Starting phenix.real_space_refine on Wed Sep 17 04:50:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j7n_61208/09_2025/9j7n_61208.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j7n_61208/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9j7n_61208/09_2025/9j7n_61208.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j7n_61208/09_2025/9j7n_61208.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9j7n_61208/09_2025/9j7n_61208.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j7n_61208/09_2025/9j7n_61208.map" } resolution = 3.14 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= 0.048 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 1.46, per 1000 atoms: 0.32 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: 0.44 Conformation dependent library (CDL) restraints added in 171.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.21 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: 0.75 Time building geometry restraints manager: 0.59 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: 1.510 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: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.910 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.890 ------------------------------------------------------------------------------- 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 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: 0.85 (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 ARG 0.003 0.000 ARG A 583 TYR 0.010 0.001 TYR A 69 PHE 0.027 0.001 PHE A 58 TRP 0.016 0.001 TRP A 470 HIS 0.003 0.001 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00636 ( 4649) covalent geometry : angle 0.82922 ( 6295) SS BOND : bond 0.00744 ( 1) SS BOND : angle 0.97581 ( 2) hydrogen bonds : bond 0.13490 ( 265) hydrogen bonds : angle 4.83397 ( 777) *********************** 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 : 0.164 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: 0.0675 time to fit residues: 5.4414 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 : 0.176 ------------------------------------------------------------------------------- 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 24 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 chunk 25 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 53 optimal weight: 0.0570 chunk 19 optimal weight: 0.1980 overall best weight: 0.5500 ------------------------------------------------------------------------------- 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 = 0.3468 r_free = 0.3468 target = 0.132016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.112081 restraints weight = 5658.089| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 1.51 r_work: 0.3028 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.0855 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= 0.119 Angle : 0.546 6.869 6297 Z= 0.276 Chirality : 0.040 0.186 683 Planarity : 0.004 0.036 744 Dihedral : 9.770 58.802 839 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.72 % Allowed : 20.69 % Favored : 77.59 % Cbeta Deviations : 0.20 % 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: 1.16 (0.39), residues: 537 helix: 1.75 (0.28), residues: 389 sheet: None (None), residues: 0 loop : -1.99 (0.49), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 583 TYR 0.015 0.001 TYR A 69 PHE 0.029 0.001 PHE A 58 TRP 0.013 0.001 TRP A 470 HIS 0.003 0.001 HIS A 170 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 4649) covalent geometry : angle 0.54557 ( 6295) SS BOND : bond 0.00025 ( 1) SS BOND : angle 1.68073 ( 2) hydrogen bonds : bond 0.04516 ( 265) hydrogen bonds : angle 3.89755 ( 777) *********************** 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 51 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.194 Fit side-chains revert: symmetry clash REVERT: A 45 SER cc_start: 0.8232 (m) cc_final: 0.7907 (p) REVERT: A 58 PHE cc_start: 0.8539 (OUTLIER) cc_final: 0.7991 (p90) REVERT: A 69 TYR cc_start: 0.8541 (OUTLIER) cc_final: 0.7815 (p90) REVERT: A 493 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.7073 (tm-30) outliers start: 8 outliers final: 5 residues processed: 50 average time/residue: 0.0455 time to fit residues: 3.4409 Evaluate side-chains 49 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.155 ------------------------------------------------------------------------------- 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 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 52 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 4 optimal weight: 0.3980 chunk 21 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 = 0.3308 r_free = 0.3308 target = 0.121385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.100112 restraints weight = 5734.398| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 1.71 r_work: 0.2965 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.1071 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= 0.128 Angle : 0.538 5.384 6297 Z= 0.276 Chirality : 0.040 0.195 683 Planarity : 0.004 0.041 744 Dihedral : 9.435 59.817 826 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.37 % Allowed : 19.40 % Favored : 78.23 % Cbeta Deviations : 0.20 % 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: 1.05 (0.38), residues: 537 helix: 1.68 (0.28), residues: 388 sheet: None (None), residues: 0 loop : -2.04 (0.49), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 583 TYR 0.018 0.001 TYR A 69 PHE 0.030 0.001 PHE A 58 TRP 0.012 0.001 TRP A 470 HIS 0.002 0.001 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 4649) covalent geometry : angle 0.53763 ( 6295) SS BOND : bond 0.00155 ( 1) SS BOND : angle 1.32526 ( 2) hydrogen bonds : bond 0.04902 ( 265) hydrogen bonds : angle 3.83645 ( 777) *********************** 