Starting phenix.real_space_refine on Wed Jul 1 23:00:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9v8y_64855/07_2026/9v8y_64855.cif Found real_map, /net/cci-nas-00/data/ceres_data/9v8y_64855/07_2026/9v8y_64855.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9v8y_64855/07_2026/9v8y_64855.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9v8y_64855/07_2026/9v8y_64855.map" model { file = "/net/cci-nas-00/data/ceres_data/9v8y_64855/07_2026/9v8y_64855.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9v8y_64855/07_2026/9v8y_64855.cif" } resolution = 3.28 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= -0.001 sd= 0.071 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 34 5.16 5 Cl 1 4.86 5 C 2540 2.51 5 N 568 2.21 5 O 623 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 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: 3766 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3765 Classifications: {'peptide': 476} Link IDs: {'PTRANS': 20, 'TRANS': 455} Chain breaks: 4 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CL': 1} Chain breaks: 1 Time building chain proxies: 1.00, per 1000 atoms: 0.27 Number of scatterers: 3766 At special positions: 0 Unit cell: (75.328, 71.048, 71.904, 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 34 16.00 O 623 8.00 N 568 7.00 C 2540 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.36 Conformation dependent library (CDL) restraints added in 96.1 milliseconds 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 862 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 1 sheets defined 66.8% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.07 Creating SS restraints... Processing helix chain 'A' and resid 65 through 70 removed outlier: 3.822A pdb=" N VAL A 70 " --> pdb=" O VAL A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 85 removed outlier: 5.322A pdb=" N TYR A 83 " --> pdb=" O PRO A 79 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ASN A 85 " --> pdb=" O LEU A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 99 removed outlier: 3.580A pdb=" N ILE A 97 " --> pdb=" O PRO A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 116 removed outlier: 3.649A pdb=" N MET A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 131 No H-bonds generated for 'chain 'A' and resid 129 through 131' Processing helix chain 'A' and resid 132 through 144 removed outlier: 3.794A pdb=" N ALA A 136 " --> pdb=" O GLY A 132 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER A 137 " --> pdb=" O LEU A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 161 removed outlier: 3.659A pdb=" N VAL A 151 " --> pdb=" O TYR A 147 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU A 152 " --> pdb=" O TYR A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 217 Processing helix chain 'A' and resid 234 through 239 Processing helix chain 'A' and resid 239 through 248 removed outlier: 3.861A pdb=" N VAL A 246 " --> pdb=" O CYS A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 276 removed outlier: 3.539A pdb=" N VAL A 271 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL A 274 " --> pdb=" O VAL A 270 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU A 276 " --> pdb=" O LEU A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 294 removed outlier: 3.684A pdb=" N ILE A 290 " --> pdb=" O LEU A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 301 removed outlier: 3.530A pdb=" N LYS A 299 " --> pdb=" O ASP A 296 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU A 300 " --> pdb=" O TRP A 297 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLY A 301 " --> pdb=" O SER A 298 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 296 through 301' Processing helix chain 'A' and resid 302 through 317 removed outlier: 4.377A pdb=" N TRP A 306 " --> pdb=" O SER A 302 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N PHE A 314 " --> pdb=" O GLY A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 371 removed outlier: 3.792A pdb=" N THR A 351 " --> pdb=" O ILE A 347 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ILE A 362 " --> pdb=" O VAL A 358 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY A 364 " --> pdb=" O PHE A 360 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N PHE A 365 " --> pdb=" O SER A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 396 removed outlier: 3.744A pdb=" N THR A 394 " --> pdb=" O PRO A 390 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU A 395 " --> pdb=" O ARG A 