Starting phenix.real_space_refine on Fri Aug 2 16:31:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xcs_38253/08_2024/8xcs_38253.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xcs_38253/08_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_38253/08_2024/8xcs_38253.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xcs_38253/08_2024/8xcs_38253.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xcs_38253/08_2024/8xcs_38253.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xcs_38253/08_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: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 2.60, per 1000 atoms: 0.77 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: 1.45 Conformation dependent library (CDL) restraints added in 585.8 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: 0.40 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: 1.04 Time building geometry restraints manager: 1.51 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 3.040 nonbonded pdb=" O ASP A 145 " pdb=" O HOH A 602 " model vdw 2.445 3.040 nonbonded pdb=" O VAL A 317 " pdb=" ND2 ASN A 344 " model vdw 2.448 3.120 nonbonded pdb=" O ARG A 65 " pdb=" O HOH A 603 " model vdw 2.461 3.040 nonbonded pdb=" O THR A 148 " pdb=" O HOH A 602 " model vdw 2.469 3.040 ... (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: 0.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 14.550 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:12.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.350 ------------------------------------------------------------------------------- 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 : 0.386 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: 1.5522 time to fit residues: 120.6299 Evaluate side-chains 49 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 46 time to evaluate : 0.374 ------------------------------------------------------------------------------- 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: 10.0000 chunk 17 optimal weight: 0.5980 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: 1.9990 chunk 23 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- 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: 0.8718 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3415 Z= 0.247 Angle : 0.523 5.391 4638 Z= 0.278 Chirality : 0.044 0.136 504 Planarity : 0.005 0.043 592 Dihedral : 10.738 154.483 477 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.11 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: 1.29 (0.44), residues: 416 helix: 1.77 (0.36), residues: 211 sheet: 0.38 (0.72), residues: 61 loop : -0.24 (0.57), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 364 HIS 0.006 0.002 HIS A 388 PHE 0.015 0.002 PHE A 341 TYR 0.013 0.002 TYR A 363 ARG 0.002 0.000 ARG A 16 *********************** 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 57 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 46 time to evaluate : 0.396 Fit side-chains REVERT: A 16 ARG cc_start: 0.8205 (ttm170) cc_final: 0.7995 (ttm170) REVERT: A 113 LYS cc_start: 0.8719 (mttp) cc_final: 0.8377 (mtpt) REVERT: A 229 LYS cc_start: 0.8785 (OUTLIER) cc_final: 0.8497 (tttp) REVERT: A 371 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.7266 (pt0) outliers start: 11 outliers final: 1 residues processed: 53 average time/residue: 1.5314 time to fit residues: 83.1994 Evaluate side-chains 44 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 41 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 LYS 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: 5.9990 chunk 11 optimal weight: 4.9990 chunk 30 optimal weight: 8.9990 chunk 25 optimal weight: 10.0000 chunk 10 optimal weight: 4.9990 chunk 37 optimal weight: 7.9990 chunk 40 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 29 optimal weight: 8.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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: 0.8776 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 3415 Z= 0.403 Angle : 0.575 5.903 4638 Z= 0.305 Chirality : 0.047 0.148 504 Planarity : 0.005 0.047 592 Dihedral : 9.387 141.602 470 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 3.76 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: 1.22 (0.43), residues: 416 helix: 1.86 (0.36), residues: 206 sheet: 0.27 (0.72), residues: 61 loop : -0.39 (0.56), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 364 HIS 0.008 0.002 HIS A 388 PHE 0.022 0.002 PHE A 341 TYR 0.017 0.002 TYR A 363 ARG 0.002 0.000 ARG A 187 *********************** 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 : 0.352 Fit side-chains REVERT: A 167 LYS cc_start: 0.8861 (mmtt) cc_final: 0.8623 (mmtt) outliers start: 9 outliers final: 3 residues processed: 48 average time/residue: 1.5953 time to fit residues: 78.4456 Evaluate side-chains 43 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 40 time to evaluate : 0.373 ------------------------------------------------------------------------------- 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 388 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 0.3980 chunk 28 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 17 optimal weight: 0.8980 chunk 25 optimal weight: 6.9990 chunk 37 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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: 0.8696 moved from start: 0.2560 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= 0.139 Angle : 0.449 4.232 4638 Z= 0.238 Chirality : 0.041 0.131 504 Planarity : 0.004 0.046 592 Dihedral : 8.042 121.864 470 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.64 % Allowed : 12.02 % Favored : 85.34 % 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: 2.11 (0.36), residues: 211 sheet: 0.39 (0.73), residues: 61 loop : -0.10 (0.59), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 