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 52 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 41 time to evaluate : 0.177 Fit side-chains revert: symmetry clash REVERT: A 45 SER cc_start: 0.8315 (m) cc_final: 0.7962 (p) REVERT: A 69 TYR cc_start: 0.8496 (OUTLIER) cc_final: 0.7644 (p90) outliers start: 11 outliers final: 6 residues processed: 49 average time/residue: 0.0515 time to fit residues: 3.6777 Evaluate side-chains 49 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.157 ------------------------------------------------------------------------------- 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 586 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 21 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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 = 0.3333 r_free = 0.3333 target = 0.121453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.101213 restraints weight = 5771.161| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 1.54 r_work: 0.2911 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 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 : 0.005 0.042 4650 Z= 0.216 Angle : 0.627 5.943 6297 Z= 0.322 Chirality : 0.044 0.215 683 Planarity : 0.005 0.044 744 Dihedral : 10.005 59.543 826 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 3.23 % Allowed : 18.97 % 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 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: 0.57 (0.38), residues: 537 helix: 1.31 (0.28), residues: 387 sheet: None (None), residues: 0 loop : -2.13 (0.47), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 41 TYR 0.025 0.001 TYR A 69 PHE 0.035 0.002 PHE A 58 TRP 0.012 0.002 TRP A 236 HIS 0.003 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00541 ( 4649) covalent geometry : angle 0.62665 ( 6295) SS BOND : bond 0.00198 ( 1) SS BOND : angle 1.74727 ( 2) hydrogen bonds : bond 0.06433 ( 265) hydrogen bonds : angle 4.08478 ( 777) *********************** 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 : 0.161 Fit side-chains revert: symmetry clash REVERT: A 45 SER cc_start: 0.8413 (m) cc_final: 0.8070 (p) REVERT: A 69 TYR cc_start: 0.8789 (OUTLIER) cc_final: 0.7898 (p90) REVERT: A 493 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.7200 (tm-30) outliers start: 15 outliers final: 10 residues processed: 55 average time/residue: 0.0468 time to fit residues: 3.8895 Evaluate side-chains 53 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 41 time to evaluate : 0.165 ------------------------------------------------------------------------------- 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 168 THR 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 415 VAL 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 586 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 21 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 14 optimal weight: 10.0000 chunk 29 optimal weight: 0.8980 chunk 2 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 47 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.120215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.098977 restraints weight = 5736.781| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 1.70 r_work: 0.2955 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.1305 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 : 0.532 5.412 6297 Z= 0.273 Chirality : 0.039 0.196 683 Planarity : 0.005 0.042 744 Dihedral : 9.367 59.600 826 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % 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 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: 0.79 (0.38), residues: 537 helix: 1.49 (0.28), residues: 388 sheet: None (None), residues: 0 loop : -2.15 (0.47), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 583 TYR 0.016 0.001 TYR A 69 PHE 0.031 0.001 PHE A 58 TRP 0.016 0.001 TRP A 470 HIS 0.002 0.001 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 4649) covalent geometry : angle 0.53119 ( 6295) SS BOND : bond 0.00115 ( 1) SS BOND : angle 1.20534 ( 2) hydrogen bonds : bond 0.04887 ( 265) hydrogen bonds : angle 3.91653 ( 777) *********************** 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 58 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 43 time to evaluate : 0.165 Fit side-chains revert: symmetry clash REVERT: A 69 TYR cc_start: 0.8451 (OUTLIER) cc_final: 0.7731 (p90) REVERT: A 205 SER cc_start: 0.7800 (OUTLIER) cc_final: 0.7196 (p) REVERT: A 493 GLU cc_start: 0.7476 (OUTLIER) cc_final: 0.7121 (tm-30) outliers start: 15 outliers final: 10 residues processed: 55 average time/residue: 0.0485 time to fit residues: 3.8898 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 : 0.160 ------------------------------------------------------------------------------- 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 168 THR 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 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 14 optimal weight: 10.0000 chunk 7 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 37 optimal weight: 0.6980 chunk 39 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.128677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.108727 restraints weight = 5732.357| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 1.50 r_work: 0.2977 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.1329 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 : 0.528 5.413 6297 Z= 0.271 Chirality : 0.039 0.196 683 Planarity : 0.005 0.043 744 Dihedral : 9.022 58.900 825 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 3.45 % Allowed : 19.40 % 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 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: 0.86 (0.38), residues: 537 helix: 1.54 (0.28), residues: 388 sheet: None (None), residues: 0 loop : -2.11 (0.48), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 41 TYR 0.018 0.001 TYR A 69 PHE 0.031 0.001 PHE A 58 TRP 0.015 0.001 TRP A 470 HIS 0.002 0.001 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 4649) covalent geometry : angle 0.52793 ( 6295) SS BOND : bond 0.00141 ( 1) SS BOND : angle 1.16875 ( 2) hydrogen bonds : bond 0.04867 ( 265) hydrogen bonds : angle 3.86322 ( 777) *********************** 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 58 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 42 time to evaluate : 0.160 Fit side-chains revert: symmetry clash REVERT: A 69 TYR cc_start: 0.8783 (OUTLIER) cc_final: 0.7961 (p90) REVERT: A 205 SER cc_start: 0.8059 (OUTLIER) cc_final: 0.7514 (p) REVERT: A 493 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7317 (tm-30) outliers start: 16 outliers final: 10 residues processed: 54 average time/residue: 0.0550 time to fit residues: 4.2350 Evaluate side-chains 54 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 41 time to evaluate : 0.158 ------------------------------------------------------------------------------- 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 168 THR 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 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 18 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 52 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 40 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 47 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.129337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.109452 restraints weight = 5626.590| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 1.48 r_work: 0.2980 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.1352 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= 0.122 Angle : 0.516 5.402 6297 Z= 0.265 Chirality : 0.039 0.193 683 Planarity : 0.005 0.043 744 Dihedral : 8.832 58.814 825 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.80 % Allowed : 19.40 % 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 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: 0.91 (0.38), residues: 537 helix: 1.57 (0.28), residues: 388 sheet: None (None), residues: 0 loop : -2.09 (0.48), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 583 TYR 0.017 0.001 TYR A 69 PHE 0.030 0.001 PHE A 58 TRP 0.015 0.001 TRP A 470 HIS 0.002 0.001 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 4649) covalent geometry : angle 0.51530 ( 6295) SS BOND : bond 0.00117 ( 1) SS BOND : angle 1.17395 ( 2) hydrogen bonds : bond 0.04672 ( 265) hydrogen bonds : angle 3.83721 ( 777) *********************** 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 54 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 41 time to evaluate : 0.195 Fit side-chains revert: symmetry clash REVERT: A 69 TYR cc_start: 0.8555 (OUTLIER) cc_final: 0.7840 (p90) REVERT: A 205 SER cc_start: 0.7919 (OUTLIER) cc_final: 0.7318 (p) REVERT: A 493 GLU cc_start: 0.7478 (OUTLIER) cc_final: 0.7116 (tm-30) outliers start: 13 outliers final: 10 residues processed: 52 average time/residue: 0.0548 time to fit residues: 4.0954 Evaluate side-chains 54 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 41 time to evaluate : 0.103 ------------------------------------------------------------------------------- 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 168 THR 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 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 6 optimal weight: 2.9990 chunk 42 optimal weight: 0.0270 chunk 11 optimal weight: 4.9990 chunk 46 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 31 optimal weight: 0.0470 chunk 39 optimal weight: 4.9990 overall best weight: 0.5536 ------------------------------------------------------------------------------- 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 = 0.3457 r_free = 0.3457 target = 0.131036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.110890 restraints weight = 5747.073| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 1.52 r_work: 0.3008 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 4650 Z= 0.108 Angle : 0.497 5.370 6297 Z= 0.255 Chirality : 0.038 0.189 683 Planarity : 0.004 0.043 744 Dihedral : 8.532 59.151 825 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.80 % Allowed : 19.40 % 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 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: 1.13 (0.38), residues: 537 helix: 1.75 (0.28), residues: 387 sheet: None (None), residues: 0 loop : -2.02 (0.48), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 583 TYR 0.015 0.001 TYR A 69 PHE 0.029 0.001 PHE A 58 TRP 0.015 0.001 TRP A 470 HIS 0.002 0.001 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 4649) covalent geometry : angle 0.49656 ( 6295) SS BOND : bond 0.00126 ( 1) SS BOND : angle 1.05970 ( 2) hydrogen bonds : bond 0.04194 ( 265) hydrogen bonds : angle 3.77009 ( 777) *********************** 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 58 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 45 time to evaluate : 0.176 Fit side-chains revert: symmetry clash REVERT: A 69 TYR cc_start: 0.8664 (OUTLIER) cc_final: 0.7938 (p90) REVERT: A 493 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.7330 (tm-30) outliers start: 13 outliers final: 11 residues processed: 55 average time/residue: 0.0521 time to fit residues: 4.1139 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 : 0.163 ------------------------------------------------------------------------------- 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 168 THR 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 22 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 40 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 