 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain A residue 494 ASP Chi-restraints excluded: chain A residue 586 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 42 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 49 optimal weight: 0.0980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 ASN A 316 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.123099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.102084 restraints weight = 5705.983| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 1.69 r_work: 0.2989 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.0857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4650 Z= 0.123 Angle : 0.553 7.028 6297 Z= 0.279 Chirality : 0.040 0.187 683 Planarity : 0.004 0.036 744 Dihedral : 9.836 58.988 839 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.94 % Allowed : 20.26 % Favored : 77.80 % Cbeta Deviations : 0.20 % 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: 1.11 (0.39), residues: 537 helix: 1.70 (0.28), residues: 389 sheet: None (None), residues: 0 loop : -1.99 (0.50), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 470 HIS 0.003 0.001 HIS A 170 PHE 0.030 0.001 PHE A 58 TYR 0.016 0.001 TYR A 69 ARG 0.002 0.000 ARG A 177 Details of bonding type rmsd hydrogen bonds : bond 0.04649 ( 265) hydrogen bonds : angle 3.91192 ( 777) SS BOND : bond 0.00288 ( 1) SS BOND : angle 1.77754 ( 2) covalent geometry : bond 0.00273 ( 4649) covalent geometry : angle 0.55238 ( 6295) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1074 Ramachandran restraints generated. 537 Oldfield, 0 Emsley, 537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1074 Ramachandran restraints generated. 537 Oldfield, 0 Emsley, 537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 43 time to evaluate : 0.427 Fit side-chains revert: symmetry clash REVERT: A 45 SER cc_start: 0.8203 (m) cc_final: 0.7858 (p) REVERT: A 58 PHE cc_start: 0.8459 (OUTLIER) cc_final: 0.7841 (p90) REVERT: A 69 TYR cc_start: 0.8425 (OUTLIER) cc_final: 0.7568 (p90) REVERT: A 493 GLU cc_start: 0.7344 (OUTLIER) cc_final: 0.6961 (tm-30) outliers start: 9 outliers final: 6 residues processed: 50 average time/residue: 0.1036 time to fit residues: 7.6883 Evaluate side-chains 50 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 41 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain A residue 586 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 11 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.127840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.107861 restraints weight = 5698.700| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 1.49 r_work: 0.2970 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.1121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4650 Z= 0.144 Angle : 0.558 5.737 6297 Z= 0.286 Chirality : 0.041 0.200 683 Planarity : 0.005 0.039 744 Dihedral : 9.618 59.824 826 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.37 % Allowed : 19.61 % Favored : 78.02 % Cbeta Deviations : 0.20 % 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: 0.91 (0.38), residues: 537 helix: 1.58 (0.28), residues: 387 sheet: None (None), residues: 0 loop : -2.07 (0.48), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 470 HIS 0.002 0.001 HIS A 161 PHE 0.032 0.002 PHE A 58 TYR 0.020 0.001 TYR A 69 ARG 0.002 0.000 ARG A 41 Details of bonding type rmsd hydrogen bonds : bond 0.05282 ( 265) hydrogen bonds : angle 3.90321 ( 777) SS BOND : bond 0.00287 ( 1) SS BOND : angle 1.39720 ( 2) covalent geometry : bond 0.00338 ( 4649) covalent geometry : angle 0.55729 ( 6295) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1074 Ramachandran restraints generated. 537 Oldfield, 0 Emsley, 537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1074 Ramachandran restraints generated. 537 Oldfield, 0 Emsley, 537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 42 time to evaluate : 0.448 Fit side-chains revert: symmetry clash REVERT: A 45 SER cc_start: 0.8403 (m) cc_final: 0.8090 (p) REVERT: A 69 TYR cc_start: 0.8848 (OUTLIER) cc_final: 0.8016 (p90) outliers start: 11 outliers final: 7 residues processed: 50 average time/residue: 0.1141 time to fit residues: 8.3672 Evaluate side-chains 50 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 586 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 4 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 27 optimal weight: 6.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.129028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.109064 restraints weight = 5676.480| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 1.50 r_work: 0.2978 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.1196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4650 Z= 0.127 Angle : 0.531 5.476 6297 Z= 0.272 Chirality : 0.039 0.195 683 Planarity : 0.005 0.042 744 Dihedral : 9.217 59.564 826 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.23 % Allowed : 18.75 % Favored : 78.02 % Cbeta Deviations : 0.20 % 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: 0.98 (0.38), residues: 537 helix: 1.64 (0.28), residues: 388 sheet: None (None), residues: 0 loop : -2.10 (0.48), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 470 HIS 0.002 0.001 HIS A 212 PHE 0.031 0.001 PHE A 58 TYR 0.017 0.001 TYR A 69 ARG 0.002 0.000 ARG A 583 Details of bonding type rmsd hydrogen bonds : bond 0.04784 ( 265) hydrogen bonds : angle 3.85463 ( 777) SS BOND : bond 0.00096 ( 1) SS BOND : angle 1.27120 ( 2) covalent geometry : bond 0.00291 ( 4649) covalent geometry : angle 0.53048 ( 6295) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1074 Ramachandran restraints generated. 