Starting phenix.real_space_refine on Sun Mar 10 17:42:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b6z_15893/03_2024/8b6z_15893.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b6z_15893/03_2024/8b6z_15893.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b6z_15893/03_2024/8b6z_15893.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b6z_15893/03_2024/8b6z_15893.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b6z_15893/03_2024/8b6z_15893.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b6z_15893/03_2024/8b6z_15893.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.007 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 8 5.49 5 S 16 5.16 5 C 2240 2.51 5 N 624 2.21 5 O 693 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 3581 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3406 Classifications: {'peptide': 442} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 415} Chain: "B" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 175 Classifications: {'RNA': 8} Modifications used: {'rna3p_pur': 6, 'rna3p_pyr': 2} Link IDs: {'rna3p': 7} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N GLY A 50 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY A 50 " occ=0.00 Time building chain proxies: 2.83, per 1000 atoms: 0.79 Number of scatterers: 3581 At special positions: 0 Unit cell: (65.934, 93.906, 67.932, 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 16 16.00 P 8 15.00 O 693 8.00 N 624 7.00 C 2240 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: 1.31 Conformation dependent library (CDL) restraints added in 745.1 milliseconds 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 806 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 5 sheets defined 25.1% alpha, 33.3% beta 1 base pairs and 4 stacking pairs defined. Time for finding SS restraints: 1.21 Creating SS restraints... Processing helix chain 'A' and resid 19 through 32 Processing helix chain 'A' and resid 35 through 50 Processing helix chain 'A' and resid 57 through 66 Processing helix chain 'A' and resid 97 through 105 Processing helix chain 'A' and resid 121 through 127 removed outlier: 3.703A pdb=" N ILE A 127 " --> pdb=" O PHE A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 144 Processing helix chain 'A' and resid 154 through 158 removed outlier: 3.836A pdb=" N SER A 157 " --> pdb=" O LYS A 154 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N THR A 158 " --> pdb=" O MET A 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 154 through 158' Processing helix chain 'A' and resid 163 through 182 removed outlier: 3.601A pdb=" N TYR A 177 " --> pdb=" O GLU A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 188 Processing helix chain 'A' and resid 227 through 234 removed outlier: 3.715A pdb=" N ALA A 231 " --> pdb=" O SER A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 421 Processing sheet with id=AA1, first strand: chain 'A' and resid 79 through 81 removed outlier: 6.557A pdb=" N ILE A 8 " --> pdb=" O THR A 88 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N ILE A 90 " --> pdb=" O ILE A 8 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N ILE A 10 " --> pdb=" O ILE A 90 " (cutoff:3.500A) removed outlier: 8.782A pdb=" N CYS A 111 " --> pdb=" O HIS A 7 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ASN A 9 " --> pdb=" O CYS A 111 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N VAL A 113 " --> pdb=" O ASN A 9 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL A 11 " --> pdb=" O VAL A 113 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ILE A 115 " --> pdb=" O VAL A 11 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N ILE A 13 " --> pdb=" O ILE A 115 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N ALA A 117 " --> pdb=" O ILE A 13 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL A 191 " --> pdb=" O VAL A 150 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 214 through 216 Processing sheet with id=AA3, first strand: chain 'A' and resid 247 through 249 removed outlier: 6.659A pdb=" N ASN A 311 " --> pdb=" O LYS A 290 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N VAL A 292 " --> pdb=" O GLY A 309 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N GLY A 309 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N MET A 294 " --> pdb=" O ASN A 307 " (cutoff:3.500A) removed outlier: 9.275A pdb=" N ASN A 307 " --> pdb=" O MET A 294 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N THR A 261 " --> pdb=" O VAL A 312 