Starting phenix.real_space_refine on Fri Dec 27 08:57:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9f6n_50235/12_2024/9f6n_50235.cif Found real_map, /net/cci-nas-00/data/ceres_data/9f6n_50235/12_2024/9f6n_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_50235/12_2024/9f6n_50235.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9f6n_50235/12_2024/9f6n_50235.map" model { file = "/net/cci-nas-00/data/ceres_data/9f6n_50235/12_2024/9f6n_50235.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9f6n_50235/12_2024/9f6n_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-5532/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: 2.85, per 1000 atoms: 0.78 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: 0.96 Conformation dependent library (CDL) restraints added in 482.6 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: 1.01 Time building geometry restraints manager: 1.08 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: 0.320 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 13.520 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.980 ------------------------------------------------------------------------------- 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 : 0.369 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: 0.1064 time to fit residues: 16.8163 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 : 0.384 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 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 : 0.407 Fit side-chains revert: symmetry clash REVERT: A 118 ASN cc_start: 0.8733 (m-40) cc_final: 0.8435 (m-40) REVERT: A 148 GLN cc_start: 0.8294 (OUTLIER) cc_final: 0.6492 (mp10) REVERT: A 158 THR cc_start: 0.8692 (OUTLIER) cc_final: 0.8370 (p) REVERT: A 305 VAL cc_start: 0.8882 (t) cc_final: 0.8548 (m) REVERT: A 345 SER cc_start: 0.8978 (t) cc_final: 0.8568 (p) REVERT: A 476 SER cc_start: 0.8653 (t) cc_final: 0.8110 (p) REVERT: A 521 MET cc_start: 0.8492 (ttp) cc_final: 0.8188 (mtp) REVERT: A 552 PHE cc_start: 0.8879 (m-10) cc_final: 0.8378 (m-80) outliers start: 23 outliers final: 9 residues processed: 108 average time/residue: 0.1022 time to fit residues: 15.1532 Evaluate side-chains 104 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 93 time to evaluate : 0.433 ------------------------------------------------------------------------------- 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 514 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 13 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 29 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 22 optimal weight: 4.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 HIS A 301 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3739 Z= 0.248 Angle : 0.617 12.654 5089 Z= 0.309 Chirality : 0.038 0.118 603 Planarity : 0.005 0.055 627 Dihedral : 5.791 58.957 510 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 6.62 % Allowed : 22.90 % Favored : 70.48 % 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: 1.89 (0.39), residues: 469 helix: 1.89 (0.26), residues: 374 sheet: None (None), residues: 0 loop : -1.34 (0.67), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 435 HIS 0.002 0.001 HIS A 301 PHE 0.021 0.001 PHE A 347 TYR 0.014 0.001 TYR A 547 ARG 0.003 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 122 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 96 time to evaluate : 0.400 Fit side-chains REVERT: A 118 ASN cc_start: 0.8750 (m-40) cc_final: 0.8297 (m110) REVERT: A 148 GLN cc_start: 0.8371 (OUTLIER) cc_final: 0.6583 (mp10) REVERT: A 158 THR cc_start: 0.8473 (OUTLIER) cc_final: 0.8169 (p) REVERT: A 249 LEU cc_start: 0.8867 (mm) cc_final: 0.8585 (mm) REVERT: A 305 VAL cc_start: 0.8919 (t) cc_final: 0.8583 (m) REVERT: A 345 SER cc_start: 0.8979 (t) cc_final: 0.8563 (p) REVERT: A 537 TYR cc_start: 0.7760 (t80) cc_final: 0.7254 (t80) REVERT: A 552 PHE cc_start: 0.8888 (m-10) cc_final: 0.8436 (m-80) outliers start: 26 outliers final: 13 residues processed: 109 average time/residue: 0.0963 time to fit residues: 14.4820 