Starting phenix.real_space_refine on Thu Jul 18 21:01:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xcs_38253/07_2024/8xcs_38253.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xcs_38253/07_2024/8xcs_38253.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xcs_38253/07_2024/8xcs_38253.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xcs_38253/07_2024/8xcs_38253.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xcs_38253/07_2024/8xcs_38253.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xcs_38253/07_2024/8xcs_38253.cif" } resolution = 2.63 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= 0.000 sd= 0.002 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 P 3 5.49 5 S 14 5.16 5 C 2121 2.51 5 N 567 2.21 5 O 655 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 371": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 3360 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3281 Classifications: {'peptide': 418} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 397} Chain: "A" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 79 Unusual residues: {'AKG': 1, 'NDP': 1, 'NH4': 1} Classifications: {'undetermined': 3, 'water': 20} Link IDs: {None: 22} Time building chain proxies: 3.98, per 1000 atoms: 1.18 Number of scatterers: 3360 At special positions: 0 Unit cell: (71.44, 69.184, 68.432, 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) S 14 16.00 P 3 15.00 O 655 8.00 N 567 7.00 C 2121 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 1.78 Conformation dependent library (CDL) restraints added in 583.9 milliseconds 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 762 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 3 sheets defined 55.5% alpha, 18.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 5 through 19 Processing helix chain 'A' and resid 24 through 32 Processing helix chain 'A' and resid 79 through 97 removed outlier: 3.815A pdb=" N VAL A 97 " --> pdb=" O LYS A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 115 Processing helix chain 'A' and resid 116 through 132 Processing helix chain 'A' and resid 133 through 135 No H-bonds generated for 'chain 'A' and resid 133 through 135' Processing helix chain 'A' and resid 149 through 165 Processing helix chain 'A' and resid 169 through 174 removed outlier: 3.919A pdb=" N ILE A 174 " --> pdb=" O PHE A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 207 Processing helix chain 'A' and resid 223 through 234 Processing helix chain 'A' and resid 256 through 268 Processing helix chain 'A' and resid 280 through 286 Processing helix chain 'A' and resid 305 through 309 removed outlier: 3.512A pdb=" N ILE A 309 " --> pdb=" O ALA A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 333 Processing helix chain 'A' and resid 339 through 344 Processing helix chain 'A' and resid 344 through 361 removed outlier: 4.472A pdb=" N VAL A 348 " --> pdb=" O ASN A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 392 Processing helix chain 'A' and resid 394 through 415 removed outlier: 3.762A pdb=" N SER A 405 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ARG A 406 " --> pdb=" O VAL A 402 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 45 removed outlier: 6.652A pdb=" N GLY A 103 " --> pdb=" O HIS A 61 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 45 removed outlier: 6.652A pdb=" N GLY A 103 " --> pdb=" O HIS A 61 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N LYS A 69 " --> pdb=" O GLY A 104 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N GLY A 106 " --> pdb=" O LYS A 69 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N THR A 68 " --> pdb=" O ILE A 141 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 277 through 279 removed outlier: 6.471A pdb=" N ILE A 215 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ALA A 241 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER A 243 " --> pdb=" O VAL A 217 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LYS A 214 " --> pdb=" O VAL A 291 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N ALA A 293 " --> pdb=" O LYS A 214 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ALA A 216 " --> pdb=" O ALA A 293 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N LEU A 292 " --> pdb=" O ALA A 315 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL A 314 " --> pdb=" O ILE A 338 " (cutoff:3.500A) 199 hydrogen bonds defined for protein. 