Starting phenix.real_space_refine on Wed Jul 1 22:49:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9f6n_50235/07_2026/9f6n_50235.cif Found real_map, /net/cci-nas-00/data/ceres_data/9f6n_50235/07_2026/9f6n_50235.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9f6n_50235/07_2026/9f6n_50235.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9f6n_50235/07_2026/9f6n_50235.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9f6n_50235/07_2026/9f6n_50235.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9f6n_50235/07_2026/9f6n_50235.map" } resolution = 3.6 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= 0.030 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 Mn 1 7.51 5 S 21 5.16 5 C 2416 2.51 5 N 591 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 4 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: 3652 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3651 Classifications: {'peptide': 471} Link IDs: {'PTRANS': 16, 'TRANS': 454} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' MN': 1} Chain breaks: 1 Time building chain proxies: 1.06, per 1000 atoms: 0.29 Number of scatterers: 3652 At special positions: 0 Unit cell: (83.328, 67.704, 70.308, 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) Mn 1 24.99 S 21 16.00 O 623 8.00 N 591 7.00 C 2416 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 363 " - pdb=" SG CYS A 394 " 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: 0.31 Conformation dependent library (CDL) restraints added in 142.7 milliseconds 938 Ramachandran restraints generated. 469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 864 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 0 sheets defined 87.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing helix chain 'A' and resid 95 through 102 removed outlier: 3.832A pdb=" N ALA A 101 " --> pdb=" O ARG A 97 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N PHE A 102 " --> pdb=" O LYS A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 113 removed outlier: 4.281A pdb=" N LEU A 108 " --> pdb=" O GLY A 104 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N TYR A 113 " --> pdb=" O MET A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 129 removed outlier: 3.624A pdb=" N ALA A 127 " --> pdb=" O LEU A 123 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA A 129 " --> pdb=" O SER A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 133 removed outlier: 3.836A pdb=" N LEU A 133 " --> pdb=" O GLY A 130 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 130 through 133' Processing helix chain 'A' and resid 134 through 158 removed outlier: 3.570A pdb=" N LEU A 138 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU A 150 " --> pdb=" O LEU A 146 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N THR A 158 " --> pdb=" O LEU A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 170 Processing helix chain 'A' and resid 171 through 205 removed outlier: 3.522A pdb=" N ARG A 175 " --> pdb=" O PRO A 171 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL A 176 " --> pdb=" O LYS A 172 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE A 177 " --> pdb=" O VAL A 173 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER A 205 " --> pdb=" O ILE A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 218 Processing helix chain 'A' and resid 219 through 232 removed outlier: 3.809A pdb=" N PHE A 223 " --> pdb=" O ILE A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 259 Processing helix chain 'A' and resid 261 through 271 Processing helix chain 'A' and resid 278 through 293 removed outlier: 4.097A pdb=" N ILE A 293 " --> pdb=" O VAL A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 308 removed outlier: 3.597A pdb=" N LEU A 300 " --> pdb=" O HIS A 296 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ARG A 308 " --> pdb=" O LEU A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 352 removed outlier: 3.642A pdb=" N PHE A 352 " --> pdb=" O ALA A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 367 removed outlier: 3.560A pdb=" N VAL A 359 " --> pdb=" O THR A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 430 removed outlier: 3.557A pdb=" N GLY A 389 " --> pdb=" O ILE A 385 " (cutoff:3.500A) Proline residue: A 398 - end of helix removed outlier: 3.758A pdb=" N LEU A 401 " --> pdb=" O GLY A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 459 Proline residue: A 451 - end of helix Processing helix chain 'A' and resid 460 through 479 Processing helix chain 'A' and resid 479 through 490 Proline residue: A 485 - end of helix Processing helix chain 'A' and resid 492 through 497 Processing helix chain 'A' and resid 502 through 532 removed outlier: 3.952A pdb=" N ASP A 530 " --> pdb=" O VAL A 526 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LEU A 531 " --> pdb=" O TYR A 527 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLY A 532 " --> pdb=" O VAL A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 562 293 hydrogen bonds defined for protein. 879 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: 0.55 Time building geometry restraints manager: 0.