Evaluate side-chains 105 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 90 time to evaluate : 0.391 ------------------------------------------------------------------------------- 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 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 4 optimal weight: 0.6980 chunk 20 optimal weight: 0.3980 chunk 28 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 40 optimal weight: 0.0170 chunk 12 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3739 Z= 0.190 Angle : 0.593 11.388 5089 Z= 0.294 Chirality : 0.039 0.170 603 Planarity : 0.005 0.056 627 Dihedral : 5.516 57.986 508 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % 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: 2.06 (0.39), residues: 469 helix: 1.98 (0.26), residues: 375 sheet: None (None), residues: 0 loop : -1.19 (0.67), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 435 HIS 0.003 0.001 HIS A 296 PHE 0.018 0.001 PHE A 347 TYR 0.011 0.001 TYR A 547 ARG 0.006 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 124 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 95 time to evaluate : 0.369 Fit side-chains revert: symmetry clash REVERT: A 118 ASN cc_start: 0.8612 (m-40) cc_final: 0.8252 (m110) REVERT: A 148 GLN cc_start: 0.8385 (OUTLIER) cc_final: 0.6617 (mp10) REVERT: A 249 LEU cc_start: 0.8773 (mm) cc_final: 0.8503 (mm) REVERT: A 305 VAL cc_start: 0.8897 (t) cc_final: 0.8593 (m) REVERT: A 345 SER cc_start: 0.8953 (t) cc_final: 0.8548 (p) REVERT: A 537 TYR cc_start: 0.7735 (t80) cc_final: 0.7208 (t80) REVERT: A 552 PHE cc_start: 0.8866 (m-10) cc_final: 0.8427 (m-80) outliers start: 29 outliers final: 16 residues processed: 113 average time/residue: 0.0984 time to fit residues: 15.3979 Evaluate side-chains 106 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 89 time to evaluate : 0.361 ------------------------------------------------------------------------------- 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 484 ILE 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 33 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 23 optimal weight: 0.7980 chunk 40 optimal weight: 0.0170 chunk 11 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.2369 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= 0.205 Angle : 0.608 13.102 5089 Z= 0.299 Chirality : 0.038 0.158 603 Planarity : 0.004 0.055 627 Dihedral : 5.426 58.302 508 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 6.87 % Allowed : 24.43 % Favored : 68.70 % 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: 2.03 (0.26), residues: 379 sheet: None (None), residues: 0 loop : -1.25 (0.68), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 435 HIS 0.003 0.001 HIS A 296 PHE 0.019 0.001 PHE A 347 TYR 0.010 0.001 TYR A 547 ARG 0.002 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: 27 poor density : 97 time to evaluate : 0.491 Fit side-chains revert: symmetry clash REVERT: A 118 ASN cc_start: 0.8624 (m-40) cc_final: 0.8288 (m110) REVERT: A 148 GLN cc_start: 0.8190 (OUTLIER) cc_final: 0.6511 (mp10) REVERT: A 158 THR cc_start: 0.8022 (OUTLIER) cc_final: 0.7352 (m) REVERT: A 191 MET cc_start: 0.8141 (ttp) cc_final: 0.7908 (ttp) REVERT: A 249 LEU cc_start: 0.8784 (mm) cc_final: 0.8509 (mm) REVERT: A 269 MET cc_start: 0.8366 (mmt) cc_final: 0.8010 (mmt) REVERT: A 305 VAL cc_start: 0.8892 (t) cc_final: 0.8590 (m) REVERT: A 345 SER cc_start: 0.8971 (t) cc_final: 0.8548 (p) REVERT: A 537 TYR cc_start: 0.7763 (t80) cc_final: 0.7233 (t80) REVERT: A 552 PHE cc_start: 0.8693 (m-10) cc_final: 0.8253 (m-80) outliers start: 27 outliers final: 17 residues processed: 111 average time/residue: 0.1139 time to fit residues: 17.0127 Evaluate side-chains 113 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 94 time to evaluate : 0.362 ------------------------------------------------------------------------------- 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 11 optimal weight: 0.0170 chunk 45 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 overall best weight: 