570 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: 1.09 Time building geometry restraints manager: 1.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1004 1.34 - 1.45: 483 1.45 - 1.57: 1899 1.57 - 1.69: 2 1.69 - 1.81: 27 Bond restraints: 3415 Sorted by residual: bond pdb=" O1N NDP A 501 " pdb=" PN NDP A 501 " ideal model delta sigma weight residual 1.477 1.550 -0.073 1.00e-02 1.00e+04 5.28e+01 bond pdb=" O2B NDP A 501 " pdb=" P2B NDP A 501 " ideal model delta sigma weight residual 1.833 1.566 0.267 3.80e-02 6.93e+02 4.94e+01 bond pdb=" O5D NDP A 501 " pdb=" PN NDP A 501 " ideal model delta sigma weight residual 1.757 1.559 0.198 3.50e-02 8.16e+02 3.22e+01 bond pdb=" C1 AKG A 502 " pdb=" C2 AKG A 502 " ideal model delta sigma weight residual 1.559 1.461 0.098 2.00e-02 2.50e+03 2.39e+01 bond pdb=" C6A NDP A 501 " pdb=" N1A NDP A 501 " ideal model delta sigma weight residual 1.368 1.253 0.115 2.90e-02 1.19e+03 1.58e+01 ... (remaining 3410 not shown) Histogram of bond angle deviations from ideal: 95.97 - 103.58: 57 103.58 - 111.20: 1368 111.20 - 118.81: 1395 118.81 - 126.42: 1742 126.42 - 134.03: 76 Bond angle restraints: 4638 Sorted by residual: angle pdb=" C1D NDP A 501 " pdb=" O4D NDP A 501 " pdb=" C4D NDP A 501 " ideal model delta sigma weight residual 105.41 127.53 -22.12 2.71e+00 1.37e-01 6.68e+01 angle pdb=" C5B NDP A 501 " pdb=" O5B NDP A 501 " pdb=" PA NDP A 501 " ideal model delta sigma weight residual 103.84 119.24 -15.40 1.91e+00 2.73e-01 6.47e+01 angle pdb=" PA NDP A 501 " pdb=" O3 NDP A 501 " pdb=" PN NDP A 501 " ideal model delta sigma weight residual 107.74 122.52 -14.78 1.95e+00 2.62e-01 5.72e+01 angle pdb=" O1X NDP A 501 " pdb=" P2B NDP A 501 " pdb=" O3X NDP A 501 " ideal model delta sigma weight residual 117.46 109.42 8.04 1.17e+00 7.36e-01 4.75e+01 angle pdb=" O2X NDP A 501 " pdb=" P2B NDP A 501 " pdb=" O3X NDP A 501 " ideal model delta sigma weight residual 117.33 108.86 8.47 1.48e+00 4.57e-01 3.28e+01 ... (remaining 4633 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.95: 1931 30.95 - 61.89: 84 61.89 - 92.84: 7 92.84 - 123.78: 0 123.78 - 154.73: 1 Dihedral angle restraints: 2023 sinusoidal: 828 harmonic: 1195 Sorted by residual: dihedral pdb=" C5B NDP A 501 " pdb=" O5B NDP A 501 " pdb=" PA NDP A 501 " pdb=" O3 NDP A 501 " ideal model delta sinusoidal sigma weight residual 175.04 20.31 154.73 1 3.00e+01 1.11e-03 2.03e+01 dihedral pdb=" CA TYR A 101 " pdb=" C TYR A 101 " pdb=" N GLY A 102 " pdb=" CA GLY A 102 " ideal model delta harmonic sigma weight residual 180.00 163.83 16.17 0 5.00e+00 4.00e-02 1.05e+01 dihedral pdb=" CB LYS A 304 " pdb=" CG LYS A 304 " pdb=" CD LYS A 304 " pdb=" CE LYS A 304 " ideal model delta sinusoidal sigma weight residual 180.00 121.19 58.81 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 2020 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 443 0.079 - 0.159: 52 0.159 - 0.238: 3 0.238 - 0.318: 3 0.318 - 0.397: 3 Chirality restraints: 504 Sorted by residual: chirality pdb=" C4D NDP A 501 " pdb=" C3D NDP A 501 " pdb=" C5D NDP A 501 " pdb=" O4D NDP A 501 " both_signs ideal model delta sigma weight residual False -2.71 -2.32 -0.40 2.00e-01 2.50e+01 3.95e+00 chirality pdb=" C2D NDP A 501 " pdb=" C1D NDP A 501 " pdb=" C3D NDP A 501 " pdb=" O2D NDP A 501 " both_signs ideal model delta sigma weight residual False -2.71 -2.34 -0.37 2.00e-01 2.50e+01 3.42e+00 chirality pdb=" C1B NDP A 501 " pdb=" C2B NDP A 501 " pdb=" N9A NDP A 501 " pdb=" O4B NDP A 501 " both_signs ideal model delta sigma weight residual False 2.59 2.24 0.36 2.00e-01 2.50e+01 3.16e+00 ... (remaining 501 not shown) Planarity restraints: 592 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2N NDP A 501 " -0.139 2.00e-02 2.50e+03 8.17e-02 8.34e+01 pdb=" C3N NDP A 501 " 0.008 2.00e-02 2.50e+03 pdb=" C4N NDP A 501 " -0.026 2.00e-02 2.50e+03 pdb=" C7N NDP A 501 " 0.058 2.00e-02 2.50e+03 pdb=" N1N NDP A 501 " 0.100 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C4N NDP A 501 " -0.035 2.00e-02 2.50e+03 6.15e-02 3.78e+01 pdb=" C5N NDP A 