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 1117 1.35 - 1.47: 936 1.47 - 1.59: 1651 1.59 - 1.71: 2 1.71 - 1.83: 33 Bond restraints: 3739 Sorted by residual: bond pdb=" CA PHE A 239 " pdb=" C PHE A 239 " ideal model delta sigma weight residual 1.524 1.485 0.039 1.27e-02 6.20e+03 9.46e+00 bond pdb=" CB ILE A 327 " pdb=" CG2 ILE A 327 " ideal model delta sigma weight residual 1.521 1.604 -0.083 3.30e-02 9.18e+02 6.27e+00 bond pdb=" CB ILE A 519 " pdb=" CG2 ILE A 519 " ideal model delta sigma weight residual 1.521 1.597 -0.076 3.30e-02 9.18e+02 5.24e+00 bond pdb=" N TYR A 527 " pdb=" CA TYR A 527 " ideal model delta sigma weight residual 1.457 1.485 -0.028 1.33e-02 5.65e+03 4.48e+00 bond pdb=" CB ILE A 288 " pdb=" CG1 ILE A 288 " ideal model delta sigma weight residual 1.530 1.572 -0.042 2.00e-02 2.50e+03 4.38e+00 ... (remaining 3734 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.06: 4724 2.06 - 4.11: 280 4.11 - 6.17: 58 6.17 - 8.23: 24 8.23 - 10.28: 3 Bond angle restraints: 5089 Sorted by residual: angle pdb=" C LEU A 228 " pdb=" N ASP A 229 " pdb=" CA ASP A 229 " ideal model delta sigma weight residual 120.44 113.90 6.54 1.30e+00 5.92e-01 2.53e+01 angle pdb=" N LEU A 145 " pdb=" CA LEU A 145 " pdb=" C LEU A 145 " ideal model delta sigma weight residual 111.07 106.69 4.38 1.07e+00 8.73e-01 1.67e+01 angle pdb=" N PHE A 239 " pdb=" CA PHE A 239 " pdb=" C PHE A 239 " ideal model delta sigma weight residual 111.07 106.72 4.35 1.07e+00 8.73e-01 1.65e+01 angle pdb=" C ASN A 297 " pdb=" N MET A 298 " pdb=" CA MET A 298 " ideal model delta sigma weight residual 120.65 115.46 5.19 1.32e+00 5.74e-01 1.55e+01 angle pdb=" N ASP A 229 " pdb=" CA ASP A 229 " pdb=" C ASP A 229 " ideal model delta sigma weight residual 111.07 106.89 4.18 1.07e+00 8.73e-01 1.53e+01 ... (remaining 5084 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.20: 1890 17.20 - 34.39: 200 34.39 - 51.58: 56 51.58 - 68.78: 12 68.78 - 85.97: 6 Dihedral angle restraints: 2164 sinusoidal: 814 harmonic: 1350 Sorted by residual: dihedral pdb=" CB CYS A 363 " pdb=" SG CYS A 363 " pdb=" SG CYS A 394 " pdb=" CB CYS A 394 " ideal model delta sinusoidal sigma weight residual 93.00 37.95 55.05 1 1.00e+01 1.00e-02 4.10e+01 dihedral pdb=" CA ASP A 469 " pdb=" CB ASP A 469 " pdb=" CG ASP A 469 " pdb=" OD1 ASP A 469 " ideal model delta sinusoidal sigma weight residual -30.00 -89.68 59.68 1 2.00e+01 2.50e-03 1.19e+01 dihedral pdb=" CA THR A 490 " pdb=" C THR A 490 " pdb=" N SER A 491 " pdb=" CA SER A 491 " ideal model delta harmonic sigma weight residual 180.00 162.89 17.11 0 5.00e+00 4.00e-02 1.17e+01 ... (remaining 2161 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 406 0.045 - 0.090: 142 0.090 - 0.135: 36 0.135 - 0.179: 12 0.179 - 0.224: 7 Chirality restraints: 603 Sorted by residual: chirality pdb=" CG LEU A 249 " pdb=" CB LEU A 249 " pdb=" CD1 LEU A 249 " pdb=" CD2 LEU A 249 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CB VAL A 442 " pdb=" CA VAL A 442 " pdb=" CG1 VAL A 442 " pdb=" CG2 VAL A 442 " both_signs ideal model delta sigma weight residual False -2.63 -2.84 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CB ILE A 447 " pdb=" CA ILE A 447 " pdb=" CG1 ILE A 447 " pdb=" CG2 ILE A 447 " both_signs ideal model delta sigma weight residual False 2.64 2.85 -0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 600 not shown) Planarity restraints: 627 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 279 " 0.059 5.00e-02 4.00e+02 8.94e-02 1.28e+01 pdb=" N PRO A 280 " -0.155 5.00e-02 4.00e+02 pdb=" CA PRO A 280 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO A 280 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 297 " -0.012 2.00e-02 2.50e+03 2.35e-02 5.50e+00 pdb=" C ASN A 297 " 0.041 2.00e-02 2.50e+03 pdb=" O ASN A 297 " -0.015 2.00e-02 2.50e+03 pdb=" N MET A 298 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 104 " 0.038 5.00e-02 4.00e+02 5.75e-02 5.30e+00 pdb=" N PRO A 105 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO A 105 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 105 " 0.032 5.00e-02 4.00e+02 ... (remaining 624 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.50: 16 2.50 - 3.10: 2690 3.10 - 3.70: 5756 3.70 - 4.30: 7655 4.30 - 4.90: 12775 Nonbonded interactions: 28892 Sorted by model distance: nonbonded pdb=" O LYS A 376 " pdb=" OD1 ASP A 377 " model vdw 1.906 3.040 nonbonded pdb=" OD2 ASP A 115 " pdb="MN MN A 701 " model vdw 2.159 3.060 nonbonded pdb=" O VAL A 215 " pdb=" OG1 THR A 218 " model vdw 2.247 3.040 nonbonded pdb=" O LEU A 514 " pdb=" OG SER A 518 " model vdw 2.261 3.040 nonbonded pdb=" OG SER A 491 " pdb=" OD1 ASN A 501 " model vdw 2.306 3.040 ... (remaining 28887 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.630 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: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.480 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 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 : 0.008 0.083 3740 Z= 0.346 Angle : 