1.1022 ------------------------------------------------------------------------------- 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 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 296 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 3739 Z= 0.292 Angle : 0.665 12.453 5089 Z= 0.327 Chirality : 0.041 0.187 603 Planarity : 0.004 0.053 627 Dihedral : 5.594 59.877 508 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 7.38 % Allowed : 25.19 % Favored : 67.43 % 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: 2.00 (0.39), residues: 469 helix: 1.90 (0.26), residues: 379 sheet: None (None), residues: 0 loop : -1.14 (0.70), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 435 HIS 0.002 0.001 HIS A 296 PHE 0.020 0.001 PHE A 347 TYR 0.009 0.001 TYR A 547 ARG 0.002 0.000 ARG A 440 *********************** 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: 29 poor density : 98 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 118 ASN cc_start: 0.8606 (m-40) cc_final: 0.8246 (m110) REVERT: A 148 GLN cc_start: 0.8069 (OUTLIER) cc_final: 0.6277 (mp10) REVERT: A 158 THR cc_start: 0.8096 (OUTLIER) cc_final: 0.7865 (p) REVERT: A 192 GLN cc_start: 0.7491 (tt0) cc_final: 0.7210 (tt0) REVERT: A 237 GLU cc_start: 0.7858 (mm-30) cc_final: 0.7540 (tm-30) REVERT: A 249 LEU cc_start: 0.8828 (mm) cc_final: 0.8542 (mm) REVERT: A 305 VAL cc_start: 0.8884 (t) cc_final: 0.8541 (m) REVERT: A 345 SER cc_start: 0.8980 (t) cc_final: 0.8571 (p) REVERT: A 537 TYR cc_start: 0.7826 (t80) cc_final: 0.7306 (t80) REVERT: A 552 PHE cc_start: 0.8719 (m-10) cc_final: 0.8384 (m-80) outliers start: 29 outliers final: 18 residues processed: 116 average time/residue: 0.1103 time to fit residues: 16.9471 Evaluate side-chains 112 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 92 time to evaluate : 0.414 ------------------------------------------------------------------------------- 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 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 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 454 LEU 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 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 25 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 28 optimal weight: 0.0270 chunk 27 optimal weight: 0.0470 chunk 20 optimal weight: 0.6980 chunk 18 optimal weight: 0.0770 chunk 13 optimal weight: 0.7980 chunk 8 optimal weight: 0.1980 chunk 30 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 overall best weight: 0.1894 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3739 Z= 0.169 Angle : 0.630 10.253 5089 Z= 0.304 Chirality : 0.039 0.201 603 Planarity : 0.004 0.057 627 Dihedral : 5.411 57.854 508 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 5.34 % Allowed : 26.97 % Favored : 67.68 % 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 (0.40), residues: 469 helix: 2.08 (0.26), residues: 381 sheet: None (None), residues: 0 loop : -0.92 (0.70), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 435 HIS 0.001 0.000 HIS A 296 PHE 0.010 0.001 PHE A 347 TYR 0.009 0.001 TYR A 547 ARG 0.002 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 127 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 106 time to evaluate : 0.413 Fit side-chains revert: symmetry clash REVERT: A 113 TYR cc_start: 0.8974 (m-80) cc_final: 0.7912 (m-80) REVERT: A 118 ASN cc_start: 0.8546 (m-40) cc_final: 0.8214 (m110) REVERT: A 148 GLN cc_start: 0.8101 (OUTLIER) cc_final: 0.6218 (mp10) REVERT: A 158 THR cc_start: 0.7956 (OUTLIER) cc_final: 0.7267 (m) REVERT: A 237 GLU cc_start: 0.7678 (mm-30) cc_final: 0.7436 (tm-30) REVERT: A 249 LEU cc_start: 0.8634 (mm) cc_final: 0.8410 (mm) REVERT: A 305 VAL cc_start: 0.9005 (t) cc_final: 0.8801 (m) REVERT: A 537 TYR cc_start: 0.8101 (t80) cc_final: 0.7584 (t80) REVERT: A 552 PHE cc_start: 0.8687 (m-10) cc_final: 0.8287 (m-80) outliers start: 21 outliers final: 11 residues processed: 121 average time/residue: 0.1016 time to fit residues: 16.6238 Evaluate side-chains 119 