501 " 0.078 2.00e-02 2.50e+03 pdb=" C6N NDP A 501 " -0.080 2.00e-02 2.50e+03 pdb=" N1N NDP A 501 " 0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS A 394 " 0.021 2.00e-02 2.50e+03 4.08e-02 1.66e+01 pdb=" C HIS A 394 " -0.071 2.00e-02 2.50e+03 pdb=" O HIS A 394 " 0.026 2.00e-02 2.50e+03 pdb=" N MET A 395 " 0.024 2.00e-02 2.50e+03 ... (remaining 589 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.88: 1265 2.88 - 3.39: 3295 3.39 - 3.89: 6079 3.89 - 4.40: 7212 4.40 - 4.90: 11655 Nonbonded interactions: 29506 Sorted by model distance: nonbonded pdb=" O HIS A 61 " pdb=" O HOH A 601 " model vdw 2.381 2.440 nonbonded pdb=" O ASP A 145 " pdb=" O HOH A 602 " model vdw 2.445 2.440 nonbonded pdb=" O VAL A 317 " pdb=" ND2 ASN A 344 " model vdw 2.448 2.520 nonbonded pdb=" O ARG A 65 " pdb=" O HOH A 603 " model vdw 2.461 2.440 nonbonded pdb=" O THR A 148 " pdb=" O HOH A 602 " model vdw 2.469 2.440 ... (remaining 29501 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.930 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 16.410 Find NCS groups from input model: 0.040 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:14.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 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 : 0.009 0.267 3415 Z= 0.517 Angle : 1.096 22.116 4638 Z= 0.584 Chirality : 0.059 0.397 504 Planarity : 0.006 0.082 592 Dihedral : 16.414 154.727 1261 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 4.69 % Allowed : 3.52 % Favored : 91.79 % 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: 0.58 (0.43), residues: 416 helix: 0.93 (0.36), residues: 210 sheet: 0.54 (0.74), residues: 60 loop : -0.33 (0.56), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 63 HIS 0.003 0.001 HIS A 388 PHE 0.008 0.001 PHE A 341 TYR 0.007 0.001 TYR A 363 ARG 0.001 0.000 ARG A 129 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 65 time to evaluate : 0.389 Fit side-chains REVERT: A 12 LYS cc_start: 0.8340 (OUTLIER) cc_final: 0.8074 (mptt) outliers start: 16 outliers final: 2 residues processed: 76 average time/residue: 1.5264 time to fit residues: 118.6691 Evaluate side-chains 49 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 46 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LYS Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 5.9990 chunk 31 optimal weight: 20.0000 chunk 17 optimal weight: 0.6980 chunk 10 optimal weight: 5.9990 chunk 20 optimal weight: 10.0000 chunk 16 optimal weight: 6.9990 chunk 32 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 23 optimal weight: 9.9990 chunk 37 optimal weight: 0.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN A 337 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3415 Z= 0.269 Angle : 0.523 5.584 4638 Z= 0.280 Chirality : 0.045 0.139 504 Planarity : 0.005 0.042 592 Dihedral : 10.956 161.997 477 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.23 % Allowed : 10.85 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.25 (0.44), residues: 416 helix: 1.88 (0.37), residues: 206 sheet: 0.37 (0.71), residues: 61 loop : -0.42 (0.56), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 364 HIS 0.006 0.002 HIS A 388 PHE 0.016 0.002 PHE A 341 TYR 0.013 0.002 TYR A 363 ARG 0.001 0.000 ARG A 65 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 45 time to evaluate : 0.340 Fit side-chains REVERT: A 113 LYS cc_start: 0.8718 (mttp) cc_final: 0.8418 (mtpt) REVERT: A 229 LYS cc_start: 0.8796 (OUTLIER) cc_final: 0.8510 (tttp) REVERT: A 303 GLU cc_start: 0.7497 (OUTLIER) cc_final: 0.7178 (pt0) REVERT: A 371 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.7305 (pt0) outliers start: 11 outliers final: 1 residues processed: 52 average time/residue: 1.6371 time to fit residues: 87.1082 Evaluate side-chains 44 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 40 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 LYS Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 7.9990 chunk 11 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 25 optimal weight: 9.9990 chunk 10 optimal weight: 2.9990 chunk 37 optimal weight: 7.9990 chunk 40 optimal weight: 4.9990 chunk 33 optimal weight: 0.6980 chunk 36 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 29 optimal