Starting phenix.real_space_refine on Thu Jul 2 00:11:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j7n_61208/07_2026/9j7n_61208.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j7n_61208/07_2026/9j7n_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_61208/07_2026/9j7n_61208.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j7n_61208/07_2026/9j7n_61208.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9j7n_61208/07_2026/9j7n_61208.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j7n_61208/07_2026/9j7n_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-dev-6108/lib/python3.11/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, 189 Ad-hoc single atom residues: {' CL': 1} Unusual residues: {'CLR': 2, 'R16': 8} Classifications: {'undetermined': 10, 'water': 5} Link IDs: {None: 13} Chain breaks: 1 Time building chain proxies: 0.90, per 1000 atoms: 0.20 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: 0.45 Conformation dependent library (CDL) restraints added in 158.7 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: 0.13 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: 0.67 Time building geometry restraints manager: 0.55 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: 1.170 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: 0.020 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.670 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:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 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 are 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/Z covalent geometry : bond 0.00636 / 0.41 ( 4649) covalent geometry : angle 0.82922 / 0.51 ( 6295) SS BOND : bond 0.00744 / 0.39 ( 1) SS BOND : angle 0.97581 / 0.65 ( 2) hydrogen bonds : bond 0.13490 / 9.14 ( 265) hydrogen bonds : angle 4.83397 / 3.35 ( 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 : 0.160 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: 0.0623 time to fit residues: 5.0485 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 : 0.157 ------------------------------------------------------------------------------- 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... 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 = 0.3336 r_free = 0.3336 target = 0.123700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.102011 restraints weight = 5703.593| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 1.83 r_work: 0.2983 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.0813 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 : 0.548 6.636 6297 Z= 0.277 Chirality : 0.040 0.187 683 Planarity : 0.004 0.035 744 Dihedral : 9.837 59.077 839 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.72 % Allowed : 20.47 % 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 are not related in a simple way. whole: 1.18 (0.39), residues: 537 helix: 1.76 (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 0.001 0.000 ARG A 583 TYR 0.015 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 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 ( 4649) covalent geometry : angle 0.54673 / 0.28 ( 6295) SS BOND : bond 0.00280 / 0.15 ( 1) SS BOND : angle 2.05441 / 1.37 ( 2) hydrogen bonds : bond 0.04597 / 3.01 ( 265) hydrogen bonds : angle 3.89865 / 2.64 ( 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 : 0.167 Fit side-chains revert: symmetry clash REVERT: A 45 SER cc_start: 0.8191 (m) cc_final: 0.7842 (p) REVERT: A 58 PHE cc_start: 0.8357 (OUTLIER) cc_final: 0.7845 (p90) REVERT: A 69 TYR cc_start: 0.8321 (OUTLIER) cc_final: 0.7591 (p90) REVERT: A 493 GLU cc_start: 0.7362 (OUTLIER) cc_final: 0.6952 (tm-30) outliers start: 8 outliers final: 5 residues processed: 50 average time/residue: 0.0454 time to fit residues: 3.4319 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 : 0.160 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 34 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 316 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.120078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.098859 restraints weight = 5752.663| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 1.71 r_work: 0.2946 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.1100 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 : 0.556 5.559 6297 Z= 0.285 Chirality : 0.041 0.200 683 Planarity : 0.005 0.040 744 Dihedral : 9.591 59.877 826 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 3.02 % Allowed : 19.40 % 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 are not related in a simple way. whole: 0.95 (0.38), residues: 537 helix: 1.59 (0.28), residues: 388 sheet: None (None), residues: 0 loop : -2.05 (0.48), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 583 TYR 0.020 0.001 TYR A 69 PHE 0.031 0.002 PHE A 58 TRP 0.012 0.001 TRP A 470 HIS 0.002 0.001 HIS A 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.14 ( 4649) covalent geometry : angle 0.55563 / 0.28 ( 6295) SS BOND : bond 0.00260 / 0.14 ( 1) SS BOND : angle 1.46599 / 0.98 ( 2) hydrogen bonds : bond 0.05238 / 3.43 ( 265) hydrogen bonds : angle 3.88626 / 2.66 ( 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 56 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 42 time to evaluate : 0.233 Fit side-chains revert: symmetry clash REVERT: A 45 SER cc_start: 0.8337 (m) cc_final: 0.7986 (p) REVERT: A 69 TYR cc_start: 0.8557 (OUTLIER) cc_final: 0.7716 (p90) REVERT: A 493 GLU cc_start: 0.7434 (OUTLIER) cc_final: 0.7062 (tm-30) outliers start: 14 outliers final: 7 residues processed: 53 average time/residue: 0.0483 time to fit residues: 3.8344 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 : 0.154 ------------------------------------------------------------------------------- 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 21 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 23 optimal weight: 0.0980 chunk 29 optimal weight: 1.9990 chunk 45 optimal weight: 0.4980 chunk 9 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 316 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.127788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.107835 restraints weight = 5654.710| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 1.50 r_work: 0.2974 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4650 Z= 0.140 Angle : 0.547 5.482 6297 Z= 0.281 Chirality : 0.040 0.199 683 Planarity : 0.005 0.043 744 Dihedral : 9.350 59.873 826 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 3.92 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.38), residues: 537 helix: 1.57 (0.28), residues: 388 sheet: None (None), residues: 0 loop : -2.12 (0.48), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 583 TYR 0.019 0.001 TYR A 69 PHE 0.031 0.002 PHE A 58 TRP 0.013 0.001 TRP A 470 HIS 0.002 0.001 HIS A 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 ( 4649) covalent geometry : angle 0.54693 / 0.28 ( 6295) SS BOND : bond 0.00118 / 0.06 ( 1) SS BOND : angle 1.32927 / 0.89 ( 2) hydrogen bonds : bond 0.05122 / 3.36 ( 265) hydrogen bonds : angle 3.90209 / 2.67 ( 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 57 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 43 time to evaluate : 0.160 Fit side-chains revert: symmetry clash REVERT: A 45 SER cc_start: 0.8405 (m) cc_final: 0.8053 (p) REVERT: A 69 TYR cc_start: 0.8693 (OUTLIER) cc_final: 0.7862 (p90) REVERT: A 493 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.7187 (tm-30) outliers start: 14 outliers final: 9 residues processed: 53 average time/residue: 0.0452 time to fit residues: 3.4877 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 : 0.151 ------------------------------------------------------------------------------- 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 423 ARG 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 21 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 27 optimal weight: 0.0000 chunk 37 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 14 optimal weight: 9.9990 chunk 29 optimal weight: 0.7980 chunk 2 optimal weight: 4.9990 chunk 4 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 chunk 1 optimal weight: 0.7980 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 316 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.130509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.110682 restraints weight = 5649.576| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 1.47 r_work: 0.3006 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.1247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4650 Z= 0.114 Angle : 0.509 5.362 6297 Z= 0.261 Chirality : 0.038 0.192 683 Planarity : 0.004 0.043 744 Dihedral : 8.858 59.943 825 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.80 % Allowed : 20.47 % 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 are not related in a simple way. whole: 1.10 (0.38), residues: 537 helix: 1.74 (0.28), residues: 387 sheet: None (None), residues: 0 loop : -2.06 (0.47), residues: 150 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 0.030 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/Z covalent geometry : bond 0.00252 / 0.11 ( 4649) covalent geometry : angle 0.50887 / 0.26 ( 6295) SS BOND : bond 0.00100 / 0.05 ( 1) SS BOND : angle 1.08580 / 0.72 ( 2) hydrogen bonds : bond 0.04405 / 2.89 ( 265) hydrogen bonds : angle 3.80224 / 2.59 ( 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 55 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 42 time to evaluate : 0.159 Fit side-chains revert: symmetry clash REVERT: A 45 SER cc_start: 0.8457 (m) cc_final: 0.8099 (p) REVERT: A 69 TYR cc_start: 0.8730 (OUTLIER) cc_final: 0.8009 (p90) REVERT: A 493 GLU cc_start: 0.7669 (OUTLIER) cc_final: 0.7312 (tm-30) outliers start: 13 outliers final: 9 residues processed: 52 average time/residue: 0.0501 time to fit residues: 3.7603 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 : 0.141 ------------------------------------------------------------------------------- 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 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: 9.9990 chunk 7 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 18 optimal weight: 0.6980 chunk 53 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 316 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.126589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.106185 restraints weight = 5761.087| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 1.55 r_work: 0.2971 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.1294 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= 0.129 Angle : 0.527 5.408 6297 Z= 0.270 Chirality : 0.039 0.196 683 Planarity : 0.005 0.042 744 Dihedral : 8.843 58.922 825 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.37 % Allowed : 20.26 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (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 ARG 