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 106 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 134 LEU 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 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 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 4 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 41 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 18 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 12 optimal weight: 0.0040 chunk 38 optimal weight: 0.7980 overall best weight: 0.5992 ------------------------------------------------------------------------------- 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 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3739 Z= 0.218 Angle : 0.687 13.416 5089 Z= 0.327 Chirality : 0.039 0.155 603 Planarity : 0.004 0.056 627 Dihedral : 5.455 59.983 508 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % 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: 2.22 (0.39), residues: 469 helix: 2.03 (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 0.012 0.001 TRP A 435 HIS 0.002 0.001 HIS A 161 PHE 0.012 0.001 PHE A 347 TYR 0.015 0.001 TYR A 547 ARG 0.001 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 129 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 106 time to evaluate : 0.412 Fit side-chains revert: symmetry clash REVERT: A 118 ASN cc_start: 0.8586 (m-40) cc_final: 0.8292 (m110) REVERT: A 148 GLN cc_start: 0.7988 (OUTLIER) cc_final: 0.6050 (mp10) REVERT: A 237 GLU cc_start: 0.7724 (mm-30) cc_final: 0.7473 (tm-30) REVERT: A 249 LEU cc_start: 0.8728 (mm) cc_final: 0.8432 (mm) REVERT: A 305 VAL cc_start: 0.8924 (t) cc_final: 0.8694 (m) REVERT: A 345 SER cc_start: 0.8959 (t) cc_final: 0.8544 (p) REVERT: A 537 TYR cc_start: 0.7966 (t80) cc_final: 0.7395 (t80) REVERT: A 552 PHE cc_start: 0.8714 (m-10) cc_final: 0.8279 (m-80) outliers start: 23 outliers final: 12 residues processed: 118 average time/residue: 0.0970 time to fit residues: 15.5019 Evaluate side-chains 109 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 0.358 ------------------------------------------------------------------------------- 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 180 LEU Chi-restraints excluded: chain A residue 206 VAL 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 475 GLN Chi-restraints excluded: chain A residue 514 LEU 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 39 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 chunk 27 optimal weight: 4.9990 chunk 44 optimal weight: 6.9990 chunk 21 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 28 optimal weight: 0.0020 overall best weight: 0.7188 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.2925 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= 0.245 Angle : 0.736 15.272 5089 Z= 0.347 Chirality : 0.040 0.146 603 Planarity : 0.005 0.055 627 Dihedral : 5.505 59.691 508 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 4.58 % Allowed : 29.26 % 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: 2.09 (0.39), residues: 469 helix: 1.93 (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 0.010 0.001 TRP A 435 HIS 0.002 0.001 HIS A 161 PHE 0.012 0.001 PHE A 523 TYR 0.015 0.001 TYR A 547 ARG 0.006 0.000 ARG A 440 *********************** 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 116 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 98 time to evaluate : 0.420 Fit side-chains revert: symmetry clash REVERT: A 118 ASN cc_start: 0.8607 (m-40) cc_final: 0.7823 (m110) REVERT: A 122 ASP cc_start: 0.7955 (m-30) cc_final: 0.7547 (m-30) REVERT: A 148 GLN cc_start: 0.8007 (OUTLIER) cc_final: 0.6120 (mp10) REVERT: A 237 GLU cc_start: 0.7714 (mm-30) cc_final: 0.7470 (tm-30) REVERT: A 249 LEU cc_start: 0.8664 (mm) cc_final: 0.8353 (mm) REVERT: A 305 VAL cc_start: 0.8938 (t) cc_final: 0.8694 (m) REVERT: A 345 SER cc_start: 0.8957 (t) cc_final: 0.8548 (p) REVERT: A 537 TYR cc_start: 0.7962 (t80) cc_final: 0.7399 (t80) REVERT: A 552 PHE cc_start: 0.8717 (m-10) cc_final: 0.8289 (m-80) outliers start: 18 outliers