391 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N MET A 396 " --> pdb=" O ALA A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 430 removed outlier: 3.835A pdb=" N TRP A 402 " --> pdb=" O VAL A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 457 Processing helix chain 'A' and resid 458 through 461 Processing helix chain 'A' and resid 466 through 476 removed outlier: 3.717A pdb=" N LEU A 472 " --> pdb=" O TYR A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 491 removed outlier: 3.879A pdb=" N LEU A 484 " --> pdb=" O GLY A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 508 Processing helix chain 'A' and resid 519 through 524 removed outlier: 4.349A pdb=" N SER A 524 " --> pdb=" O LYS A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 541 removed outlier: 3.631A pdb=" N PHE A 537 " --> pdb=" O GLY A 533 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL A 539 " --> pdb=" O PHE A 535 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N TYR A 541 " --> pdb=" O PHE A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 550 No H-bonds generated for 'chain 'A' and resid 548 through 550' Processing helix chain 'A' and resid 554 through 570 removed outlier: 3.544A pdb=" N GLY A 561 " --> pdb=" O GLY A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 581 removed outlier: 3.689A pdb=" N HIS A 575 " --> pdb=" O CYS A 571 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LEU A 576 " --> pdb=" O VAL A 572 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU A 577 " --> pdb=" O PRO A 573 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLY A 578 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU A 581 " --> pdb=" O LEU A 577 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 546 through 547 177 hydrogen bonds defined for protein. 525 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: 0.37 Time building geometry restraints manager: 0.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1079 1.34 - 1.46: 1024 1.46 - 1.58: 1733 1.58 - 1.69: 1 1.69 - 1.81: 50 Bond restraints: 3887 Sorted by residual: bond pdb=" CB PRO A 303 " pdb=" CG PRO A 303 " ideal model delta sigma weight residual 1.492 1.609 -0.117 5.00e-02 4.00e+02 5.51e+00 bond pdb=" C VAL A 572 " pdb=" N PRO A 573 " ideal model delta sigma weight residual 1.336 1.356 -0.020 1.20e-02 6.94e+03 2.89e+00 bond pdb=" CB THR A 311 " pdb=" CG2 THR A 311 " ideal model delta sigma weight residual 1.521 1.480 0.041 3.30e-02 9.18e+02 1.55e+00 bond pdb=" CG LEU A 159 " pdb=" CD2 LEU A 159 " ideal model delta sigma weight residual 1.521 1.480 0.041 3.30e-02 9.18e+02 1.52e+00 bond pdb=" CB ARG A 77 " pdb=" CG ARG A 77 " ideal model delta sigma weight residual 1.520 1.488 0.032 3.00e-02 1.11e+03 1.16e+00 ... (remaining 3882 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 5142 1.99 - 3.97: 130 3.97 - 5.96: 22 5.96 - 7.95: 5 7.95 - 9.93: 4 Bond angle restraints: 5303 Sorted by residual: angle pdb=" CA PRO A 303 " pdb=" N PRO A 303 " pdb=" CD PRO A 303 " ideal model delta sigma weight residual 112.00 102.61 9.39 1.40e+00 5.10e-01 4.50e+01 angle pdb=" N VAL A 261 " pdb=" CA VAL A 261 " pdb=" C VAL A 261 " ideal model delta sigma weight residual 112.04 107.78 4.26 1.40e+00 5.10e-01 9.24e+00 angle pdb=" N GLY A 310 " pdb=" CA GLY A 310 " pdb=" C GLY A 310 " ideal model delta sigma weight residual 115.31 111.62 3.69 1.24e+00 6.50e-01 8.86e+00 angle pdb=" CA LEU A 167 " pdb=" CB LEU A 167 " pdb=" CG LEU A 167 " ideal model delta sigma weight residual 116.30 125.58 -9.28 3.50e+00 8.16e-02 7.03e+00 angle pdb=" N PRO A 303 " pdb=" CD PRO A 303 " pdb=" CG PRO A 303 " ideal model delta sigma weight residual 103.20 99.48 3.72 1.50e+00 4.44e-01 6.17e+00 ... (remaining 5298 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 2003 17.62 - 35.25: 131 35.25 - 52.87: 20 52.87 - 70.49: 2 70.49 - 88.11: 2 Dihedral angle restraints: 2158 sinusoidal: 797 harmonic: 1361 Sorted by residual: dihedral pdb=" CA PRO A 79 " pdb=" C PRO A 79 " pdb=" N TYR A 80 " pdb=" CA TYR A 80 " ideal model delta harmonic sigma weight residual 180.00 145.02 34.98 0 5.00e+00 4.00e-02 4.90e+01 dihedral pdb=" CA THR A 463 " pdb=" C THR A 463 " pdb=" N ASP A 464 " pdb=" CA ASP A 464 " ideal model delta harmonic sigma weight residual 180.00 157.43 22.57 0 5.00e+00 4.00e-02 2.04e+01 dihedral pdb=" CA LEU A 324 " pdb=" C LEU A 324 " pdb=" N THR A 325 " pdb=" CA THR A 325 " ideal model delta harmonic sigma weight residual 180.00 158.76 21.24 0 5.00e+00 4.00e-02 1.80e+01 ... (remaining 2155 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 265 0.026 - 0.051: 187 0.051 - 0.077: 90 0.077 - 0.103: 35 0.103 - 0.128: 11 Chirality restraints: 588 Sorted by residual: chirality pdb=" CA ARG A 77 " pdb=" N ARG A 77 " pdb=" C ARG A 77 " pdb=" CB ARG A 77 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.11e-01 chirality pdb=" CA GLU A 109 " pdb=" N GLU A 109 " pdb=" C GLU A 109 " pdb=" CB GLU A 109 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.54e-01 chirality pdb=" CA PRO A 104 " pdb=" N PRO A 104 " pdb=" C PRO A 104 " pdb=" CB PRO A 104 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.53e-01 ... (remaining 585 not shown) Planarity restraints: 640 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 302 " -0.088 5.00e-02 4.00e+02 1.26e-01 2.56e+01 pdb=" N PRO A 303 " 0.218 5.00e-02 4.00e+02 pdb=" CA PRO A 303 " -0.065 5.00e-02 4.00e+02 pdb=" CD PRO A 303 " -0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 92 " 0.026 5.00e-02 4.00e+02 3.85e-02 2.37e+00 pdb=" N PRO A 93 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 93 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 93 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 389 " -0.022 5.00e-02 4.00e+02 3.35e-02 1.79e+00 pdb=" N PRO A 390 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 390 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 390 " -0.019 5.00e-02 4.00e+02 ... (remaining 637 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 49 2.64 - 3.20: 3593 3.20 - 3.77: 5936 3.77 - 4.33: 8357 4.33 - 4.90: 13537 Nonbonded interactions: 31472 Sorted by model distance: nonbonded pdb=" OH TYR A 80 " pdb=" OD2 ASP A 474 " model vdw 2.070 3.040 nonbonded pdb=" O VAL A 100 " pdb=" OG1 THR A 527 " model vdw 2.075 3.040 nonbonded pdb=" OH TYR A 317 " pdb=" OG SER A 349 " model vdw 2.119 3.040 nonbonded pdb=" O PHE A 473 " pdb=" OG SER A 477 " model vdw 2.207 3.040 nonbonded pdb=" O PRO A 104 " pdb=" NE1 TRP A 523 " model vdw 2.220 3.120 ... (remaining 31467 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: 1.220 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: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 4.940 Find NCS groups from input model: 0.010 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 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 : 0.004 0.117 3887 Z= 0.184 Angle : 0.809 9.934 5303 Z= 0.436 Chirality : 0.043 0.128 588 Planarity : 0.007 0.126 640 Dihedral : 12.349 88.114 1296 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.58 % Favored : 91.42 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -3.01 (0.37), residues: 466 helix: -1.84 (0.27), residues: 313 sheet: None (None), residues: 0 loop : -1.95 (0.52), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 332 TYR 0.016 0.002 TYR A 292 PHE 0.020 0.002 PHE A 353 TRP 0.011 0.001 TRP A 251 HIS 0.001 0.001 HIS A 575 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.18 ( 3887) covalent geometry : angle 0.80942 / 0.44 ( 5303) hydrogen bonds : bond 0.20247 / 13.78 ( 177) hydrogen bonds : angle 8.36146 / 5.88 ( 525) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.079 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 0.0512 time to fit residues: 4.6692 Evaluate side-chains 66 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 24 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 0.0470 chunk 16 optimal weight: 4.9990 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 0.4980 chunk 19 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 114 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.199393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.172763 restraints weight = 4412.429| |-----------------------------------------------------------------------------| r_work (start): 0.4024 rms_B_bonded: 2.08 r_work: 0.3871 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.1284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 3887 Z= 0.148 Angle : 0.696 9.928 5303 Z= 0.343 Chirality : 0.043 0.129 588 Planarity : 0.005 0.072 640 Dihedral : 5.420 29.406 510 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 1.26 % Allowed : 9.85 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.35 (0.38), residues: 466 helix: -1.35 (0.28), residues: 318 sheet: None (None), residues: 0 loop : -1.67 (0.54), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 332 TYR 0.010 0.001 TYR A 291 PHE 0.012 0.001 PHE A 90 TRP 0.010 0.001 TRP A 251 HIS 0.001 0.000 HIS A 