1.197 10.281 5091 Z= 0.628 Chirality : 0.054 0.224 603 Planarity : 0.008 0.089 627 Dihedral : 16.583 85.972 1297 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.80 % Allowed : 23.41 % Favored : 73.79 % 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: -0.74 (0.34), residues: 469 helix: -0.07 (0.23), residues: 372 sheet: None (None), residues: 0 loop : -1.69 (0.64), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 440 TYR 0.033 0.002 TYR A 324 PHE 0.028 0.002 PHE A 347 TRP 0.011 0.001 TRP A 135 HIS 0.006 0.002 HIS A 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00789 / 0.35 ( 3739) covalent geometry : angle 1.19486 / 0.63 ( 5089) SS BOND : bond 0.00959 / 0.50 ( 1) SS BOND : angle 3.68490 / 2.15 ( 2) hydrogen bonds : bond 0.11422 / 7.53 ( 293) hydrogen bonds : angle 5.53104 / 3.90 ( 879) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 938 Ramachandran restraints generated. 469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 938 Ramachandran restraints generated. 469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 113 time to evaluate : 0.162 Fit side-chains revert: symmetry clash REVERT: A 164 GLU cc_start: 0.8451 (mt-10) cc_final: 0.7951 (mp0) REVERT: A 305 VAL cc_start: 0.8895 (t) cc_final: 0.8600 (m) REVERT: A 471 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8428 (mp) REVERT: A 476 SER cc_start: 0.8750 (t) cc_final: 0.8168 (p) REVERT: A 521 MET cc_start: 0.8345 (ttp) cc_final: 0.8027 (mtp) REVERT: A 537 TYR cc_start: 0.7734 (t80) cc_final: 0.7363 (t80) REVERT: A 552 PHE cc_start: 0.8790 (m-10) cc_final: 0.8205 (m-80) outliers start: 11 outliers final: 8 residues processed: 118 average time/residue: 0.0429 time to fit residues: 7.0031 Evaluate side-chains 108 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 99 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 148 GLN Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 518 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 24 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 32 optimal weight: 0.5980 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 30 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 118 ASN ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.127434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.105181 restraints weight = 5946.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.108924 restraints weight = 3014.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.111517 restraints weight = 1950.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.112877 restraints weight = 1458.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.114270 restraints weight = 1226.118| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3740 Z= 0.149 Angle : 0.592 9.818 5091 Z= 0.303 Chirality : 0.038 0.137 603 Planarity : 0.005 0.061 627 Dihedral : 6.251 58.181 517 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 5.60 % Allowed : 22.65 % Favored : 71.76 % 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: 1.29 (0.37), residues: 469 helix: 1.46 (0.25), residues: 373 sheet: None (None), residues: 0 loop : -1.49 (0.65), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 440 TYR 0.010 0.001 TYR A 547 PHE 0.016 0.001 PHE A 438 TRP 0.008 0.001 TRP A 556 HIS 0.004 0.001 HIS A 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 ( 3739) covalent geometry : angle 0.59226 / 0.30 ( 5089) SS BOND : bond 0.00705 / 0.37 ( 1) SS BOND : angle 0.94835 / 0.56 ( 2) hydrogen bonds : bond 0.04361 / 2.97 ( 293) hydrogen bonds : angle 4.09689 / 2.89 ( 879) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 938 Ramachandran restraints generated. 469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 938 Ramachandran restraints generated. 469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 97 time to evaluate : 0.131 Fit side-chains revert: symmetry clash REVERT: A 148 GLN cc_start: 0.8650 (OUTLIER) cc_final: 0.6755 (mp10) REVERT: A 158 THR cc_start: 0.9111 (OUTLIER) cc_final: 0.8775 (p) REVERT: A 191 MET cc_start: 0.8257 (ttp) cc_final: 0.8010 (ttp) REVERT: A 305 VAL cc_start: 0.9144 (t) cc_final: 0.8832 (m) REVERT: A 345 SER cc_start: 0.9198 (t) cc_final: 0.8802 (p) REVERT: A 521 MET cc_start: 0.8452 (ttp) cc_final: 0.8164 (mtp) REVERT: A 552 PHE cc_start: 0.8847 (m-10) cc_final: 0.8402 (m-80) outliers start: 22 outliers final: 8 residues processed: 109 average time/residue: 0.0395 time to fit residues: 6.0747 Evaluate side-chains 104 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 94 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 GLN Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 422 SER Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 514 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 2 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 28 optimal weight: 0.0770 chunk 4 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 overall best weight: 0.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 118 ASN ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 301 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.125583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.102833 restraints weight = 5973.