Starting phenix.real_space_refine on Mon Jan 13 19:27:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9f6n_50235/01_2025/9f6n_50235.cif Found real_map, /net/cci-nas-00/data/ceres_data/9f6n_50235/01_2025/9f6n_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9f6n_50235/01_2025/9f6n_50235.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9f6n_50235/01_2025/9f6n_50235.map" model { file = "/net/cci-nas-00/data/ceres_data/9f6n_50235/01_2025/9f6n_50235.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9f6n_50235/01_2025/9f6n_50235.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.47, per 1000 atoms: 0.68 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: 0.86 Conformation dependent library (CDL) restraints added in 459.0 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: 0.33 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: 0.97 Time building geometry restraints manager: 0.99 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 2.320 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: 0.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.480 Find NCS groups from input model: 0.030 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 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 3739 Z= 0.497 Angle : 1.195 10.281 5089 Z= 0.627 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (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 TRP 0.011 0.001 TRP A 135 HIS 0.006 0.002 HIS A 161 PHE 0.028 0.002 PHE A 347 TYR 0.033 0.002 TYR A 324 ARG 0.012 0.001 ARG A 440 *********************** 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 : 0.410 Fit side-chains revert: symmetry clash REVERT: A 164 GLU cc_start: 0.8451 (mt-10) cc_final: 0.7953 (mp0) REVERT: A 305 VAL cc_start: 0.8895 (t) cc_final: 0.8601 (m) REVERT: A 471 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8427 (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: 0.7362 (t80) REVERT: A 552 PHE cc_start: 0.8790 (m-10) cc_final: 0.8204 (m-80) outliers start: 11 outliers final: 8 residues processed: 118 average time/residue: 0.1038 time to fit residues: 16.5321 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 : 0.378 ------------------------------------------------------------------------------- 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 39 optimal weight: 0.6980 chunk 35 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 36 optimal weight: 0.4980 chunk 14 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3485 r_free = 0.3485 target = 0.127540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.105283 restraints weight = 5849.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.109001 restraints weight = 3009.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.111533 restraints weight = 1962.970| |-----------------------------------------------------------------------------| r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3739 Z= 0.210 Angle : 0.592 9.811 5089 Z= 0.303 Chirality : 0.038 0.140 603 Planarity : 0.005 0.060 627 Dihedral : 6.269 58.205 517 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 5.85 % Allowed : 21.88 % Favored : 72.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.37), residues: 469 helix: 1.46 (0.25), residues: 373 sheet: None (None), residues: 0 loop : -1.50 (0.65), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 556 HIS 0.004 0.001 HIS A 296 PHE 0.016 0.001 PHE A 438 TYR 0.010 0.001 TYR A 547 ARG 0.006 0.001 ARG A 440 *********************** 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: 23 poor density : 96 time to evaluate : 0.430 Fit side-chains revert: symmetry clash REVERT: A 118 ASN cc_start: 0.9009 (m-40) cc_final: 0.8724 (m-40) REVERT: A 148 GLN cc_start: 0.8676 (OUTLIER) cc_final: 0.6741 (mp10) REVERT: A 158 THR cc_start: 0.9126 (OUTLIER) cc_final: 0.8789 (p) REVERT: A 305 VAL cc_start: 0.9167 (t) cc_final: 0.8854 (m) REVERT: A 345 SER cc_start: 0.9195 (t) cc_final: 0.8813 (p) REVERT: A 476 SER cc_start: 0.8648 (t) cc_final: 0.8166 (p) REVERT: A 477 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8891 (tp) REVERT: A 521 MET cc_start: 0.8471 (ttp) cc_final: 0.8180 (mtp) REVERT: A 552 PHE cc_start: 0.8863 (m-10) cc_final: 0.8382 (m-80) outliers start: 23 outliers final: 9 residues processed: 108 average time/residue: 0.1013 time to fit residues: 15.0658 Evaluate side-chains 105 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 0.388 ------------------------------------------------------------------------------- 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 327 ILE Chi-restraints excluded: chain A residue 422 SER Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 477 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 35 optimal weight: 0.3980 chunk 42 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 31 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 chunk 33 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 16 optimal weight: 0.2980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 HIS ** 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 = 0.3496 r_free = 0.3496 target = 0.127493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.104932 restraints weight = 5811.