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 ( 3887) covalent geometry : angle 0.69618 / 0.34 ( 5303) hydrogen bonds : bond 0.04314 / 2.69 ( 177) hydrogen bonds : angle 5.03413 / 3.50 ( 525) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 63 time to evaluate : 0.124 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 64 average time/residue: 0.0523 time to fit residues: 4.5033 Evaluate side-chains 62 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 60 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 453 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 13 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 20 optimal weight: 0.1980 chunk 0 optimal weight: 6.9990 chunk 16 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 33 optimal weight: 0.0570 chunk 35 optimal weight: 0.6980 chunk 8 optimal weight: 0.4980 chunk 45 optimal weight: 1.9990 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.200100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.174397 restraints weight = 4337.255| |-----------------------------------------------------------------------------| r_work (start): 0.4042 rms_B_bonded: 2.03 r_work: 0.3888 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 3887 Z= 0.131 Angle : 0.676 9.953 5303 Z= 0.324 Chirality : 0.042 0.187 588 Planarity : 0.004 0.058 640 Dihedral : 5.205 29.124 510 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 2.27 % Allowed : 11.87 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.13 (0.39), residues: 466 helix: -1.19 (0.28), residues: 320 sheet: None (None), residues: 0 loop : -1.54 (0.56), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 332 TYR 0.013 0.001 TYR A 80 PHE 0.019 0.001 PHE A 470 TRP 0.010 0.001 TRP A 251 HIS 0.001 0.001 HIS A 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 ( 3887) covalent geometry : angle 0.67575 / 0.32 ( 5303) hydrogen bonds : bond 0.03902 / 2.42 ( 177) hydrogen bonds : angle 4.74474 / 3.26 ( 525) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 67 time to evaluate : 0.154 Fit side-chains REVERT: A 307 ILE cc_start: 0.7054 (OUTLIER) cc_final: 0.6551 (mm) REVERT: A 342 ILE cc_start: 0.8225 (OUTLIER) cc_final: 0.7900 (mp) REVERT: A 357 PHE cc_start: 0.8013 (OUTLIER) cc_final: 0.7716 (t80) REVERT: A 365 PHE cc_start: 0.7007 (t80) cc_final: 0.6748 (t80) REVERT: A 504 MET cc_start: 0.8838 (mmt) cc_final: 0.8595 (mmm) outliers start: 9 outliers final: 4 residues processed: 70 average time/residue: 0.0513 time to fit residues: 4.8530 Evaluate side-chains 68 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 61 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 357 PHE Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 453 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 46 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 34 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 42 optimal weight: 0.0980 chunk 27 optimal weight: 0.8980 chunk 37 optimal weight: 0.6980 chunk 35 optimal weight: 0.3980 chunk 15 optimal weight: 0.9980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.197077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.170272 restraints weight = 4348.490| |-----------------------------------------------------------------------------| r_work (start): 0.4021 rms_B_bonded: 2.08 r_work: 0.3868 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 3887 Z= 0.131 Angle : 0.662 9.991 5303 Z= 0.317 Chirality : 0.042 0.162 588 Planarity : 0.004 0.053 640 Dihedral : 5.080 25.844 510 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 3.03 % Allowed : 14.14 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.08 (0.39), residues: 466 helix: -1.15 (0.28), residues: 324 sheet: None (None), residues: 0 loop : -1.54 (0.57), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 332 TYR 0.014 0.001 TYR A 80 PHE 0.019 0.001 PHE A 406 TRP 0.010 0.001 TRP A 251 HIS 0.001 0.001 HIS A 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.13 ( 3887) covalent geometry : angle 0.66223 / 0.32 ( 5303) hydrogen bonds : bond 0.03694 / 2.30 ( 177) hydrogen bonds : angle 4.55550 / 3.12 ( 525) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 67 time to evaluate : 0.130 Fit side-chains REVERT: A 133 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8000 (tt) REVERT: A 342 ILE cc_start: 0.8156 (OUTLIER) cc_final: 0.7804 (mp) REVERT: A 357 PHE cc_start: 0.8029 (OUTLIER) cc_final: 0.7711 (t80) REVERT: A 504 MET cc_start: 0.8875 (mmt) cc_final: 0.8601 (mmm) outliers start: 12 outliers final: 5 