0.001 0.000 ARG A 583 TYR 0.019 0.001 TYR A 69 PHE 0.031 0.002 PHE A 58 TRP 0.013 0.001 TRP A 470 HIS 0.002 0.001 HIS A 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 ( 4649) covalent geometry : angle 0.52640 / 0.27 ( 6295) SS BOND : bond 0.00135 / 0.07 ( 1) SS BOND : angle 1.18712 / 0.79 ( 2) hydrogen bonds : bond 0.04856 / 3.18 ( 265) hydrogen bonds : angle 3.82532 / 2.62 ( 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 53 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 42 time to evaluate : 0.140 Fit side-chains revert: symmetry clash REVERT: A 45 SER cc_start: 0.8441 (m) cc_final: 0.8050 (p) REVERT: A 69 TYR cc_start: 0.8624 (OUTLIER) cc_final: 0.7807 (p90) REVERT: A 493 GLU cc_start: 0.7496 (OUTLIER) cc_final: 0.7116 (tm-30) outliers start: 11 outliers final: 9 residues processed: 50 average time/residue: 0.0434 time to fit residues: 3.2821 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 : 0.098 ------------------------------------------------------------------------------- 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 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 18 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 chunk 53 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 40 optimal weight: 0.3980 chunk 21 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 316 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.129982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.110068 restraints weight = 5632.467| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 1.49 r_work: 0.3003 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.1314 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= 0.119 Angle : 0.510 5.382 6297 Z= 0.262 Chirality : 0.038 0.193 683 Planarity : 0.004 0.042 744 Dihedral : 8.683 58.970 825 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.02 % Allowed : 20.04 % Favored : 76.94 % 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 are not related in a simple way. whole: 1.07 (0.38), residues: 537 helix: 1.71 (0.28), residues: 388 sheet: None (None), residues: 0 loop : -2.07 (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/Z covalent geometry : bond 0.00268 / 0.12 ( 4649) covalent geometry : angle 0.50998 / 0.26 ( 6295) SS BOND : bond 0.00100 / 0.05 ( 1) SS BOND : angle 1.14305 / 0.76 ( 2) hydrogen bonds : bond 0.04538 / 2.97 ( 265) hydrogen bonds : angle 3.78704 / 2.59 ( 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 57 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 43 time to evaluate : 0.155 Fit side-chains revert: symmetry clash REVERT: A 69 TYR cc_start: 0.8609 (OUTLIER) cc_final: 0.7884 (p90) REVERT: A 205 SER cc_start: 0.7955 (OUTLIER) cc_final: 0.7368 (p) REVERT: A 493 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.7179 (tm-30) outliers start: 14 outliers final: 11 residues processed: 54 average time/residue: 0.0510 time to fit residues: 3.9834 Evaluate side-chains 55 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 41 time to evaluate : 0.166 ------------------------------------------------------------------------------- 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 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 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: 1.9990 chunk 11 optimal weight: 4.9990 chunk 46 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 32 optimal weight: 0.0770 chunk 35 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 31 optimal weight: 0.0170 chunk 39 optimal weight: 3.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 316 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.131216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.111108 restraints weight = 5746.836| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 1.51 r_work: 0.3013 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.1332 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 : 0.496 5.345 6297 Z= 0.254 Chirality : 0.038 0.188 683 Planarity : 0.004 0.042 744 Dihedral : 8.456 59.227 825 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.80 % Allowed : 20.26 % Favored : 76.94 % 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 are not related in a simple way. whole: 1.24 (0.38), residues: 537 helix: 1.84 (0.28), residues: 387 sheet: None (None), residues: 0 loop : -2.01 (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/Z covalent geometry : bond 0.00238 / 0.11 ( 4649) covalent geometry : angle 0.49537 / 0.25 ( 6295) SS BOND : bond 0.00098 / 0.05 ( 1) SS BOND : angle 1.03517 / 0.69 ( 2) hydrogen bonds : bond 0.04159 / 2.72 ( 265) hydrogen bonds : angle 3.72929 / 2.54 ( 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 57 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 44 time to evaluate : 0.189 Fit side-chains revert: symmetry clash REVERT: A 69 TYR cc_start: 0.8492 (OUTLIER) cc_final: 0.7761 (p90) REVERT: A 423 ARG cc_start: 0.5997 (OUTLIER) cc_final: 0.5725 (mmm160) REVERT: A 493 GLU cc_start: 0.7491 (OUTLIER) cc_final: 0.7114 (tm-30) outliers start: 13 outliers final: 10 residues processed: 54 average time/residue: 0.0541 time to fit residues: 4.1661 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 : 0.184 ------------------------------------------------------------------------------- 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 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: 0.7980 chunk 41 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 