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.108593 restraints weight = 3082.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.110906 restraints weight = 2048.519| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3739 Z= 0.179 Angle : 0.591 12.474 5089 Z= 0.290 Chirality : 0.037 0.113 603 Planarity : 0.005 0.057 627 Dihedral : 5.664 57.615 510 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 5.60 % Allowed : 23.66 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.38), residues: 469 helix: 2.01 (0.26), residues: 374 sheet: None (None), residues: 0 loop : -1.45 (0.66), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 435 HIS 0.003 0.001 HIS A 296 PHE 0.018 0.001 PHE A 347 TYR 0.014 0.001 TYR A 547 ARG 0.002 0.000 ARG A 440 *********************** 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 119 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 97 time to evaluate : 0.383 Fit side-chains revert: symmetry clash REVERT: A 118 ASN cc_start: 0.8948 (m-40) cc_final: 0.8607 (m110) REVERT: A 148 GLN cc_start: 0.8681 (OUTLIER) cc_final: 0.6749 (mp10) REVERT: A 158 THR cc_start: 0.8921 (OUTLIER) cc_final: 0.8630 (p) REVERT: A 249 LEU cc_start: 0.8710 (mm) cc_final: 0.8493 (mm) REVERT: A 305 VAL cc_start: 0.9217 (t) cc_final: 0.8959 (m) REVERT: A 345 SER cc_start: 0.9188 (t) cc_final: 0.8763 (p) REVERT: A 476 SER cc_start: 0.8636 (t) cc_final: 0.8172 (p) REVERT: A 537 TYR cc_start: 0.7744 (t80) cc_final: 0.7228 (t80) REVERT: A 552 PHE cc_start: 0.8890 (m-10) cc_final: 0.8418 (m-80) outliers start: 22 outliers final: 11 residues processed: 106 average time/residue: 0.1052 time to fit residues: 15.2358 Evaluate side-chains 106 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 time to evaluate : 0.382 ------------------------------------------------------------------------------- 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 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 484 ILE Chi-restraints excluded: chain A residue 514 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 1 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 chunk 29 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 43 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 301 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.126432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.103392 restraints weight = 5962.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.107003 restraints weight = 3158.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.109338 restraints weight = 2097.571| |-----------------------------------------------------------------------------| r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3739 Z= 0.214 Angle : 0.600 11.330 5089 Z= 0.297 Chirality : 0.038 0.162 603 Planarity : 0.004 0.057 627 Dihedral : 5.579 59.457 508 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 7.38 % Allowed : 23.41 % Favored : 69.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.14 (0.39), residues: 469 helix: 2.06 (0.26), residues: 374 sheet: None (None), residues: 0 loop : -1.25 (0.68), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 435 HIS 0.003 0.001 HIS A 301 PHE 0.020 0.001 PHE A 347 TYR 0.011 0.001 TYR A 547 ARG 0.005 0.000 ARG A 440 *********************** 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 120 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 91 time to evaluate : 0.392 Fit side-chains revert: symmetry clash REVERT: A 148 GLN cc_start: 0.8673 (OUTLIER) cc_final: 0.6595 (mp10) REVERT: A 158 THR cc_start: 0.8918 (OUTLIER) cc_final: 0.8646 (p) REVERT: A 249 LEU cc_start: 0.8710 (mm) cc_final: 0.8506 (mm) REVERT: A 305 VAL cc_start: 0.9199 (t) cc_final: 0.8931 (m) REVERT: A 345 SER cc_start: 0.9186 (t) cc_final: 0.8814 (p) REVERT: A 476 SER cc_start: 0.8597 (t) cc_final: 0.8153 (p) REVERT: A 537 TYR cc_start: 0.7748 (t80) cc_final: 0.7234 (t80) REVERT: A 552 PHE cc_start: 0.8843 (m-10) cc_final: 0.8398 (m-80) outliers start: 29 outliers final: 16 residues processed: 110 average time/residue: 0.1023 time to fit residues: 15.5058 Evaluate side-chains 103 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 85 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 475 GLN Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 514 LEU 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 36 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 22 optimal weight: 0.3980 chunk 43 optimal weight: 0.0870 chunk 10 optimal weight: 0.5980 chunk 6 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 chunk 31 optimal weight: 0.6980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 ASN ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 192 GLN ** 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 = 0.3507 r_free = 0.3507 target = 0.128685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.105832 restraints weight = 6034.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.109539 restraints weight = 3181.