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 = 0.3300 r_free = 0.3300 target = 0.121048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.099835 restraints weight = 5715.400| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 1.71 r_work: 0.2970 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.1390 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= 0.123 Angle : 0.513 5.397 6297 Z= 0.263 Chirality : 0.039 0.194 683 Planarity : 0.005 0.042 744 Dihedral : 8.660 59.074 825 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 3.23 % Allowed : 19.18 % Favored : 77.59 % Cbeta Deviations : 0.20 % 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: 1.06 (0.38), residues: 537 helix: 1.69 (0.28), residues: 388 sheet: None (None), residues: 0 loop : -2.03 (0.48), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 583 TYR 0.018 0.001 TYR A 69 PHE 0.030 0.001 PHE A 58 TRP 0.013 0.001 TRP A 470 HIS 0.002 0.001 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 4649) covalent geometry : angle 0.51232 ( 6295) SS BOND : bond 0.00141 ( 1) SS BOND : angle 1.15517 ( 2) hydrogen bonds : bond 0.04651 ( 265) hydrogen bonds : angle 3.79500 ( 777) *********************** 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 58 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 43 time to evaluate : 0.158 Fit side-chains revert: symmetry clash REVERT: A 69 TYR cc_start: 0.8479 (OUTLIER) cc_final: 0.7775 (p90) REVERT: A 493 GLU cc_start: 0.7399 (OUTLIER) cc_final: 0.7039 (tm-30) outliers start: 15 outliers final: 13 residues processed: 54 average time/residue: 0.0549 time to fit residues: 4.2573 Evaluate side-chains 58 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 43 time to evaluate : 0.163 ------------------------------------------------------------------------------- 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 168 THR Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 296 THR 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 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 49 optimal weight: 0.6980 chunk 2 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 chunk 5 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 35 optimal weight: 0.6980 chunk 41 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.127643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.107376 restraints weight = 5676.949| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 1.53 r_work: 0.3008 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.1391 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 : 0.505 5.380 6297 Z= 0.259 Chirality : 0.038 0.192 683 Planarity : 0.004 0.043 744 Dihedral : 8.601 59.175 825 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.23 % Allowed : 18.97 % 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 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: 1.11 (0.38), residues: 537 helix: 1.73 (0.28), residues: 388 sheet: None (None), residues: 0 loop : -2.03 (0.48), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 583 TYR 0.017 0.001 TYR A 69 PHE 0.030 0.001 PHE A 58 TRP 0.014 0.001 TRP A 470 HIS 0.002 0.001 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 4649) covalent geometry : angle 0.50476 ( 6295) SS BOND : bond 0.00111 ( 1) SS BOND : angle 1.09265 ( 2) hydrogen bonds : bond 0.04486 ( 265) hydrogen bonds : angle 3.78151 ( 777) ********************** 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 58 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 43 time to evaluate : 0.117 Fit side-chains revert: symmetry clash REVERT: A 69 TYR cc_start: 0.8608 (OUTLIER) cc_final: 0.7891 (p90) REVERT: A 423 ARG cc_start: 0.6044 (OUTLIER) cc_final: 0.5683 (mmm160) REVERT: A 493 GLU cc_start: 0.7536 (OUTLIER) cc_final: 0.7187 (tm-30) outliers start: 15 outliers final: 12 residues processed: 54 average time/residue: 0.0489 time to fit residues: 3.7943 Evaluate side-chains 58 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 43 time to evaluate : 0.196 ------------------------------------------------------------------------------- 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 168 THR Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 296 THR 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 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 12 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 16 optimal weight: 0.0020 overall best weight: 0.5788 ------------------------------------------------------------------------------- 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 = 0.3425 r_free = 0.3425 target = 0.128998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.108629 restraints weight = 5688.666| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 1.54 r_work: 0.3019 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.1427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 4650 Z= 0.108 Angle : 0.491 5.344 6297 Z= 0.252 Chirality : 0.038 0.189 683 Planarity : 0.004 0.041 744 Dihedral : 8.393 59.293 825 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.23 % Allowed : 18.97 % 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 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: 1.20 (0.38), residues: 537 helix: 1.81 (0.28), residues: 389 sheet: None (None), residues: 0 loop : -2.07 (0.48), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 583 TYR 0.015 0.001 TYR A 69 PHE 0.029 0.001 PHE A 58 TRP 0.015 0.001 TRP A 470 HIS 0.002 0.001 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 4649) covalent geometry : angle 0.49081 ( 6295) SS BOND : bond 0.00111 ( 1) SS BOND : angle 1.01797 ( 2) hydrogen bonds : bond 0.04152 ( 265) hydrogen bonds : angle 3.73958 ( 777) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1221.41 seconds wall clock time: 21 minutes 36.48 seconds (1296.48 seconds total)