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 247 through 249 Processing sheet with id=AA5, first strand: chain 'A' and resid 386 through 389 removed outlier: 6.610A pdb=" N ALA A 373 " --> pdb=" O VAL A 405 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N VAL A 405 " --> pdb=" O ALA A 373 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N LEU A 375 " --> pdb=" O GLU A 403 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N GLU A 403 " --> pdb=" O LEU A 375 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N ALA A 338 " --> pdb=" O PRO A 406 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLN A 339 " --> pdb=" O GLU A 442 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N GLN A 343 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N ILE A 438 " --> pdb=" O GLN A 343 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N ILE A 345 " --> pdb=" O GLY A 436 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N GLY A 436 " --> pdb=" O ILE A 345 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N THR A 432 " --> pdb=" O ASP A 428 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ASP A 428 " --> pdb=" O THR A 432 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VAL A 360 " --> pdb=" O ARG A 427 " (cutoff:3.500A) 136 hydrogen bonds defined for protein. 366 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2 hydrogen bonds 4 hydrogen bond angles 0 basepair planarities 1 basepair parallelities 4 stacking parallelities Total time for adding SS restraints: 1.22 Time building geometry restraints manager: 1.41 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: 1126 1.34 - 1.46: 522 1.46 - 1.57: 1984 1.57 - 1.69: 15 1.69 - 1.81: 26 Bond restraints: 3673 Sorted by residual: bond pdb=" C ILE A 235 " pdb=" N LEU A 236 " ideal model delta sigma weight residual 1.327 1.339 -0.012 1.39e-02 5.18e+03 7.88e-01 bond pdb=" N VAL A 152 " pdb=" CA VAL A 152 " ideal model delta sigma weight residual 1.465 1.476 -0.011 1.38e-02 5.25e+03 5.94e-01 bond pdb=" CA GLY A 351 " pdb=" C GLY A 351 " ideal model delta sigma weight residual 1.514 1.505 0.010 1.41e-02 5.03e+03 4.55e-01 bond pdb=" CA HIS A 364 " pdb=" CB HIS A 364 " ideal model delta sigma weight residual 1.530 1.541 -0.011 1.69e-02 3.50e+03 4.23e-01 bond pdb=" C LYS A 165 " pdb=" O LYS A 165 " ideal model delta sigma weight residual 1.236 1.228 0.008 1.26e-02 6.30e+03 4.09e-01 ... (remaining 3668 not shown) Histogram of bond angle deviations from ideal: 100.40 - 107.13: 190 107.13 - 113.87: 2104 113.87 - 120.61: 1326 120.61 - 127.34: 1322 127.34 - 134.08: 66 Bond angle restraints: 5008 Sorted by residual: angle pdb=" N GLY A 182 " pdb=" CA GLY A 182 " pdb=" C GLY A 182 " ideal model delta sigma weight residual 113.18 120.51 -7.33 2.37e+00 1.78e-01 9.56e+00 angle pdb=" N SER A 157 " pdb=" CA SER A 157 " pdb=" C SER A 157 " ideal model delta sigma weight residual 112.88 115.26 -2.38 1.29e+00 6.01e-01 3.40e+00 angle pdb=" CB LYS A 172 " pdb=" CG LYS A 172 " pdb=" CD LYS A 172 " ideal model delta sigma weight residual 111.30 115.15 -3.85 2.30e+00 1.89e-01 2.80e+00 angle pdb=" CA GLY A 182 " pdb=" C GLY A 182 " pdb=" N TYR A 183 " ideal model delta sigma weight residual 116.69 119.99 -3.30 2.04e+00 2.40e-01 2.62e+00 angle pdb=" N ASN A 200 " pdb=" CA ASN A 200 " pdb=" CB ASN A 200 " ideal model delta sigma weight residual 113.15 110.58 2.57 1.63e+00 3.76e-01 2.48e+00 ... (remaining 5003 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.56: 2078 14.56 - 29.12: 95 29.12 - 43.68: 36 43.68 - 58.25: 16 58.25 - 72.81: 11 Dihedral angle restraints: 2236 sinusoidal: 977 harmonic: 1259 Sorted by residual: dihedral pdb=" CA VAL A 152 " pdb=" C VAL A 152 " pdb=" N ASN A 153 " pdb=" CA ASN A 153 " ideal model delta harmonic sigma weight residual -180.00 -161.01 -18.99 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CA PRO A 160 " pdb=" C PRO A 160 " pdb=" N ALA A 161 " pdb=" CA ALA A 161 " ideal model delta harmonic sigma weight residual -180.00 -162.08 -17.92 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" CA ILE A 178 " pdb=" C ILE A 178 " pdb=" N LYS A 179 " pdb=" CA LYS A 179 " ideal model delta harmonic sigma weight residual 180.00 162.10 17.90 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 2233 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 309 0.025 - 0.050: 155 0.050 - 0.075: 37 0.075 - 0.100: 31 0.100 - 0.125: 37 Chirality restraints: 569 Sorted by residual: chirality pdb=" CA ILE A 401 " pdb=" N ILE A 401 " pdb=" C ILE A 401 " pdb=" CB ILE A 401 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.93e-01 chirality pdb=" CA VAL A 405 " pdb=" N VAL A 405 " pdb=" C VAL A 405 " pdb=" CB VAL A 405 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.12 2.00e-01 2.50e+01 3.84e-01 chirality pdb=" CA VAL A 292 " pdb=" N VAL A 292 " pdb=" C VAL A 292 " pdb=" CB VAL A 292 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.81e-01 ... (remaining 566 not shown) Planarity restraints: 613 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 419 " 0.027 5.00e-02 4.00e+02 4.10e-02 2.69e+00 pdb=" N PRO A 420 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 420 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 420 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 418 " -0.021 5.00e-02 4.00e+02 3.26e-02 1.70e+00 pdb=" N PRO A 419 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO A 419 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 419 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 358 " 0.016 5.00e-02 4.00e+02 2.43e-02 9.41e-01 pdb=" N PRO A 359 " -0.042 5.00e-02 4.00e+02 pdb=" CA PRO A 359 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 359 " 0.013 5.00e-02 4.00e+02 ... (remaining 610 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 924 2.81 - 3.33: 3215 3.33 - 3.85: 5926 3.85 - 4.38: 6908 4.38 - 4.90: 11870 Nonbonded interactions: 28843 Sorted by model distance: nonbonded pdb=" OD2 ASP A 74 " pdb=" OG SER A 76 " model vdw 2.286 2.440 nonbonded pdb=" O ALA A 231 " pdb=" OG1 THR A 234 " model vdw 2.388 2.440 nonbonded pdb=" O VAL A 277 " pdb=" OG SER A 329 " model vdw 2.390 2.440 nonbonded pdb=" OH TYR A 29 " pdb=" NE1 TRP A 58 " model vdw 2.391 2.520 nonbonded pdb=" OE2 GLU A 68 " pdb=" N ARG A 96 " model vdw 2.413 2.520 ... (remaining 28838 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=0.00 max=1.00 mean=0.70 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: 6.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 24.440 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.840 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5668 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 : 0.002 0.023 3673 Z= 0.146 Angle : 0.507 7.329 5008 Z= 0.273 Chirality : 0.044 0.125 569 Planarity : 0.004 0.041 613 Dihedral : 12.065 72.808 1430 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 0.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 0.27 % Allowed : 2.14 % Favored : 97.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.69 (0.37), residues: 440 helix: -0.07 (0.48), residues: 93 sheet: -0.11 (0.60), residues: 83 loop : -0.67 (0.35), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 78 HIS 0.005 0.001 HIS A 364 PHE 0.005 0.001 PHE A 123 TYR 0.012 0.002 TYR A 167 ARG 0.003 0.000 ARG A 134 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 69 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 THR cc_start: 0.6986 (p) cc_final: 0.5495 (t) REVERT: A 243 ASP cc_start: 0.5976 (m-30) cc_final: 0.5723 (t0) REVERT: A 254 TYR cc_start: 0.4476 (m-80) cc_final: 0.4154 (m-80) outliers start: 1 outliers final: 0 residues processed: 70 average time/residue: 1.4113 time to fit residues: 101.5669 Evaluate side-chains 34 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 37 optimal weight: 50.0000 chunk 33 optimal weight: 30.0000 chunk 18 optimal weight: 0.8980 chunk 11 optimal weight: 50.0000 chunk 22 optimal weight: 50.0000 chunk 17 optimal weight: 9.9990 chunk 34 optimal weight: 4.9990 chunk 13 optimal weight: 50.0000 chunk 20 optimal weight: 9.9990 chunk 25 optimal weight: 6.9990 chunk 39 optimal weight: 30.0000 overall best weight: 6.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 GLN A 349 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5853 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3673 Z= 0.221 Angle : 0.691 13.285 5008 Z= 0.346 Chirality : 0.047 0.151 569 Planarity : 0.005 0.041 613 Dihedral : 11.749 73.941 590 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.88 % Allowed : 13.94 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.31 (0.39), residues: 440 helix: 0.62 (0.53), residues: 95 sheet: 0.16 (0.54), residues: 93 loop : -0.64 (0.37), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 78 HIS 0.006 0.001 HIS A 364 PHE 0.009 0.001 PHE A 310 TYR 0.018 0.002 TYR A 183 ARG 0.006 0.001 ARG A 37 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 33 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 THR cc_start: 0.6786 (p) cc_final: 