weight: 10.0000 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 62 ASN A 337 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3415 Z= 0.261 Angle : 0.507 5.123 4638 Z= 0.269 Chirality : 0.044 0.138 504 Planarity : 0.004 0.045 592 Dihedral : 9.828 161.393 470 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.64 % Allowed : 11.73 % Favored : 85.63 % 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: 1.40 (0.44), residues: 416 helix: 2.03 (0.36), residues: 206 sheet: 0.36 (0.71), residues: 61 loop : -0.35 (0.56), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 30 HIS 0.006 0.002 HIS A 388 PHE 0.017 0.002 PHE A 341 TYR 0.014 0.002 TYR A 363 ARG 0.001 0.000 ARG A 65 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 42 time to evaluate : 0.437 Fit side-chains REVERT: A 246 ARG cc_start: 0.7876 (OUTLIER) cc_final: 0.7384 (mtt180) REVERT: A 371 GLU cc_start: 0.7621 (pt0) cc_final: 0.7348 (pt0) outliers start: 9 outliers final: 2 residues processed: 48 average time/residue: 1.6277 time to fit residues: 80.0133 Evaluate side-chains 42 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 39 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 3.9990 chunk 28 optimal weight: 7.9990 chunk 19 optimal weight: 5.9990 chunk 4 optimal weight: 6.9990 chunk 17 optimal weight: 0.9980 chunk 25 optimal weight: 9.9990 chunk 37 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 10 optimal weight: 6.9990 chunk 33 optimal weight: 0.2980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 337 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3415 Z= 0.140 Angle : 0.443 5.167 4638 Z= 0.233 Chirality : 0.041 0.129 504 Planarity : 0.004 0.045 592 Dihedral : 9.394 162.685 470 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.35 % Allowed : 12.61 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.64 (0.44), residues: 416 helix: 2.12 (0.36), residues: 211 sheet: 0.40 (0.72), residues: 61 loop : -0.10 (0.58), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 382 HIS 0.003 0.001 HIS A 388 PHE 0.009 0.001 PHE A 341 TYR 0.008 0.001 TYR A 363 ARG 0.001 0.000 ARG A 406 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 47 time to evaluate : 0.347 Fit side-chains REVERT: A 246 ARG cc_start: 0.7842 (OUTLIER) cc_final: 0.7339 (mtt180) REVERT: A 371 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.7359 (pt0) REVERT: A 388 HIS cc_start: 0.8815 (OUTLIER) cc_final: 0.7966 (t70) outliers start: 8 outliers final: 1 residues processed: 51 average time/residue: 1.5749 time to fit residues: 82.2939 Evaluate side-chains 48 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 44 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 29 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 33 optimal weight: 9.9990 chunk 27 optimal weight: 8.9990 chunk 20 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 10 optimal weight: 8.9990 chunk 13 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 337 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 3415 Z= 0.311 Angle : 0.520 5.315 4638 Z= 0.277 Chirality : 0.045 0.140 504 Planarity : 0.005 0.046 592 Dihedral : 9.609 156.724 470 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.52 % Allowed : 12.02 % Favored : 84.46 % 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: 1.49 (0.44), residues: 416 helix: 2.13 (0.36), residues: 206 sheet: 0.56 (0.73), residues: 59 loop : -0.42 (0.56), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 30 HIS 0.007 0.002 HIS A 388 PHE 0.020 0.002 PHE A 341 TYR 0.015 0.002 TYR A 363 ARG 0.002 0.000 ARG A 118 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 41 time to evaluate : 0.480 Fit side-chains REVERT: A 246 ARG cc_start: 0.7870 (OUTLIER) cc_final: 0.7312 (mtt180) REVERT: A 371 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.7398 (pt0) outliers start: 12 outliers final: 3 residues processed: 48 average time/residue: 1.6164 time to fit residues: 79.4348 Evaluate side-chains 45 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 40 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 9.9990 chunk 9 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 3 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 38 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 