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.106494 restraints weight = 3140.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.108895 restraints weight = 2087.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.110385 restraints weight = 1597.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.111558 restraints weight = 1342.851| |-----------------------------------------------------------------------------| r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3740 Z= 0.149 Angle : 0.595 12.061 5091 Z= 0.297 Chirality : 0.038 0.113 603 Planarity : 0.005 0.055 627 Dihedral : 5.755 58.547 510 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 6.11 % Allowed : 23.16 % Favored : 70.74 % 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: 1.96 (0.39), residues: 469 helix: 1.94 (0.26), residues: 374 sheet: None (None), residues: 0 loop : -1.37 (0.67), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 440 TYR 0.014 0.001 TYR A 547 PHE 0.019 0.001 PHE A 347 TRP 0.010 0.001 TRP A 435 HIS 0.002 0.001 HIS A 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 ( 3739) covalent geometry : angle 0.59390 / 0.30 ( 5089) SS BOND : bond 0.00494 / 0.26 ( 1) SS BOND : angle 2.08453 / 1.22 ( 2) hydrogen bonds : bond 0.04191 / 2.84 ( 293) hydrogen bonds : angle 3.94778 / 2.80 ( 879) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 938 Ramachandran restraints generated. 469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 938 Ramachandran restraints generated. 469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 102 time to evaluate : 0.131 Fit side-chains REVERT: A 148 GLN cc_start: 0.8729 (OUTLIER) cc_final: 0.6884 (mp10) REVERT: A 158 THR cc_start: 0.8969 (OUTLIER) cc_final: 0.8663 (p) REVERT: A 249 LEU cc_start: 0.8864 (mm) cc_final: 0.8608 (mm) REVERT: A 305 VAL cc_start: 0.9214 (t) cc_final: 0.8924 (m) REVERT: A 345 SER cc_start: 0.9214 (t) cc_final: 0.8805 (p) REVERT: A 537 TYR cc_start: 0.7772 (t80) cc_final: 0.7279 (t80) REVERT: A 552 PHE cc_start: 0.8860 (m-10) cc_final: 0.8421 (m-80) outliers start: 24 outliers final: 13 residues processed: 113 average time/residue: 0.0403 time to fit residues: 6.3764 Evaluate side-chains 109 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 94 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 148 GLN Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 377 ASP Chi-restraints excluded: chain A residue 422 SER Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 548 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 44 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 20 optimal weight: 0.5980 chunk 18 optimal weight: 6.9990 chunk 10 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 = 0.3438 r_free = 0.3438 target = 0.122337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.099645 restraints weight = 6024.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.103116 restraints weight = 3162.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.105337 restraints weight = 2099.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.107047 restraints weight = 1618.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.107499 restraints weight = 1347.097| |-----------------------------------------------------------------------------| r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3740 Z= 0.168 Angle : 0.611 9.104 5091 Z= 0.309 Chirality : 0.039 0.172 603 Planarity : 0.005 0.055 627 Dihedral : 5.588 58.941 508 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 8.14 % Allowed : 22.90 % Favored : 68.96 % 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: 2.06 (0.39), residues: 469 helix: 2.00 (0.26), residues: 374 sheet: None (None), residues: 0 loop : -1.26 (0.67), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 440 TYR 0.010 0.001 TYR A 547 PHE 0.021 0.001 PHE A 347 TRP 0.009 0.001 TRP A 435 HIS 0.002 0.001 HIS A 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.17 ( 3739) covalent geometry : angle 0.60503 / 0.31 ( 5089) SS BOND : bond 0.00382 / 0.20 ( 1) SS BOND : angle 4.39741 / 2.32 ( 2) hydrogen bonds : bond 0.04273 / 2.89 ( 293) hydrogen bonds : angle 4.03760 / 2.87 ( 879) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 938 Ramachandran restraints generated. 469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 938 Ramachandran restraints generated. 