residues processed: 74 average time/residue: 0.0506 time to fit residues: 5.0612 Evaluate side-chains 72 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 MET Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 357 PHE Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 453 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 44 optimal weight: 0.3980 chunk 6 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 22 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 41 optimal weight: 0.0670 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 312 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.197762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.170041 restraints weight = 4414.343| |-----------------------------------------------------------------------------| r_work (start): 0.4009 rms_B_bonded: 2.13 r_work: 0.3854 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3887 Z= 0.132 Angle : 0.655 9.962 5303 Z= 0.314 Chirality : 0.042 0.154 588 Planarity : 0.004 0.049 640 Dihedral : 5.051 24.966 510 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 4.04 % Allowed : 14.65 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.00 (0.39), residues: 466 helix: -1.06 (0.28), residues: 324 sheet: None (None), residues: 0 loop : -1.62 (0.57), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 332 TYR 0.010 0.001 TYR A 292 PHE 0.020 0.001 PHE A 406 TRP 0.010 0.001 TRP A 251 HIS 0.001 0.001 HIS A 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.13 ( 3887) covalent geometry : angle 0.65474 / 0.31 ( 5303) hydrogen bonds : bond 0.03580 / 2.22 ( 177) hydrogen bonds : angle 4.46704 / 3.05 ( 525) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 65 time to evaluate : 0.133 Fit side-chains REVERT: A 133 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8029 (tt) REVERT: A 342 ILE cc_start: 0.8139 (OUTLIER) cc_final: 0.7766 (mp) REVERT: A 357 PHE cc_start: 0.8049 (OUTLIER) cc_final: 0.7703 (t80) outliers start: 16 outliers final: 5 residues processed: 76 average time/residue: 0.0483 time to fit residues: 4.8821 Evaluate side-chains 71 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 357 PHE Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 453 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 18 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 14 optimal weight: 0.0770 chunk 25 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 35 optimal weight: 0.4980 chunk 39 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.198186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.170786 restraints weight = 4491.806| |-----------------------------------------------------------------------------| r_work (start): 0.4017 rms_B_bonded: 2.17 r_work: 0.3863 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 3887 Z= 0.130 Angle : 0.677 10.724 5303 Z= 0.322 Chirality : 0.043 0.175 588 Planarity : 0.004 0.047 640 Dihedral : 4.999 25.117 510 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 3.54 % Allowed : 16.41 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.83 (0.39), residues: 466 helix: -0.94 (0.28), residues: 323 sheet: None (None), residues: 0 loop : -1.50 (0.57), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 332 TYR 0.018 0.001 TYR A 80 PHE 0.020 0.001 PHE A 406 TRP 0.009 0.001 TRP A 251 HIS 0.001 0.000 HIS A 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.13 ( 3887) covalent geometry : angle 0.67675 / 0.32 ( 5303) hydrogen bonds : bond 0.03595 / 2.20 ( 177) hydrogen bonds : angle 4.49789 / 3.07 ( 525) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 0.128 Fit side-chains REVERT: A 133 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.7976 (tt) REVERT: A 262 TYR cc_start: 0.7403 (m-80) cc_final: 0.6532 (t80) REVERT: A 342 ILE cc_start: 0.8131 (OUTLIER) cc_final: 0.7730 (mp) REVERT: A 357 PHE cc_start: 0.8025 (OUTLIER) cc_final: 0.7691 (t80) outliers start: 14 outliers final: 7 residues processed: 71 average time/residue: 0.0465 time to fit residues: 4.4967 Evaluate side-chains 71 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 MET Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 357 PHE Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 453 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 21 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 13 optimal weight: 0.2980 chunk 9 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 2 optimal weight: 0.0870 chunk 17 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 40 optimal