final: 16 residues processed: 108 average time/residue: 0.1054 time to fit residues: 15.2567 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 : 0.419 ------------------------------------------------------------------------------- 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 180 LEU Chi-restraints excluded: chain A residue 206 VAL 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 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 22 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 39 optimal weight: 0.4980 chunk 11 optimal weight: 0.0770 chunk 34 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 37 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 overall best weight: 0.5138 ------------------------------------------------------------------------------- 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 192 GLN A 413 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3739 Z= 0.211 Angle : 0.718 14.333 5089 Z= 0.338 Chirality : 0.039 0.149 603 Planarity : 0.005 0.056 627 Dihedral : 5.495 59.597 508 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 5.34 % Allowed : 28.50 % 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: 2.10 (0.39), residues: 469 helix: 1.94 (0.26), residues: 382 sheet: None (None), residues: 0 loop : -1.09 (0.70), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 435 HIS 0.001 0.001 HIS A 161 PHE 0.010 0.001 PHE A 523 TYR 0.015 0.001 TYR A 547 ARG 0.005 0.000 ARG A 440 ********************** 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 125 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 104 time to evaluate : 0.458 Fit side-chains revert: symmetry clash REVERT: A 118 ASN cc_start: 0.8563 (m-40) cc_final: 0.7768 (m110) REVERT: A 122 ASP cc_start: 0.7913 (m-30) cc_final: 0.7515 (m-30) REVERT: A 148 GLN cc_start: 0.7957 (OUTLIER) cc_final: 0.6038 (mp10) REVERT: A 237 GLU cc_start: 0.7708 (mm-30) cc_final: 0.7467 (tm-30) REVERT: A 249 LEU cc_start: 0.8697 (mm) cc_final: 0.8474 (mm) REVERT: A 305 VAL cc_start: 0.8954 (t) cc_final: 0.8718 (m) REVERT: A 345 SER cc_start: 0.8964 (t) cc_final: 0.8528 (p) REVERT: A 537 TYR cc_start: 0.7982 (t80) cc_final: 0.7417 (t80) REVERT: A 552 PHE cc_start: 0.8720 (m-10) cc_final: 0.8291 (m-80) outliers start: 21 outliers final: 16 residues processed: 116 average time/residue: 0.1098 time to fit residues: 17.0113 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 : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 134 LEU 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 180 LEU Chi-restraints excluded: chain A residue 206 VAL 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 414 SER Chi-restraints excluded: chain A residue 431 LEU 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 548 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 6 optimal weight: 3.9990 chunk 32 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.123268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.100285 restraints weight = 6044.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.103807 restraints weight = 3248.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.106179 restraints weight = 2167.658| |-----------------------------------------------------------------------------| r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 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 : 0.004 0.038 3739 Z= 0.268 Angle : 0.760 15.318 5089 Z= 0.358 Chirality : 0.040 0.160 603 Planarity : 0.005 0.054 627 Dihedral : 5.519 58.875 508 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 5.60 % Allowed : 27.99 % 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: 1.96 (0.39), residues: 469 helix: 1.84 (0.26), residues: 381 sheet: None (None), residues: 0 loop : -1.08 (0.71), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 435 HIS 0.002 0.001 HIS A 161 PHE 0.009 0.001 PHE A 523 TYR 0.015 0.001 TYR A 547 ARG 0.007 0.000 ARG A 440 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1084.43 seconds wall clock time: 20 minutes 23.17 seconds (1223.17 seconds total)