469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 91 time to evaluate : 0.127 Fit side-chains REVERT: A 148 GLN cc_start: 0.8760 (OUTLIER) cc_final: 0.6912 (mp10) REVERT: A 158 THR cc_start: 0.8966 (OUTLIER) cc_final: 0.8614 (p) REVERT: A 249 LEU cc_start: 0.8902 (mm) cc_final: 0.8630 (mm) REVERT: A 305 VAL cc_start: 0.9198 (t) cc_final: 0.8908 (m) REVERT: A 345 SER cc_start: 0.9193 (t) cc_final: 0.8808 (p) REVERT: A 537 TYR cc_start: 0.7775 (t80) cc_final: 0.7283 (t80) REVERT: A 552 PHE cc_start: 0.8842 (m-10) cc_final: 0.8440 (m-80) outliers start: 32 outliers final: 15 residues processed: 112 average time/residue: 0.0403 time to fit residues: 6.3274 Evaluate side-chains 107 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 90 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 148 GLN Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 377 ASP Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 422 SER Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 435 TRP Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 548 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 1 optimal weight: 0.2980 chunk 16 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 6 optimal weight: 0.2980 chunk 15 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 14 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 192 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.125931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.103277 restraints weight = 5976.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.106897 restraints weight = 3116.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.109340 restraints weight = 2052.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.110770 restraints weight = 1557.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.112012 restraints weight = 1308.270| |-----------------------------------------------------------------------------| r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3740 Z= 0.136 Angle : 0.579 7.402 5091 Z= 0.293 Chirality : 0.038 0.144 603 Planarity : 0.005 0.056 627 Dihedral : 5.473 58.752 508 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 7.12 % Allowed : 25.70 % Favored : 67.18 % 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: 2.23 (0.39), residues: 469 helix: 2.14 (0.26), residues: 374 sheet: None (None), residues: 0 loop : -1.30 (0.66), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 278 TYR 0.010 0.001 TYR A 547 PHE 0.019 0.001 PHE A 347 TRP 0.007 0.001 TRP A 435 HIS 0.001 0.001 HIS A 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 ( 3739) covalent geometry : angle 0.57720 / 0.29 ( 5089) SS BOND : bond 0.00117 / 0.06 ( 1) SS BOND : angle 2.30578 / 1.22 ( 2) hydrogen bonds : bond 0.04065 / 2.74 ( 293) hydrogen bonds : angle 3.91955 / 2.81 ( 879) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 938 Ramachandran restraints generated. 469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 938 Ramachandran restraints generated. 469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 105 time to evaluate : 0.128 Fit side-chains REVERT: A 148 GLN cc_start: 0.8778 (OUTLIER) cc_final: 0.6988 (mp10) REVERT: A 158 THR cc_start: 0.8756 (OUTLIER) cc_final: 0.8435 (p) REVERT: A 164 GLU cc_start: 0.8507 (mt-10) cc_final: 0.8187 (mt-10) REVERT: A 249 LEU cc_start: 0.8812 (mm) cc_final: 0.8611 (mm) REVERT: A 305 VAL cc_start: 0.9173 (t) cc_final: 0.8886 (m) REVERT: A 345 SER cc_start: 0.9244 (t) cc_final: 0.8824 (p) REVERT: A 537 TYR cc_start: 0.7787 (t80) cc_final: 0.7247 (t80) REVERT: A 552 PHE cc_start: 0.8880 (m-10) cc_final: 0.8452 (m-80) outliers start: 28 outliers final: 15 residues processed: 121 average time/residue: 0.0425 time to fit residues: 7.0679 Evaluate side-chains 111 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 94 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 148 GLN Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 377 ASP Chi-restraints excluded: chain A residue 422 SER Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 435 TRP Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 548 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 4 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 20 optimal weight: 0.1980 chunk 7 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 43 optimal weight: 0.0470 chunk 3 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 25 optimal weight: 0.5980 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 118 ASN ** A 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 281 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.126301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.103666 restraints weight = 6022.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.107340 restraints weight = 3128.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.109797 restraints weight = 2051.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.111566 restraints weight = 1555.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.112616 restraints weight = 1280.091| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3740 Z= 0.129 Angle : 0.597 7.054 5091 Z= 0.297 Chirality : 0.038 0.183 603 Planarity : 0.004 0.058 627 Dihedral : 5.405 58.224 508 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 7.12 % Allowed : 25.95 % Favored : 66.92 % 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: 2.31 (0.39), residues: 469 helix: 2.16 (0.26), residues: 380 sheet: None (None), residues: 0 loop : -1.32 (0.68), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 278 TYR 0.009 0.001 TYR A 547 PHE 0.018 0.001 PHE A 347 TRP 0.009 0.001 TRP A 556 HIS 0.001 0.000 HIS A 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 ( 3739) covalent geometry : angle 0.59623 / 0.30 ( 5089) SS BOND : bond 0.00405 / 0.21 ( 1) SS BOND : angle 1.63480 / 0.89 ( 2) hydrogen bonds : bond 0.03962 / 2.69 ( 293) hydrogen bonds : angle 3.86820 / 2.79 ( 879) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 938 Ramachandran restraints generated. 