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.111892 restraints weight = 2104.763| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3739 Z= 0.183 Angle : 0.604 12.979 5089 Z= 0.294 Chirality : 0.038 0.144 603 Planarity : 0.004 0.057 627 Dihedral : 5.384 57.578 508 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 7.12 % Allowed : 24.43 % Favored : 68.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.27 (0.39), residues: 469 helix: 2.16 (0.26), residues: 374 sheet: None (None), residues: 0 loop : -1.26 (0.66), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 556 HIS 0.002 0.001 HIS A 296 PHE 0.020 0.001 PHE A 347 TYR 0.010 0.001 TYR A 547 ARG 0.004 0.000 ARG A 440 *********************** 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 124 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 96 time to evaluate : 0.397 Fit side-chains revert: symmetry clash REVERT: A 148 GLN cc_start: 0.8743 (OUTLIER) cc_final: 0.6747 (mp10) REVERT: A 158 THR cc_start: 0.8764 (OUTLIER) cc_final: 0.7957 (m) REVERT: A 294 MET cc_start: 0.7833 (mmm) cc_final: 0.7593 (mmm) REVERT: A 305 VAL cc_start: 0.9149 (t) cc_final: 0.8881 (m) REVERT: A 345 SER cc_start: 0.9242 (t) cc_final: 0.8834 (p) REVERT: A 476 SER cc_start: 0.8672 (t) cc_final: 0.8167 (p) REVERT: A 537 TYR cc_start: 0.8016 (t80) cc_final: 0.7494 (t80) REVERT: A 552 PHE cc_start: 0.8870 (m-10) cc_final: 0.8410 (m-80) outliers start: 28 outliers final: 17 residues processed: 110 average time/residue: 0.1108 time to fit residues: 16.2649 Evaluate side-chains 110 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 91 time to evaluate : 0.379 ------------------------------------------------------------------------------- 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 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 414 SER 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 477 LEU Chi-restraints excluded: chain A residue 484 ILE 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 10 optimal weight: 0.5980 chunk 8 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 1 optimal weight: 0.0370 chunk 23 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 chunk 42 optimal weight: 0.7980 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 161 HIS ** 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 = 0.3488 r_free = 0.3488 target = 0.127096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.104307 restraints weight = 6045.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.107907 restraints weight = 3156.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.110464 restraints weight = 2087.405| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3739 Z= 0.193 Angle : 0.621 11.767 5089 Z= 0.301 Chirality : 0.038 0.141 603 Planarity : 0.004 0.056 627 Dihedral : 5.356 58.390 508 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.31 (0.39), residues: 469 helix: 2.14 (0.26), residues: 380 sheet: None (None), residues: 0 loop : -1.23 (0.69), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 435 HIS 0.002 0.001 HIS A 296 PHE 0.018 0.001 PHE A 347 TYR 0.010 0.001 TYR A 553 ARG 0.002 0.000 ARG A 445 *********************** 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 131 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 102 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 113 TYR cc_start: 0.9005 (m-80) cc_final: 0.8381 (m-80) REVERT: A 148 GLN cc_start: 0.8575 (OUTLIER) cc_final: 0.6438 (mp10) REVERT: A 158 THR cc_start: 0.8657 (OUTLIER) cc_final: 0.7853 (m) REVERT: A 305 VAL cc_start: 0.9177 (t) cc_final: 0.8909 (m) REVERT: A 345 SER cc_start: 0.9221 (t) cc_final: 0.8820 (p) REVERT: A 476 SER cc_start: 0.8670 (t) cc_final: 0.8178 (p) REVERT: A 537 TYR cc_start: 0.8079 (t80) cc_final: 0.7586 (t80) REVERT: A 552 PHE cc_start: 0.8855 (m-10) cc_final: 0.8384 (m-80) outliers start: 29 outliers final: 17 residues processed: 116 average time/residue: 0.1123 time to fit residues: 17.3645 Evaluate side-chains 110 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 91 time to evaluate : 0.407 ------------------------------------------------------------------------------- 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 265 VAL Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 377 ASP Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 435 TRP Chi-restraints excluded: chain A residue 475 GLN Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 514 LEU 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 26 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 chunk 18 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 22 optimal weight: 0.0020 chunk 8 optimal weight: 1.9990 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 296 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.126347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.103595 restraints weight = 6009.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.107116 restraints weight = 3213.