weight: 0.0970 overall best weight: 0.3956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.198171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.171678 restraints weight = 4444.095| |-----------------------------------------------------------------------------| r_work (start): 0.4039 rms_B_bonded: 2.10 r_work: 0.3886 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 3887 Z= 0.122 Angle : 0.670 10.015 5303 Z= 0.315 Chirality : 0.042 0.152 588 Planarity : 0.004 0.044 640 Dihedral : 4.925 25.727 510 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 3.79 % Allowed : 15.66 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.70 (0.39), residues: 466 helix: -0.83 (0.28), residues: 325 sheet: None (None), residues: 0 loop : -1.50 (0.57), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 332 TYR 0.015 0.001 TYR A 80 PHE 0.019 0.001 PHE A 406 TRP 0.010 0.001 TRP A 485 HIS 0.001 0.001 HIS A 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.12 ( 3887) covalent geometry : angle 0.66968 / 0.32 ( 5303) hydrogen bonds : bond 0.03497 / 2.14 ( 177) hydrogen bonds : angle 4.40518 / 3.01 ( 525) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 65 time to evaluate : 0.157 Fit side-chains REVERT: A 342 ILE cc_start: 0.8098 (OUTLIER) cc_final: 0.7735 (mp) REVERT: A 357 PHE cc_start: 0.8016 (OUTLIER) cc_final: 0.7615 (t80) outliers start: 15 outliers final: 9 residues processed: 75 average time/residue: 0.0470 time to fit residues: 4.7627 Evaluate side-chains 72 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 MET Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 357 PHE Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 453 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 15 optimal weight: 0.6980 chunk 3 optimal weight: 0.0060 chunk 21 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 30 optimal weight: 0.8980 chunk 46 optimal weight: 10.0000 chunk 35 optimal weight: 2.9990 chunk 44 optimal weight: 0.0980 chunk 43 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.199511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.173739 restraints weight = 4408.481| |-----------------------------------------------------------------------------| r_work (start): 0.4035 rms_B_bonded: 2.06 r_work: 0.3881 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3887 Z= 0.128 Angle : 0.683 10.009 5303 Z= 0.322 Chirality : 0.043 0.150 588 Planarity : 0.004 0.045 640 Dihedral : 4.928 26.104 510 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 3.79 % Allowed : 17.17 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.39), residues: 466 helix: -0.75 (0.29), residues: 323 sheet: None (None), residues: 0 loop : -1.47 (0.57), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 332 TYR 0.015 0.001 TYR A 80 PHE 0.019 0.001 PHE A 406 TRP 0.009 0.001 TRP A 485 HIS 0.001 0.000 HIS A 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 ( 3887) covalent geometry : angle 0.68324 / 0.32 ( 5303) hydrogen bonds : bond 0.03472 / 2.14 ( 177) hydrogen bonds : angle 4.34627 / 2.96 ( 525) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 65 time to evaluate : 0.130 Fit side-chains REVERT: A 262 TYR cc_start: 0.7397 (m-80) cc_final: 0.6496 (t80) REVERT: A 342 ILE cc_start: 0.8087 (OUTLIER) cc_final: 0.7690 (mp) REVERT: A 357 PHE cc_start: 0.8017 (OUTLIER) cc_final: 0.7596 (t80) outliers start: 15 outliers final: 10 residues processed: 75 average time/residue: 0.0504 time to fit residues: 5.0935 Evaluate side-chains 77 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 116 MET Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 357 PHE Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 453 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 36 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 23 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 6 optimal weight: 0.3980 chunk 30 optimal weight: 0.0980 chunk 11 optimal weight: 0.0970 chunk 0 optimal weight: 6.9990 chunk 24 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.200126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.172842 restraints weight = 4410.814| |-----------------------------------------------------------------------------| r_work (start): 0.4042 rms_B_bonded: 2.16 r_work: 0.3891 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3887 Z= 0.124 Angle : 0.677 10.006 5303 Z= 0.320 Chirality : 0.042 0.149 588 Planarity : 0.004 0.043 640 Dihedral : 4.921 26.772 510 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 3.79 % Allowed : 17.17 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.46 (0.40), residues: 466 helix: -0.65 (0.29), residues: 322 sheet: None (None), residues: 0 loop : -1.40 (0.56), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 332 TYR 0.016 0.001 TYR A 80 PHE 0.020 0.001 PHE A 406 TRP 0.010 0.001 TRP A 485 HIS 0.001 0.000 HIS A 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.12 ( 3887) covalent geometry : angle 0.67678 / 0.32 ( 5303) hydrogen bonds : bond 0.03469 / 2.21 ( 177) hydrogen bonds : angle 4.26962 / 2.91 ( 525) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 68 time to evaluate : 0.130 Fit side-chains REVERT: A 342 ILE cc_start: 0.8056 (OUTLIER) cc_final: 0.7662 (mp) REVERT: A 357 PHE cc_start: 0.8016 (OUTLIER) cc_final: 0.7595 (t80) outliers start: 15 outliers final: 10 residues processed: 77 average time/residue: 0.0439 time to fit residues: 4.6797 Evaluate side-chains 76 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 116 MET Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 357 PHE Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 453 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 4 optimal weight: 0.2980 chunk 40 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 36 optimal weight: 0.5980 chunk 46 optimal weight: 0.9990 chunk 38 optimal weight: 0.0970 chunk 22 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.196836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.169631 restraints weight = 4480.493| |-----------------------------------------------------------------------------| r_work (start): 0.4014 rms_B_bonded: 2.16 r_work: 0.3863 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3887 Z= 0.140 Angle : 0.695 10.005 5303 Z= 0.330 Chirality : 0.043 0.151 588 Planarity : 0.004 0.043 640 Dihedral : 4.928 26.530 510 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 3.54 % Allowed : 18.18 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.40), residues: 466 helix: -0.69 (0.29), residues: 322 sheet: None (None), residues: 0 loop : -1.34 (0.57), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 332 TYR 0.016 0.001 TYR A 80 PHE 0.020 0.001 PHE A 406 TRP 0.010 0.001 TRP A 485 HIS 0.001 0.000 HIS A 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.14 ( 3887) covalent geometry : angle 0.69479 / 0.33 ( 5303) hydrogen bonds : bond 0.03506 / 2.23 ( 177) hydrogen bonds : angle 4.32913 / 2.95 ( 525) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 0.078 Fit side-chains REVERT: A 342 ILE cc_start: 0.8067 (OUTLIER) cc_final: 0.7691 (mp) REVERT: A 357 PHE cc_start: 0.8057 (OUTLIER) cc_final: 0.7630 (t80) outliers start: 14 outliers final: 9 residues processed: 74 average time/residue: 0.0422 time to fit residues: 4.3094 Evaluate side-chains 78 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 116 MET Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 357 PHE Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 453 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 6 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 27 optimal weight: 0.0470 chunk 30 optimal weight: 0.0980 chunk 34 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 36 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 chunk 15 optimal weight: 0.9980 overall best weight: 0.4078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.196571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.170564 restraints weight = 4367.988| |-----------------------------------------------------------------------------| r_work (start): 0.4041 rms_B_bonded: 2.10 r_work: 0.3893 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3887 Z= 0.128 Angle : 0.707 14.191 5303 Z= 0.331 Chirality : 0.042 0.154 588 Planarity : 0.004 0.043 640 Dihedral : 4.905 27.113 510 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 3.28 % Allowed : 18.18 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.40), residues: 466 helix: -0.62 (0.29), residues: 323 sheet: None (None), residues: 0 loop : -1.32 (0.57), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 332 TYR 0.019 0.001 TYR A 80 PHE 0.020 0.001 PHE A 406 TRP 0.011 0.001 TRP A 485 HIS 0.001 0.000 HIS A 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 ( 3887) covalent geometry : angle 0.70654 / 0.33 ( 5303) hydrogen bonds : bond 0.03485 / 2.24 ( 177) hydrogen bonds : angle 4.33672 / 2.94 ( 525) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1025.41 seconds wall clock time: 18 minutes 17.91 seconds (1097.91 seconds total)