30 HIS 0.003 0.001 HIS A 388 PHE 0.008 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 54 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 45 time to evaluate : 0.379 Fit side-chains REVERT: A 16 ARG cc_start: 0.8294 (ttm-80) cc_final: 0.8086 (ttm170) REVERT: A 246 ARG cc_start: 0.7867 (OUTLIER) cc_final: 0.7426 (mtt180) REVERT: A 371 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.7415 (pt0) REVERT: A 388 HIS cc_start: 0.8808 (OUTLIER) cc_final: 0.7975 (t70) outliers start: 9 outliers final: 0 residues processed: 49 average time/residue: 1.6663 time to fit residues: 83.5552 Evaluate side-chains 44 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 41 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 9.9990 chunk 16 optimal weight: 5.9990 chunk 33 optimal weight: 7.9990 chunk 27 optimal weight: 0.1980 chunk 20 optimal weight: 0.0980 chunk 35 optimal weight: 0.8980 chunk 10 optimal weight: 8.9990 chunk 13 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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: 0.8683 moved from start: 0.2558 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= 0.141 Angle : 0.445 4.233 4638 Z= 0.235 Chirality : 0.041 0.131 504 Planarity : 0.004 0.045 592 Dihedral : 7.203 99.063 470 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.64 % Allowed : 12.90 % 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: 1.78 (0.44), residues: 416 helix: 2.26 (0.36), residues: 211 sheet: 0.40 (0.73), residues: 61 loop : -0.04 (0.59), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 30 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 396 *********************** 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 56 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 47 time to evaluate : 0.379 Fit side-chains REVERT: A 246 ARG cc_start: 0.7871 (OUTLIER) cc_final: 0.7406 (mtt180) REVERT: A 388 HIS cc_start: 0.8741 (OUTLIER) cc_final: 0.8178 (t70) outliers start: 9 outliers final: 0 residues processed: 52 average time/residue: 1.5477 time to fit residues: 82.4631 Evaluate side-chains 45 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 43 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 ARG 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: 0.4980 chunk 9 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 18 optimal weight: 9.9990 chunk 3 optimal weight: 7.9990 chunk 13 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 38 optimal weight: 0.9990 chunk 4 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- 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: 0.8747 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3415 Z= 0.266 Angle : 0.507 4.601 4638 Z= 0.270 Chirality : 0.044 0.137 504 Planarity : 0.004 0.046 592 Dihedral : 7.615 99.972 470 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.93 % Allowed : 12.61 % 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: 1.61 (0.44), residues: 416 helix: 2.23 (0.35), residues: 206 sheet: 0.40 (0.73), residues: 61 loop : -0.25 (0.57), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 30 HIS 0.007 0.001 HIS A 388 PHE 0.018 0.002 PHE A 341 TYR 0.014 0.002 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: 10 poor density : 43 time to evaluate : 0.391 Fit side-chains REVERT: A 229 LYS cc_start: 0.8820 (OUTLIER) cc_final: 0.8598 (tttp) REVERT: A 246 ARG cc_start: 0.7889 (OUTLIER) cc_final: 0.7337 (mtt180) outliers start: 10 outliers final: 3 residues processed: 49 average time/residue: 1.6724 time to fit residues: 83.8964 Evaluate side-chains 45 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 40 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ARG Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 229 LYS Chi-restraints excluded: chain A residue 246 ARG 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: 9.9990 chunk 22 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 39 optimal weight: 5.9990 chunk 24 optimal weight: 7.9990 chunk 18 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 chunk 11 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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: 0.8712 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3415 Z= 0.175 Angle : 0.467 4.703 4638 Z= 0.247 Chirality : 0.042 0.132 504 Planarity : 0.004 0.046 592 Dihedral : 7.307 97.341 470 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % 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: 1.69 (0.44), residues: 416 helix: 2.17 (0.35), residues: 211 sheet: 0.40 (0.73), residues: 61 loop : -0.07 (0.59), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 30 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 396 *********************** 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 52 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 42 time to evaluate : 0.375 Fit side-chains REVERT: A 78 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.8203 (tt0) REVERT: A 246 ARG cc_start: 0.7873 (OUTLIER) cc_final: 0.7304 (mtt180) REVERT: A 388 HIS cc_start: 0.8947 (OUTLIER) cc_final: 0.7957 (t70) outliers start: 10 outliers final: 2 residues processed: 47 average time/residue: 1.6084 time to fit residues: 77.5042 Evaluate side-chains 46 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 41 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ARG 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 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: 5.9990 chunk 31 optimal weight: 9.9990 chunk 35 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 28 optimal weight: 10.0000 overall best weight: 2.9788 ------------------------------------------------------------------------------- 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: 0.8754 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3415 Z= 0.289 Angle : 0.518 4.956 4638 Z= 0.275 Chirality : 0.045 0.136 504 Planarity : 0.004 0.046 592 Dihedral : 7.620 98.369 470 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.64 % Allowed : 12.90 % 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: 1.54 (0.43), residues: 416 helix: 2.19 (0.35), residues: 206 sheet: 0.37 (0.73), residues: 61 loop : -0.33 (0.56), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 30 HIS 0.007 0.001 HIS A 388 PHE 0.020 0.002 PHE A 341 TYR 0.014 0.002 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 51 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 42 time to evaluate : 0.399 Fit side-chains REVERT: A 78 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.8213 (tt0) REVERT: A 246 ARG cc_start: 0.7877 (OUTLIER) cc_final: 0.7323 (mtt180) outliers start: 9 outliers final: 3 residues processed: 46 average time/residue: 1.6784 time to fit residues: 79.0142 Evaluate side-chains 44 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 39 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ARG 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 388 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 6.9990 chunk 33 optimal weight: 7.9990 chunk 34 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 chunk 24 optimal weight: 9.9990 chunk 38 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 27 optimal weight: 0.0010 chunk 40 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.7388 ------------------------------------------------------------------------------- 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: 0.8685 moved from start: 0.2671 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= 0.141 Angle : 0.458 4.873 4638 Z= 0.241 Chirality : 0.041 0.135 504 Planarity : 0.004 0.047 592 Dihedral : 7.118 95.217 470 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.64 % Allowed : 13.78 % 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: 1.79 (0.44), residues: 416 helix: 2.27 (0.35), residues: 211 sheet: 0.39 (0.73), residues: 61 loop : -0.03 (0.59), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 30 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 122 *********************** 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 54 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 45 time to evaluate : 0.384 Fit side-chains REVERT: A 246 ARG cc_start: 0.7865 (OUTLIER) cc_final: 0.7283 (mtt180) REVERT: A 388 HIS cc_start: 0.8693 (OUTLIER) cc_final: 0.8178 (t70) outliers start: 9 outliers final: 2 residues processed: 49 average time/residue: 1.5693 time to fit residues: 78.9347 Evaluate side-chains 46 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 42 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 246 ARG 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: 2.9990 chunk 25 optimal weight: 0.0770 chunk 19 optimal weight: 6.9990 chunk 34 optimal weight: 7.9990 chunk 9 optimal weight: 0.9980 chunk 29 optimal weight: 5.9990 chunk 4 optimal weight: 0.9980 chunk 13 optimal weight: 0.0030 chunk 33 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 overall best weight: 0.5948 ------------------------------------------------------------------------------- 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: 0.8661 moved from start: 0.2711 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= 0.131 Angle : 0.452 4.988 4638 Z= 0.236 Chirality : 0.041 0.129 504 Planarity : 0.004 0.045 592 Dihedral : 6.897 91.746 470 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.05 % Allowed : 14.08 % 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: 1.89 (0.44), residues: 416 helix: 2.38 (0.35), residues: 211 sheet: 0.46 (0.73), residues: 61 loop : -0.05 (0.58), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 30 HIS 0.002 0.000 HIS A 388 PHE 0.007 0.001 PHE A 341 TYR 0.006 0.001 TYR A 363 ARG 0.001 0.000 ARG A 396 ********************** 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: 7 poor density : 46 time to evaluate : 0.369 Fit side-chains REVERT: A 238 THR cc_start: 0.9160 (OUTLIER) cc_final: 0.8938 (p) REVERT: A 246 ARG cc_start: 0.7871 (OUTLIER) cc_final: 0.7230 (mtt180) REVERT: A 388 HIS cc_start: 0.8564 (OUTLIER) cc_final: 0.8110 (t70) outliers start: 7 outliers final: 0 residues processed: 49 average time/residue: 1.6371 time to fit residues: 82.2341 Evaluate side-chains 48 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 45 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 246 ARG 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: 9.9990 chunk 1 optimal weight: 6.9990 chunk 23 optimal weight: 9.9990 chunk 37 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 26 optimal weight: 7.9990 chunk 24 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.105052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.079364 restraints weight = 4345.846| |-----------------------------------------------------------------------------| r_work (start): 0.2727 rms_B_bonded: 1.47 r_work: 0.2630 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2528 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.2528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9020 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3415 Z= 0.224 Angle : 0.500 5.191 4638 Z= 0.264 Chirality : 0.043 0.126 504 Planarity : 0.004 0.046 592 Dihedral : 7.366 93.842 470 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.47 % Allowed : 14.66 % 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: 1.74 (0.44), residues: 416 helix: 2.23 (0.35), residues: 211 sheet: 0.42 (0.73), residues: 61 loop : -0.09 (0.58), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 382 HIS 0.006 0.001 HIS A 388 PHE 0.017 0.002 PHE A 341 TYR 0.013 0.001 TYR A 363 ARG 0.001 0.000 ARG A 118 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1815.85 seconds wall clock time: 32 minutes 25.16 seconds (1945.16 seconds total)