469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 938 Ramachandran restraints generated. 469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 99 time to evaluate : 0.133 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 113 TYR cc_start: 0.8950 (m-80) cc_final: 0.8448 (m-80) REVERT: A 148 GLN cc_start: 0.8571 (OUTLIER) cc_final: 0.6520 (mp10) REVERT: A 158 THR cc_start: 0.8597 (OUTLIER) cc_final: 0.7775 (m) REVERT: A 305 VAL cc_start: 0.9215 (t) cc_final: 0.9002 (m) REVERT: A 345 SER cc_start: 0.9209 (t) cc_final: 0.8795 (p) REVERT: A 537 TYR cc_start: 0.7906 (t80) cc_final: 0.7410 (t80) REVERT: A 552 PHE cc_start: 0.8707 (m-10) cc_final: 0.8270 (m-80) outliers start: 28 outliers final: 14 residues processed: 112 average time/residue: 0.0426 time to fit residues: 6.5735 Evaluate side-chains 107 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 148 GLN Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 377 ASP Chi-restraints excluded: chain A residue 414 SER Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 435 TRP Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 548 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 8 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 37 optimal weight: 0.5980 chunk 14 optimal weight: 0.0060 chunk 40 optimal weight: 1.9990 chunk 27 optimal weight: 0.0020 chunk 19 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 overall best weight: 0.3604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 148 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 = 0.3505 r_free = 0.3505 target = 0.128498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.105835 restraints weight = 6142.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.109589 restraints weight = 3201.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.112036 restraints weight = 2103.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.113795 restraints weight = 1599.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.115105 restraints weight = 1317.751| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3740 Z= 0.124 Angle : 0.616 10.159 5091 Z= 0.301 Chirality : 0.038 0.137 603 Planarity : 0.004 0.057 627 Dihedral : 5.314 57.833 508 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 7.38 % Allowed : 25.45 % Favored : 67.18 % 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: 2.34 (0.39), residues: 469 helix: 2.18 (0.26), residues: 381 sheet: None (None), residues: 0 loop : -1.35 (0.67), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 278 TYR 0.009 0.001 TYR A 547 PHE 0.016 0.001 PHE A 347 TRP 0.007 0.001 TRP A 556 HIS 0.001 0.000 HIS A 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 ( 3739) covalent geometry : angle 0.61550 / 0.30 ( 5089) SS BOND : bond 0.00274 / 0.14 ( 1) SS BOND : angle 1.35510 / 0.74 ( 2) hydrogen bonds : bond 0.03816 / 2.60 ( 293) hydrogen bonds : angle 3.84605 / 2.78 ( 879) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 938 Ramachandran restraints generated. 469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 938 Ramachandran restraints generated. 469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 100 time to evaluate : 0.165 Fit side-chains revert: symmetry clash REVERT: A 122 ASP cc_start: 0.8299 (m-30) cc_final: 0.8082 (m-30) REVERT: A 148 GLN cc_start: 0.8466 (OUTLIER) cc_final: 0.6362 (mp10) REVERT: A 158 THR cc_start: 0.8568 (OUTLIER) cc_final: 0.7795 (m) REVERT: A 305 VAL cc_start: 0.9211 (t) cc_final: 0.9005 (m) REVERT: A 345 SER cc_start: 0.9205 (t) cc_final: 0.8778 (p) REVERT: A 476 SER cc_start: 0.8871 (t) cc_final: 0.8630 (p) REVERT: A 537 TYR cc_start: 0.8105 (t80) cc_final: 0.7628 (t80) REVERT: A 552 PHE cc_start: 0.8807 (m-10) cc_final: 0.8366 (m-80) outliers start: 29 outliers final: 17 residues processed: 117 average time/residue: 0.0461 time to fit residues: 7.3376 Evaluate side-chains 117 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 98 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 148 GLN Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 377 ASP Chi-restraints excluded: chain A residue 414 SER Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 435 TRP Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 548 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 2 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 20 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 15 optimal weight: 0.5980 chunk 1 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 148 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 = 0.3463 r_free = 0.3463 target = 0.125038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.102765 restraints weight = 6082.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.106357 restraints weight = 3197.