0.5959 (t) REVERT: A 276 MET cc_start: 0.4385 (mtp) cc_final: 0.3767 (ttm) outliers start: 7 outliers final: 1 residues processed: 39 average time/residue: 1.3767 time to fit residues: 55.4706 Evaluate side-chains 25 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 24 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 22 optimal weight: 20.0000 chunk 12 optimal weight: 20.0000 chunk 33 optimal weight: 0.0670 chunk 27 optimal weight: 7.9990 chunk 11 optimal weight: 50.0000 chunk 40 optimal weight: 9.9990 chunk 43 optimal weight: 6.9990 chunk 35 optimal weight: 0.7980 chunk 39 optimal weight: 30.0000 chunk 13 optimal weight: 50.0000 chunk 32 optimal weight: 8.9990 overall best weight: 4.9724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5882 moved from start: 0.3587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3673 Z= 0.200 Angle : 0.658 13.550 5008 Z= 0.330 Chirality : 0.046 0.142 569 Planarity : 0.005 0.047 613 Dihedral : 11.619 73.593 590 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.61 % Allowed : 15.28 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.23 (0.38), residues: 440 helix: 0.74 (0.52), residues: 95 sheet: -0.12 (0.50), residues: 106 loop : -0.46 (0.37), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 196 HIS 0.007 0.001 HIS A 349 PHE 0.029 0.003 PHE A 310 TYR 0.012 0.001 TYR A 183 ARG 0.004 0.000 ARG A 37 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 25 time to evaluate : 0.430 Fit side-chains revert: symmetry clash REVERT: A 82 THR cc_start: 0.6962 (p) cc_final: 0.6093 (t) REVERT: A 276 MET cc_start: 0.4422 (mtp) cc_final: 0.3777 (ttm) REVERT: A 290 LYS cc_start: 0.6476 (OUTLIER) cc_final: 0.5781 (tppt) REVERT: A 310 PHE cc_start: 0.8353 (p90) cc_final: 0.7468 (p90) outliers start: 6 outliers final: 1 residues processed: 28 average time/residue: 1.1855 time to fit residues: 34.6948 Evaluate side-chains 24 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 22 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 290 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 39 optimal weight: 30.0000 chunk 30 optimal weight: 20.0000 chunk 20 optimal weight: 8.9990 chunk 4 optimal weight: 10.0000 chunk 19 optimal weight: 20.0000 chunk 26 optimal weight: 0.7980 chunk 40 optimal weight: 7.9990 chunk 42 optimal weight: 20.0000 chunk 38 optimal weight: 30.0000 chunk 11 optimal weight: 50.0000 chunk 35 optimal weight: 0.9990 overall best weight: 5.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5911 moved from start: 0.4062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3673 Z= 0.187 Angle : 0.627 10.989 5008 Z= 0.313 Chirality : 0.046 0.139 569 Planarity : 0.005 0.051 613 Dihedral : 11.629 73.598 590 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.61 % Allowed : 14.75 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.48 (0.37), residues: 440 helix: 0.51 (0.50), residues: 95 sheet: -0.23 (0.54), residues: 90 loop : -0.63 (0.35), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 58 HIS 0.004 0.001 HIS A 349 PHE 0.034 0.002 PHE A 211 TYR 0.011 0.002 TYR A 56 ARG 0.003 0.000 ARG A 37 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 23 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 MET cc_start: -0.2136 (mmt) cc_final: -0.2978 (mmm) REVERT: A 82 THR cc_start: 0.7115 (p) cc_final: 0.6202 (t) REVERT: A 276 MET cc_start: 0.4647 (mtp) cc_final: 0.4009 (ttm) REVERT: A 290 LYS cc_start: 0.6598 (OUTLIER) cc_final: 0.5657 (tppt) REVERT: A 310 PHE cc_start: 0.8387 (p90) cc_final: 0.7478 (p90) outliers start: 6 outliers final: 1 residues processed: 26 average time/residue: 1.2428 time to fit residues: 33.7086 Evaluate side-chains 22 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 20 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 290 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 3.9990 chunk 0 optimal weight: 70.0000 chunk 31 optimal weight: 20.0000 chunk 17 optimal weight: 50.0000 chunk 36 optimal weight: 7.9990 chunk 29 optimal weight: 4.9990 chunk 21 optimal weight: 10.0000 chunk 38 optimal weight: 10.0000 chunk 10 optimal weight: 7.9990 chunk 14 optimal weight: 40.0000 chunk 8 optimal weight: 6.