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.109627 restraints weight = 2147.870| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3739 Z= 0.200 Angle : 0.659 10.762 5089 Z= 0.315 Chirality : 0.042 0.331 603 Planarity : 0.004 0.054 627 Dihedral : 5.350 58.701 508 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 7.12 % Allowed : 26.46 % Favored : 66.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.29 (0.39), residues: 469 helix: 2.10 (0.26), residues: 380 sheet: None (None), residues: 0 loop : -1.08 (0.70), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 435 HIS 0.002 0.001 HIS A 296 PHE 0.017 0.001 PHE A 347 TYR 0.009 0.001 TYR A 547 ARG 0.005 0.000 ARG A 278 *********************** 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 121 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 93 time to evaluate : 0.423 Fit side-chains revert: symmetry clash REVERT: A 148 GLN cc_start: 0.8623 (OUTLIER) cc_final: 0.6433 (mp10) REVERT: A 158 THR cc_start: 0.8628 (OUTLIER) cc_final: 0.7808 (m) REVERT: A 305 VAL cc_start: 0.9247 (t) cc_final: 0.9034 (m) REVERT: A 345 SER cc_start: 0.9213 (t) cc_final: 0.8837 (p) REVERT: A 363 CYS cc_start: 0.5943 (t) cc_final: 0.5417 (t) REVERT: A 476 SER cc_start: 0.8627 (t) cc_final: 0.8154 (p) REVERT: A 537 TYR cc_start: 0.8086 (t80) cc_final: 0.7562 (t80) REVERT: A 552 PHE cc_start: 0.8908 (m-10) cc_final: 0.8459 (m-80) outliers start: 28 outliers final: 21 residues processed: 108 average time/residue: 0.1052 time to fit residues: 15.2055 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 : 0.401 ------------------------------------------------------------------------------- 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 249 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 475 GLN Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 514 LEU 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 0 optimal weight: 5.9990 chunk 19 optimal weight: 0.5980 chunk 28 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 39 optimal weight: 0.0870 chunk 4 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 13 optimal weight: 0.6980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 GLN ** 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 = 0.3486 r_free = 0.3486 target = 0.126783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.104785 restraints weight = 5997.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.108330 restraints weight = 3145.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.110833 restraints weight = 2074.255| |-----------------------------------------------------------------------------| r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3739 Z= 0.207 Angle : 0.681 13.230 5089 Z= 0.321 Chirality : 0.042 0.331 603 Planarity : 0.004 0.055 627 Dihedral : 5.338 58.393 508 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 7.12 % Allowed : 26.46 % Favored : 66.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.29 (0.39), residues: 469 helix: 2.09 (0.26), residues: 380 sheet: None (None), residues: 0 loop : -1.07 (0.69), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 435 HIS 0.001 0.001 HIS A 161 PHE 0.007 0.001 PHE A 438 TYR 0.009 0.001 TYR A 547 ARG 0.002 0.000 ARG A 440 *********************** 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 121 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 93 time to evaluate : 0.379 Fit side-chains REVERT: A 122 ASP cc_start: 0.8244 (m-30) cc_final: 0.8038 (m-30) REVERT: A 158 THR cc_start: 0.8614 (OUTLIER) cc_final: 0.7829 (m) REVERT: A 305 VAL cc_start: 0.9244 (t) cc_final: 0.9017 (m) REVERT: A 476 SER cc_start: 0.8642 (t) cc_final: 0.8157 (p) REVERT: A 537 TYR cc_start: 0.8132 (t80) cc_final: 0.7623 (t80) outliers start: 28 outliers final: 23 residues processed: 110 average time/residue: 0.0969 time to fit residues: 14.6369 Evaluate side-chains 112 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 88 time to evaluate : 0.399 ------------------------------------------------------------------------------- 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 249 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 475 GLN Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 559 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 8 optimal weight: 0.0770 chunk 28 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 192 GLN A 281 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.124982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.102565 restraints weight = 5966.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.106161 restraints weight = 3145.