337 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3415 Z= 0.146 Angle : 0.444 4.397 4638 Z= 0.235 Chirality : 0.042 0.132 504 Planarity : 0.004 0.045 592 Dihedral : 9.058 153.652 470 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.35 % Allowed : 13.78 % Favored : 83.87 % 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: 1.67 (0.44), residues: 416 helix: 2.17 (0.36), residues: 211 sheet: 0.54 (0.73), residues: 59 loop : -0.18 (0.58), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 30 HIS 0.003 0.001 HIS A 388 PHE 0.010 0.001 PHE A 341 TYR 0.010 0.001 TYR A 363 ARG 0.001 0.000 ARG A 118 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 45 time to evaluate : 0.405 Fit side-chains REVERT: A 246 ARG cc_start: 0.7835 (OUTLIER) cc_final: 0.7264 (mtt180) REVERT: A 371 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.7377 (pt0) REVERT: A 388 HIS cc_start: 0.8825 (OUTLIER) cc_final: 0.8135 (t70) outliers start: 8 outliers final: 2 residues processed: 49 average time/residue: 1.5745 time to fit residues: 79.0209 Evaluate side-chains 48 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 43 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 33 optimal weight: 9.9990 chunk 39 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 chunk 18 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 23 optimal weight: 7.9990 chunk 11 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 25 optimal weight: 0.6980 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 337 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3415 Z= 0.230 Angle : 0.482 4.583 4638 Z= 0.257 Chirality : 0.043 0.132 504 Planarity : 0.004 0.044 592 Dihedral : 9.151 151.879 470 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.93 % Allowed : 12.90 % Favored : 84.16 % 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: 1.63 (0.44), residues: 416 helix: 2.28 (0.36), residues: 206 sheet: 0.54 (0.72), residues: 59 loop : -0.36 (0.57), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 30 HIS 0.006 0.001 HIS A 388 PHE 0.016 0.002 PHE A 341 TYR 0.013 0.001 TYR A 363 ARG 0.001 0.000 ARG A 118 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 43 time to evaluate : 0.372 Fit side-chains REVERT: A 78 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.8203 (tt0) REVERT: A 246 ARG cc_start: 0.7861 (OUTLIER) cc_final: 0.7290 (mtt180) REVERT: A 371 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.7393 (pt0) outliers start: 10 outliers final: 3 residues processed: 48 average time/residue: 1.7325 time to fit residues: 85.1121 Evaluate side-chains 44 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 38 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 7.9990 chunk 19 optimal weight: 5.9990 chunk 3 optimal weight: 4.9990 chunk 31 optimal weight: 10.0000 chunk 35 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 28 optimal weight: 6.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 337 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3415 Z= 0.221 Angle : 0.484 4.797 4638 Z= 0.257 Chirality : 0.043 0.134 504 Planarity : 0.004 0.046 592 Dihedral : 9.081 150.157 470 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.64 % Allowed : 14.08 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.64 (0.44), residues: 416 helix: 2.27 (0.36), residues: 206 sheet: 0.57 (0.72), residues: 59 loop : -0.35 (0.57), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 382 HIS 0.005 0.001 HIS A 388 PHE 0.016 0.002 PHE A 341 TYR 0.013 0.001 TYR A 363 ARG 0.001 0.000 ARG A 118 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 41 time to evaluate : 0.389 Fit side-chains REVERT: A 78 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.8204 (tt0) REVERT: A 246 ARG cc_start: 0.7867 (OUTLIER) cc_final: 0.7314 (mtt180) REVERT: A 371 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.7393 (pt0) outliers start: 9 outliers final: 3 residues processed: 46 average time/residue: 1.6656 time to fit residues: 78.4808 Evaluate side-chains 45 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 39 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 34 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 chunk 38 optimal weight: 8.9990 chunk 