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.108822 restraints weight = 2105.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.110209 restraints weight = 1589.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.111511 restraints weight = 1331.811| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3740 Z= 0.154 Angle : 0.688 11.846 5091 Z= 0.332 Chirality : 0.041 0.347 603 Planarity : 0.004 0.056 627 Dihedral : 5.490 59.927 508 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 6.11 % Allowed : 27.74 % Favored : 66.16 % 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: 2.22 (0.39), residues: 469 helix: 2.08 (0.26), residues: 380 sheet: None (None), residues: 0 loop : -1.30 (0.68), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 440 TYR 0.015 0.001 TYR A 547 PHE 0.018 0.001 PHE A 347 TRP 0.006 0.001 TRP A 556 HIS 0.001 0.001 HIS A 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 ( 3739) covalent geometry : angle 0.68482 / 0.33 ( 5089) SS BOND : bond 0.00428 / 0.23 ( 1) SS BOND : angle 3.62257 / 1.91 ( 2) hydrogen bonds : bond 0.04084 / 2.77 ( 293) hydrogen bonds : angle 4.06122 / 2.91 ( 879) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 938 Ramachandran restraints generated. 469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 938 Ramachandran restraints generated. 469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 91 time to evaluate : 0.135 Fit side-chains REVERT: A 122 ASP cc_start: 0.8329 (m-30) cc_final: 0.8105 (m-30) REVERT: A 148 GLN cc_start: 0.8641 (OUTLIER) cc_final: 0.6560 (mp10) REVERT: A 158 THR cc_start: 0.8565 (OUTLIER) cc_final: 0.7786 (m) REVERT: A 305 VAL cc_start: 0.9236 (t) cc_final: 0.9006 (m) REVERT: A 345 SER cc_start: 0.9228 (t) cc_final: 0.8808 (p) REVERT: A 476 SER cc_start: 0.8901 (t) cc_final: 0.8626 (p) REVERT: A 496 MET cc_start: 0.8497 (mmm) cc_final: 0.8150 (mmm) REVERT: A 537 TYR cc_start: 0.7988 (t80) cc_final: 0.7464 (t80) REVERT: A 552 PHE cc_start: 0.8848 (m-10) cc_final: 0.8423 (m-80) outliers start: 24 outliers final: 20 residues processed: 107 average time/residue: 0.0388 time to fit residues: 5.8875 Evaluate side-chains 109 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 87 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 148 GLN Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 377 ASP Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 414 SER Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 435 TRP Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 548 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 6 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 14 optimal weight: 0.0050 chunk 26 optimal weight: 0.9980 chunk 22 optimal weight: 4.9990 chunk 9 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 192 GLN A 413 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.125431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.103013 restraints weight = 6031.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.106616 restraints weight = 3179.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.109121 restraints weight = 2093.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.110712 restraints weight = 1575.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.111924 restraints weight = 1301.404| |-----------------------------------------------------------------------------| r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3740 Z= 0.153 Angle : 0.710 15.266 5091 Z= 0.336 Chirality : 0.042 0.326 603 Planarity : 0.004 0.054 627 Dihedral : 5.481 58.914 508 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 6.87 % Allowed : 27.23 % Favored : 65.90 % 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: 2.11 (0.39), residues: 469 helix: 2.00 (0.26), residues: 380 sheet: None (None), residues: 0 loop : -1.26 (0.68), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 440 TYR 0.015 0.001 TYR A 547 PHE 0.007 0.001 PHE A 347 TRP 0.005 0.001 TRP A 435 HIS 0.001 0.001 HIS A 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 ( 3739) covalent geometry : angle 0.70656 / 0.33 ( 5089) SS BOND : bond 0.00093 / 0.05 ( 1) SS BOND : angle 3.39302 / 1.79 ( 2) hydrogen bonds : bond 0.04087 / 2.77 ( 293) hydrogen bonds : angle 4.09303 / 2.94 ( 879) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 938 Ramachandran restraints generated. 469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 938 Ramachandran restraints generated. 469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 92 time to evaluate : 0.133 Fit side-chains REVERT: A 148 GLN cc_start: 0.8591 (OUTLIER) cc_final: 0.6746 (mp10) REVERT: A 158 THR cc_start: 0.8587 (OUTLIER) cc_final: 0.7780 (m) REVERT: A 305 VAL cc_start: 0.9234 (t) cc_final: 0.8997 (m) REVERT: A 345 SER cc_start: 0.9207 (t) cc_final: 0.8788 (p) REVERT: A 476 SER cc_start: 0.8890 (t) cc_final: 0.8621 (p) REVERT: A 537 TYR cc_start: 0.7996 (t80) cc_final: 0.7477 (t80) REVERT: A 552 PHE cc_start: 0.8863 (m-10) cc_final: 0.8430 (m-80) outliers start: 27 outliers final: 21 residues processed: 109 average time/residue: 0.0358 time to fit residues: 5.4757 Evaluate side-chains 111 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 88 time to evaluate : 0.