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.108473 restraints weight = 2070.355| |-----------------------------------------------------------------------------| r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3739 Z= 0.223 Angle : 0.710 13.356 5089 Z= 0.335 Chirality : 0.044 0.355 603 Planarity : 0.005 0.054 627 Dihedral : 5.397 58.894 508 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 7.63 % Allowed : 26.21 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.23 (0.39), residues: 469 helix: 2.05 (0.26), residues: 380 sheet: None (None), residues: 0 loop : -1.07 (0.69), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 135 HIS 0.002 0.001 HIS A 161 PHE 0.010 0.001 PHE A 523 TYR 0.009 0.001 TYR A 547 ARG 0.015 0.001 ARG A 278 *********************** 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 120 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 90 time to evaluate : 0.409 Fit side-chains REVERT: A 158 THR cc_start: 0.8465 (OUTLIER) cc_final: 0.7646 (m) REVERT: A 305 VAL cc_start: 0.9245 (t) cc_final: 0.9016 (m) REVERT: A 345 SER cc_start: 0.9166 (t) cc_final: 0.8764 (p) REVERT: A 476 SER cc_start: 0.8625 (t) cc_final: 0.8157 (p) REVERT: A 537 TYR cc_start: 0.7992 (t80) cc_final: 0.7428 (t80) REVERT: A 552 PHE cc_start: 0.8751 (m-10) cc_final: 0.8364 (m-80) outliers start: 30 outliers final: 22 residues processed: 108 average time/residue: 0.0983 time to fit residues: 14.5320 Evaluate side-chains 114 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 91 time to evaluate : 0.404 ------------------------------------------------------------------------------- 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 249 LEU Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 363 CYS 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 475 GLN Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 514 LEU 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 26 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 16 optimal weight: 0.4980 chunk 19 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 chunk 43 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 HIS A 413 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.123769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.101288 restraints weight = 6004.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.104775 restraints weight = 3152.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.107176 restraints weight = 2097.418| |-----------------------------------------------------------------------------| r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.2932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3739 Z= 0.241 Angle : 0.738 15.441 5089 Z= 0.348 Chirality : 0.043 0.364 603 Planarity : 0.005 0.062 627 Dihedral : 5.434 59.294 508 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 5.85 % Allowed : 28.24 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.14 (0.39), residues: 469 helix: 1.97 (0.26), residues: 381 sheet: None (None), residues: 0 loop : -1.05 (0.70), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 135 HIS 0.002 0.001 HIS A 296 PHE 0.008 0.001 PHE A 523 TYR 0.008 0.001 TYR A 547 ARG 0.003 0.000 ARG A 278 ********************** 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 116 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 93 time to evaluate : 0.475 Fit side-chains REVERT: A 158 THR cc_start: 0.8526 (OUTLIER) cc_final: 0.8230 (p) REVERT: A 305 VAL cc_start: 0.9200 (t) cc_final: 0.8904 (m) REVERT: A 476 SER cc_start: 0.8605 (t) cc_final: 0.8136 (p) REVERT: A 537 TYR cc_start: 0.8017 (t80) cc_final: 0.7462 (t80) REVERT: A 552 PHE cc_start: 0.8765 (m-10) cc_final: 0.8416 (m-80) outliers start: 23 outliers final: 21 residues processed: 106 average time/residue: 0.0964 time to fit residues: 14.0008 Evaluate side-chains 114 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 92 time to evaluate : 0.408 ------------------------------------------------------------------------------- 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 249 LEU Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 363 CYS 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 475 GLN Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 514 LEU 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 43 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 4 optimal weight: 0.0870 chunk 34 optimal weight: 0.3980 chunk 11 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 chunk 37 optimal weight: 0.5980 chunk 18 optimal weight: 0.0270 overall best weight: 0.3416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.128883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.106102 restraints weight = 6003.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.109852 restraints weight = 3148.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.112388 restraints weight = 2073.475| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3739 Z= 0.188 Angle : 0.743 15.185 5089 Z= 0.342 Chirality : 0.042 0.365 603 Planarity : 0.004 0.055 627 Dihedral : 5.384 58.491 508 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 5.09 % Allowed : 28.75 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.23 (0.39), residues: 469 helix: 2.04 (0.26), residues: 382 sheet: None (None), residues: 0 loop : -1.11 (0.69), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 435 HIS 0.003 0.001 HIS A 296 PHE 0.014 0.001 PHE A 347 TYR 0.008 0.001 TYR A 547 ARG 0.003 0.000 ARG A 278 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1333.18 seconds wall clock time: 24 minutes 45.47 seconds (1485.47 seconds total)