23 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 27 optimal weight: 7.9990 chunk 40 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 337 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3415 Z= 0.250 Angle : 0.501 5.113 4638 Z= 0.265 Chirality : 0.044 0.135 504 Planarity : 0.004 0.046 592 Dihedral : 9.149 149.268 470 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.64 % Allowed : 14.37 % Favored : 82.99 % 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: 1.60 (0.44), residues: 416 helix: 2.24 (0.36), residues: 206 sheet: 0.56 (0.72), residues: 59 loop : -0.37 (0.57), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 382 HIS 0.006 0.001 HIS A 388 PHE 0.017 0.002 PHE A 341 TYR 0.014 0.001 TYR A 363 ARG 0.001 0.000 ARG A 118 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 40 time to evaluate : 0.325 Fit side-chains REVERT: A 78 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.8225 (tt0) REVERT: A 246 ARG cc_start: 0.7891 (OUTLIER) cc_final: 0.7331 (mtt180) REVERT: A 371 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.7402 (pt0) outliers start: 9 outliers final: 2 residues processed: 45 average time/residue: 1.7171 time to fit residues: 79.1164 Evaluate side-chains 44 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 39 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 19 optimal weight: 6.9990 chunk 34 optimal weight: 6.9990 chunk 9 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 4 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 6 optimal weight: 0.1980 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 19 GLN A 337 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 3415 Z= 0.134 Angle : 0.445 5.455 4638 Z= 0.233 Chirality : 0.041 0.130 504 Planarity : 0.004 0.046 592 Dihedral : 8.483 145.602 470 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.76 % Allowed : 14.96 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.78 (0.44), residues: 416 helix: 2.27 (0.36), residues: 211 sheet: 0.57 (0.72), residues: 59 loop : -0.14 (0.59), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 63 HIS 0.002 0.000 HIS A 388 PHE 0.008 0.001 PHE A 381 TYR 0.008 0.001 TYR A 363 ARG 0.001 0.000 ARG A 265 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 47 time to evaluate : 0.395 Fit side-chains REVERT: A 246 ARG cc_start: 0.7858 (OUTLIER) cc_final: 0.7219 (mtt180) REVERT: A 371 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.7388 (pt0) REVERT: A 388 HIS cc_start: 0.8548 (OUTLIER) cc_final: 0.8060 (t70) outliers start: 6 outliers final: 1 residues processed: 50 average time/residue: 1.6007 time to fit residues: 82.0633 Evaluate side-chains 50 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 46 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.0070 chunk 1 optimal weight: 4.9990 chunk 23 optimal weight: 10.0000 chunk 37 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 chunk 27 optimal weight: 0.3980 chunk 26 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 overall best weight: 1.4602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.106988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.081867 restraints weight = 4329.764| |-----------------------------------------------------------------------------| r_work (start): 0.2716 rms_B_bonded: 1.42 r_work: 0.2619 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2517 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.2517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9003 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3415 Z= 0.173 Angle : 0.469 6.177 4638 Z= 0.245 Chirality : 0.042 0.129 504 Planarity : 0.004 0.045 592 Dihedral : 8.544 145.922 470 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.47 % Allowed : 14.96 % Favored : 83.58 % 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: 1.77 (0.44), residues: 416 helix: 2.26 (0.35), residues: 211 sheet: 0.56 (0.73), residues: 59 loop : -0.13 (0.59), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 382 HIS 0.004 0.001 HIS A 388 PHE 0.012 0.001 PHE A 341 TYR 0.010 0.001 TYR A 363 ARG 0.001 0.000 ARG A 129 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1816.77 seconds wall clock time: 32 minutes 24.63 seconds (1944.63 seconds total)