537 Oldfield, 0 Emsley, 537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1074 Ramachandran restraints generated. 537 Oldfield, 0 Emsley, 537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 45 time to evaluate : 0.448 Fit side-chains revert: symmetry clash REVERT: A 45 SER cc_start: 0.8368 (m) cc_final: 0.8009 (p) REVERT: A 69 TYR cc_start: 0.8558 (OUTLIER) cc_final: 0.7837 (p90) REVERT: A 493 GLU cc_start: 0.7476 (OUTLIER) cc_final: 0.7113 (tm-30) outliers start: 15 outliers final: 7 residues processed: 56 average time/residue: 0.1249 time to fit residues: 9.9152 Evaluate side-chains 53 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 44 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain A residue 423 ARG Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 586 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 1 optimal weight: 4.9990 chunk 32 optimal weight: 0.0670 chunk 17 optimal weight: 2.9990 chunk 16 optimal weight: 10.0000 chunk 13 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 overall best weight: 1.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.122690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.102330 restraints weight = 5838.446| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 1.55 r_work: 0.2923 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4650 Z= 0.181 Angle : 0.593 5.635 6297 Z= 0.304 Chirality : 0.042 0.209 683 Planarity : 0.005 0.042 744 Dihedral : 9.649 59.172 825 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 2.37 % Allowed : 20.47 % Favored : 77.16 % Cbeta Deviations : 0.20 % 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: 0.64 (0.38), residues: 537 helix: 1.37 (0.28), residues: 388 sheet: None (None), residues: 0 loop : -2.15 (0.48), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 470 HIS 0.002 0.001 HIS A 161 PHE 0.033 0.002 PHE A 58 TYR 0.023 0.001 TYR A 69 ARG 0.002 0.000 ARG A 41 Details of bonding type rmsd hydrogen bonds : bond 0.06000 ( 265) hydrogen bonds : angle 4.01736 ( 777) SS BOND : bond 0.00219 ( 1) SS BOND : angle 1.41153 ( 2) covalent geometry : bond 0.00444 ( 4649) covalent geometry : angle 0.59231 ( 6295) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1074 Ramachandran restraints generated. 537 Oldfield, 0 Emsley, 537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1074 Ramachandran restraints generated. 537 Oldfield, 0 Emsley, 537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.444 Fit side-chains revert: symmetry clash REVERT: A 69 TYR cc_start: 0.8756 (OUTLIER) cc_final: 0.7858 (p90) REVERT: A 493 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.7247 (tm-30) outliers start: 11 outliers final: 8 residues processed: 54 average time/residue: 0.1082 time to fit residues: 8.7179 Evaluate side-chains 53 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 43 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 586 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 18 optimal weight: 0.8980 chunk 1 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 26 optimal weight: 0.0470 chunk 8 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 13 optimal weight: 5.9990 chunk 7 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.129290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.109328 restraints weight = 5642.003| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 1.49 r_work: 0.2985 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4650 Z= 0.117 Angle : 0.519 5.389 6297 Z= 0.266 Chirality : 0.039 0.193 683 Planarity : 0.005 0.043 744 Dihedral : 8.993 59.941 825 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.23 % Allowed : 20.04 % Favored : 76.72 % Cbeta Deviations : 0.20 % 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: 0.91 (0.38), residues: 537 helix: 1.57 (0.28), residues: 388 sheet: None (None), residues: 0 loop : -2.06 (0.47), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 470 HIS 0.002 0.001 HIS A 161 PHE 0.030 0.001 PHE A 58 TYR 0.015 0.001 TYR A 69 ARG 0.001 0.000 ARG A 583 Details of bonding type rmsd hydrogen bonds : bond 0.04603 ( 265) hydrogen bonds : angle 3.87052 ( 777) SS BOND : bond 0.00099 ( 1) SS BOND : angle 1.14447 ( 2) covalent geometry : bond 0.00260 ( 4649) covalent geometry : angle 0.51841 ( 6295) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1074 Ramachandran restraints generated. 537 Oldfield, 0 Emsley, 537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1074 Ramachandran restraints generated. 