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 148 GLN Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 377 ASP Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 414 SER Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 435 TRP Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 548 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 12 optimal weight: 0.2980 chunk 17 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 4 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 chunk 22 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 148 GLN A 192 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.124442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.102065 restraints weight = 6071.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.105642 restraints weight = 3156.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.108130 restraints weight = 2073.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.109689 restraints weight = 1563.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.110558 restraints weight = 1299.696| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3740 Z= 0.149 Angle : 0.708 12.797 5091 Z= 0.336 Chirality : 0.042 0.312 603 Planarity : 0.004 0.056 627 Dihedral : 5.459 58.317 508 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 7.38 % Allowed : 28.24 % Favored : 64.38 % 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: 2.11 (0.39), residues: 469 helix: 2.00 (0.26), residues: 381 sheet: None (None), residues: 0 loop : -1.33 (0.68), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 440 TYR 0.015 0.001 TYR A 547 PHE 0.020 0.001 PHE A 347 TRP 0.006 0.001 TRP A 556 HIS 0.002 0.001 HIS A 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 ( 3739) covalent geometry : angle 0.70511 / 0.33 ( 5089) SS BOND : bond 0.00133 / 0.07 ( 1) SS BOND : angle 3.07009 / 1.62 ( 2) hydrogen bonds : bond 0.04074 / 2.77 ( 293) hydrogen bonds : angle 4.09959 / 2.95 ( 879) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 938 Ramachandran restraints generated. 469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 938 Ramachandran restraints generated. 469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 89 time to evaluate : 0.133 Fit side-chains REVERT: A 158 THR cc_start: 0.8562 (OUTLIER) cc_final: 0.7779 (m) REVERT: A 305 VAL cc_start: 0.9226 (t) cc_final: 0.8981 (m) REVERT: A 345 SER cc_start: 0.9222 (t) cc_final: 0.8827 (p) REVERT: A 347 PHE cc_start: 0.8732 (OUTLIER) cc_final: 0.7521 (t80) REVERT: A 476 SER cc_start: 0.8895 (t) cc_final: 0.8623 (p) REVERT: A 537 TYR cc_start: 0.7979 (t80) cc_final: 0.7457 (t80) REVERT: A 552 PHE cc_start: 0.8915 (m-10) cc_final: 0.8475 (m-80) outliers start: 29 outliers final: 22 residues processed: 108 average time/residue: 0.0388 time to fit residues: 5.9449 Evaluate side-chains 113 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 89 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 148 GLN Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 377 ASP Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 414 SER Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 435 TRP Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 475 GLN Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 548 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 38 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 27 optimal weight: 0.5980 chunk 46 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3451 r_free = 0.3451 target = 0.124132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.102066 restraints weight = 5972.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.105604 restraints weight = 3124.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.108013 restraints weight = 2054.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.109429 restraints weight = 1549.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.110730 restraints weight = 1298.998| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3740 Z= 0.161 Angle : 0.720 12.868 5091 Z= 0.342 Chirality : 0.042 0.315 603 Planarity : 0.004 0.054 627 Dihedral : 4.861 56.108 506 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 6.62 % Allowed : 28.24 % Favored : 65.14 % 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: 2.04 (0.39), residues: 469 helix: 1.94 (0.26), residues: 381 sheet: None (None), residues: 0 loop : -1.29 (0.69), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 440 TYR 0.015 0.001 TYR A 547 PHE 0.015 0.001 PHE A 347 TRP 0.006 0.001 TRP A 556 HIS 0.002 0.001 HIS A 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 ( 3739) covalent geometry : angle 0.71728 / 0.34 ( 5089) SS BOND : bond 0.00190 / 0.10 ( 1) SS BOND : angle 3.12358 / 1.64 ( 2) hydrogen bonds : bond 0.04190 / 2.85 ( 293) hydrogen bonds : angle 4.14167 / 2.98 ( 879) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 750.74 seconds wall clock time: 13 minutes 39.70 seconds (819.70 seconds total)