316 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.127151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.106917 restraints weight = 5683.339| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 1.53 r_work: 0.2979 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1371 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 : 0.516 5.387 6297 Z= 0.265 Chirality : 0.039 0.194 683 Planarity : 0.004 0.040 744 Dihedral : 8.623 59.236 825 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 3.02 % Allowed : 20.04 % Favored : 76.94 % 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 are not related in a simple way. whole: 1.12 (0.38), residues: 537 helix: 1.73 (0.28), residues: 388 sheet: None (None), residues: 0 loop : -2.01 (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 0.031 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/Z covalent geometry : bond 0.00283 / 0.12 ( 4649) covalent geometry : angle 0.51544 / 0.26 ( 6295) SS BOND : bond 0.00145 / 0.08 ( 1) SS BOND : angle 1.13905 / 0.76 ( 2) hydrogen bonds : bond 0.04648 / 3.03 ( 265) hydrogen bonds : angle 3.77816 / 2.58 ( 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 55 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 41 time to evaluate : 0.162 Fit side-chains revert: symmetry clash REVERT: A 69 TYR cc_start: 0.8588 (OUTLIER) cc_final: 0.7895 (p90) REVERT: A 423 ARG cc_start: 0.6001 (OUTLIER) cc_final: 0.5614 (mmm160) REVERT: A 493 GLU cc_start: 0.7487 (OUTLIER) cc_final: 0.7107 (tm-30) outliers start: 14 outliers final: 11 residues processed: 52 average time/residue: 0.0529 time to fit residues: 3.9741 Evaluate side-chains 55 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 41 time to evaluate : 0.156 ------------------------------------------------------------------------------- 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 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 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 49 optimal weight: 0.0050 chunk 2 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 316 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.128622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.108290 restraints weight = 5680.912| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 1.54 r_work: 0.2995 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.1372 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= 0.111 Angle : 0.498 5.364 6297 Z= 0.256 Chirality : 0.038 0.189 683 Planarity : 0.004 0.040 744 Dihedral : 8.468 59.308 825 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.02 % Allowed : 20.04 % Favored : 76.94 % 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 are not related in a simple way. whole: 1.21 (0.38), residues: 537 helix: 1.81 (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 0.016 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/Z covalent geometry : bond 0.00246 / 0.11 ( 4649) covalent geometry : angle 0.49822 / 0.26 ( 6295) SS BOND : bond 0.00111 / 0.06 ( 1) SS BOND : angle 1.03107 / 0.69 ( 2) hydrogen bonds : bond 0.04270 / 2.79 ( 265) hydrogen bonds : angle 3.74506 / 2.55 ( 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 57 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 43 time to evaluate : 0.155 Fit side-chains revert: symmetry clash REVERT: A 69 TYR cc_start: 0.8502 (OUTLIER) cc_final: 0.7786 (p90) REVERT: A 423 ARG cc_start: 0.5967 (OUTLIER) cc_final: 0.5691 (mmm160) REVERT: A 493 GLU cc_start: 0.7480 (OUTLIER) cc_final: 0.7104 (tm-30) outliers start: 14 outliers final: 11 residues processed: 54 average time/residue: 0.0530 time to fit residues: 4.0382 Evaluate side-chains 58 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 44 time to evaluate : 0.152 ------------------------------------------------------------------------------- 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 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 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 12 optimal weight: 0.0070 chunk 21 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 43 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 16 optimal weight: 0.0970 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 316 ASN A 567 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.129699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.109372 restraints weight = 5686.847| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 1.54 r_work: 0.3013 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.1433 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= 0.107 Angle : 0.489 5.334 6297 Z= 0.251 Chirality : 0.038 0.187 683 Planarity : 0.004 0.041 744 Dihedral : 8.275 59.568 825 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % 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 are not related in a simple way. whole: 1.27 (0.38), residues: 537 helix: 1.87 (0.28), residues: 389 sheet: None (None), residues: 0 loop : -2.09 (0.47), 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 0.014 0.001 TRP A 470 HIS 0.002 0.001 HIS A 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 ( 4649) covalent geometry : angle 0.48899 / 0.25 ( 6295) SS BOND : bond 0.00102 / 0.05 ( 1) SS BOND : angle 0.97428 / 0.65 ( 2) hydrogen bonds : bond 0.04039 / 2.64 ( 265) hydrogen bonds : angle 3.70597 / 2.52 ( 777) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1242.10 seconds wall clock time: 21 minutes 59.71 seconds (1319.71 seconds total)