537 Oldfield, 0 Emsley, 537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 42 time to evaluate : 0.423 Fit side-chains revert: symmetry clash REVERT: A 69 TYR cc_start: 0.8719 (OUTLIER) cc_final: 0.8003 (p90) REVERT: A 205 SER cc_start: 0.8068 (OUTLIER) cc_final: 0.7531 (p) REVERT: A 493 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7375 (tm-30) outliers start: 15 outliers final: 10 residues processed: 54 average time/residue: 0.1227 time to fit residues: 9.3557 Evaluate side-chains 55 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 42 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain A residue 423 ARG Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain A residue 495 MET Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 586 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 20 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 31 optimal weight: 0.0870 chunk 13 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 42 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.127712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.107463 restraints weight = 5646.205| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 1.52 r_work: 0.2992 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4650 Z= 0.115 Angle : 0.509 5.371 6297 Z= 0.261 Chirality : 0.038 0.192 683 Planarity : 0.005 0.043 744 Dihedral : 8.678 58.822 825 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.80 % Allowed : 20.04 % Favored : 77.16 % Cbeta Deviations : 0.20 % 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: 1.02 (0.38), residues: 537 helix: 1.68 (0.28), residues: 388 sheet: None (None), residues: 0 loop : -2.10 (0.48), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 470 HIS 0.002 0.001 HIS A 212 PHE 0.030 0.001 PHE A 58 TYR 0.017 0.001 TYR A 69 ARG 0.002 0.000 ARG A 583 Details of bonding type rmsd hydrogen bonds : bond 0.04489 ( 265) hydrogen bonds : angle 3.79209 ( 777) SS BOND : bond 0.00086 ( 1) SS BOND : angle 1.09696 ( 2) covalent geometry : bond 0.00256 ( 4649) covalent geometry : angle 0.50913 ( 6295) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1074 Ramachandran restraints generated. 537 Oldfield, 0 Emsley, 537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1074 Ramachandran restraints generated. 537 Oldfield, 0 Emsley, 537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 44 time to evaluate : 0.434 Fit side-chains revert: symmetry clash REVERT: A 69 TYR cc_start: 0.8537 (OUTLIER) cc_final: 0.7819 (p90) REVERT: A 205 SER cc_start: 0.7905 (OUTLIER) cc_final: 0.7298 (p) REVERT: A 493 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.7159 (tm-30) outliers start: 13 outliers final: 10 residues processed: 55 average time/residue: 0.1235 time to fit residues: 9.6526 Evaluate side-chains 55 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 42 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain A residue 423 ARG Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain A residue 495 MET Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 586 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 48 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 52 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 38 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.126975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.106795 restraints weight = 5694.206| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 1.52 r_work: 0.2987 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.1354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4650 Z= 0.125 Angle : 0.520 5.405 6297 Z= 0.267 Chirality : 0.039 0.195 683 Planarity : 0.005 0.042 744 Dihedral : 8.734 58.900 825 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.80 % Allowed : 19.83 % Favored : 77.37 % Cbeta Deviations : 0.20 % 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: 0.99 (0.38), residues: 537 helix: 1.65 (0.28), residues: 388 sheet: None (None), residues: 0 loop : -2.10 (0.48), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 470 HIS 0.002 0.001 HIS A 212 PHE 0.031 0.001 PHE A 58 TYR 0.018 0.001 TYR A 69 ARG 0.001 0.000 ARG A 583 Details of bonding type rmsd hydrogen bonds : bond 0.04691 ( 265) hydrogen bonds : angle 3.81651 ( 777) SS BOND : bond 0.00128 ( 1) SS BOND : angle 1.15189 ( 2) covalent geometry : bond 0.00289 ( 4649) covalent geometry : angle 0.52006 ( 6295) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1074 Ramachandran restraints generated. 537 Oldfield, 0 Emsley, 537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1074 Ramachandran restraints generated. 537 Oldfield, 0 Emsley, 537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 43 time to evaluate : 0.555 Fit side-chains revert: symmetry clash REVERT: A 69 TYR cc_start: 0.8607 (OUTLIER) cc_final: 0.7906 (p90) REVERT: A 493 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.7166 (tm-30) outliers start: 13 outliers final: 11 residues processed: 54 average time/residue: 0.1268 time to fit residues: 9.7555 Evaluate side-chains 55 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 42 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain A residue 423 ARG Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain A residue 495 MET Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 586 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 31 optimal weight: 0.0980 chunk 2 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 35 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.126973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.106792 restraints weight = 5702.632| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 1.52 r_work: 0.2982 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4650 Z= 0.121 Angle : 0.515 5.381 6297 Z= 0.265 Chirality : 0.039 0.194 683 Planarity : 0.005 0.042 744 Dihedral : 8.688 59.049 825 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 3.02 % Allowed : 19.61 % Favored : 77.37 % Cbeta Deviations : 0.20 % 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: 1.03 (0.38), residues: 537 helix: 1.67 (0.28), residues: 388 sheet: None (None), residues: 0 loop : -2.07 (0.48), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 470 HIS 0.002 0.001 HIS A 212 PHE 0.030 0.001 PHE A 58 TYR 0.017 0.001 TYR A 69 ARG 0.001 0.000 ARG A 583 Details of bonding type rmsd hydrogen bonds : bond 0.04606 ( 265) hydrogen bonds : angle 3.80778 ( 777) SS BOND : bond 0.00124 ( 1) SS BOND : angle 1.13087 ( 2) covalent geometry : bond 0.00276 ( 4649) covalent geometry : angle 0.51496 ( 6295) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1074 Ramachandran restraints generated. 537 Oldfield, 0 Emsley, 537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1074 Ramachandran restraints generated. 537 Oldfield, 0 Emsley, 537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 42 time to evaluate : 0.432 Fit side-chains revert: symmetry clash REVERT: A 69 TYR cc_start: 0.8555 (OUTLIER) cc_final: 0.7845 (p90) REVERT: A 493 GLU cc_start: 0.7491 (OUTLIER) cc_final: 0.7144 (tm-30) outliers start: 14 outliers final: 12 residues processed: 54 average time/residue: 0.1186 time to fit residues: 9.0662 Evaluate side-chains 56 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 42 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain A residue 423 ARG Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain A residue 495 MET Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 586 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 9 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 chunk 42 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.126878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.106637 restraints weight = 5651.333| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 1.53 r_work: 0.2982 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.1388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4650 Z= 0.121 Angle : 0.516 5.401 6297 Z= 0.265 Chirality : 0.039 0.194 683 Planarity : 0.005 0.043 744 Dihedral : 8.674 59.155 825 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.80 % Allowed : 19.83 % Favored : 77.37 % Cbeta Deviations : 0.20 % 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: 1.02 (0.38), residues: 537 helix: 1.67 (0.28), residues: 388 sheet: None (None), residues: 0 loop : -2.07 (0.48), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 470 HIS 0.002 0.001 HIS A 161 PHE 0.030 0.001 PHE A 58 TYR 0.018 0.001 TYR A 69 ARG 0.001 0.000 ARG A 583 Details of bonding type rmsd hydrogen bonds : bond 0.04632 ( 265) hydrogen bonds : angle 3.80988 ( 777) SS BOND : bond 0.00105 ( 1) SS BOND : angle 1.11521 ( 2) covalent geometry : bond 0.00277 ( 4649) covalent geometry : angle 0.51549 ( 6295) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1074 Ramachandran restraints generated. 537 Oldfield, 0 Emsley, 537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1074 Ramachandran restraints generated. 537 Oldfield, 0 Emsley, 537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 43 time to evaluate : 0.507 Fit side-chains revert: symmetry clash REVERT: A 69 TYR cc_start: 0.8563 (OUTLIER) cc_final: 0.7862 (p90) REVERT: A 493 GLU cc_start: 0.7485 (OUTLIER) cc_final: 0.7137 (tm-30) outliers start: 13 outliers final: 11 residues processed: 54 average time/residue: 0.1296 time to fit residues: 9.8436 Evaluate side-chains 55 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 42 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain A residue 423 ARG Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain A residue 495 MET Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 586 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 43 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.126690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.106477 restraints weight = 5661.518| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 1.52 r_work: 0.2987 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4650 Z= 0.124 Angle : 0.518 5.400 6297 Z= 0.266 Chirality : 0.039 0.194 683 Planarity : 0.004 0.041 744 Dihedral : 8.691 59.239 825 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 3.02 % Allowed : 19.61 % Favored : 77.37 % Cbeta Deviations : 0.20 % 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: 1.02 (0.38), residues: 537 helix: 1.65 (0.28), residues: 388 sheet: None (None), residues: 0 loop : -2.05 (0.48), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 470 HIS 0.002 0.001 HIS A 212 PHE 0.031 0.001 PHE A 58 TYR 0.018 0.001 TYR A 69 ARG 0.001 0.000 ARG A 583 Details of bonding type rmsd hydrogen bonds : bond 0.04681 ( 265) hydrogen bonds : angle 3.81846 ( 777) SS BOND : bond 0.00136 ( 1) SS BOND : angle 1.14112 ( 2) covalent geometry : bond 0.00284 ( 4649) covalent geometry : angle 0.51740 ( 6295) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2455.03 seconds wall clock time: 43 minutes 14.66 seconds (2594.66 seconds total)