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 GLN ** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5959 moved from start: 0.4553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3673 Z= 0.188 Angle : 0.610 9.194 5008 Z= 0.304 Chirality : 0.045 0.135 569 Planarity : 0.005 0.053 613 Dihedral : 11.633 73.559 590 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.14 % Allowed : 15.82 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.32 (0.37), residues: 440 helix: 0.63 (0.50), residues: 97 sheet: 0.17 (0.53), residues: 97 loop : -0.67 (0.36), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 58 HIS 0.004 0.001 HIS A 364 PHE 0.040 0.002 PHE A 211 TYR 0.009 0.001 TYR A 357 ARG 0.004 0.001 ARG A 37 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 20 time to evaluate : 0.475 Fit side-chains revert: symmetry clash REVERT: A 82 THR cc_start: 0.7137 (p) cc_final: 0.6198 (t) REVERT: A 165 LYS cc_start: 0.7460 (mmpt) cc_final: 0.6939 (pmtt) REVERT: A 276 MET cc_start: 0.4723 (mtp) cc_final: 0.4246 (ttm) REVERT: A 290 LYS cc_start: 0.6764 (OUTLIER) cc_final: 0.5443 (tppt) REVERT: A 310 PHE cc_start: 0.8501 (p90) cc_final: 0.7453 (p90) outliers start: 8 outliers final: 2 residues processed: 26 average time/residue: 1.0950 time to fit residues: 30.0597 Evaluate side-chains 23 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 20 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 290 LYS Chi-restraints excluded: chain A residue 330 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 50.0000 chunk 10 optimal weight: 30.0000 chunk 42 optimal weight: 7.9990 chunk 35 optimal weight: 10.0000 chunk 19 optimal weight: 9.9990 chunk 3 optimal weight: 9.9990 chunk 14 optimal weight: 30.0000 chunk 22 optimal weight: 40.0000 chunk 41 optimal weight: 7.9990 chunk 4 optimal weight: 10.0000 chunk 31 optimal weight: 0.0770 overall best weight: 7.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5993 moved from start: 0.5106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3673 Z= 0.195 Angle : 0.594 8.737 5008 Z= 0.300 Chirality : 0.046 0.133 569 Planarity : 0.005 0.057 613 Dihedral : 11.607 73.558 590 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.14 % Allowed : 15.55 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.19 (0.38), residues: 440 helix: 0.74 (0.51), residues: 97 sheet: 0.31 (0.54), residues: 97 loop : -0.63 (0.36), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 58 HIS 0.003 0.001 HIS A 364 PHE 0.034 0.002 PHE A 211 TYR 0.009 0.001 TYR A 357 ARG 0.003 0.001 ARG A 266 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 21 time to evaluate : 0.425 Fit side-chains revert: symmetry clash REVERT: A 49 MET cc_start: -0.2529 (mmt) cc_final: -0.3074 (tpp) REVERT: A 82 THR cc_start: 0.7206 (p) cc_final: 0.6276 (t) REVERT: A 165 LYS cc_start: 0.7403 (mmpt) cc_final: 0.7200 (mmpt) REVERT: A 276 MET cc_start: 0.4887 (mtp) cc_final: 0.4318 (ttm) REVERT: A 290 LYS cc_start: 0.6588 (OUTLIER) cc_final: 0.4980 (tppt) REVERT: A 310 PHE cc_start: 0.8512 (p90) cc_final: 0.7491 (p90) outliers start: 8 outliers final: 5 residues processed: 27 average time/residue: 1.1730 time to fit residues: 33.1538 Evaluate side-chains 27 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 21 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 290 LYS Chi-restraints excluded: chain A residue 319 ASP Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 429 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 40.0000 chunk 35 optimal weight: 7.9990 chunk 23 optimal weight: 5.9990 chunk 42 optimal weight: 7.9990 chunk 26 optimal weight: 5.9990 chunk 25 optimal weight: 20.0000 chunk 19 optimal weight: 0.3980 chunk 16 optimal weight: 8.9990 chunk 12 optimal weight: 50.0000 chunk 8 optimal weight: 9.9990 chunk 28 optimal weight: 20.0000 overall best weight: 5.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5987 moved from start: 0.5364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3673 Z= 0.168 Angle : 0.565 8.883 5008 Z= 0.283 Chirality : 0.045 0.136 569 Planarity : 0.005 0.055 613 Dihedral : 11.666 73.521 590 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.88 % Allowed : 16.62 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.10 (0.38), residues: 440 helix: 0.94 (0.51), residues: 97 sheet: 0.36 (0.53), residues: 97 loop : -0.62 (0.36), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 210 HIS 0.005 0.001 HIS A 26 PHE 0.030 0.002 PHE A 211 TYR 0.008 0.001 TYR A 162 ARG 0.003 0.001 ARG A 423 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 21 time to evaluate : 0.428 Fit side-chains revert: symmetry clash REVERT: A 49 MET cc_start: -0.1852 (mmt) cc_final: -0.2500 (mmm) REVERT: A 82 THR cc_start: 0.7192 (p) cc_final: 0.6228 (t) REVERT: A 165 LYS cc_start: 0.7496 (mmpt) cc_final: 0.7143 (pmtt) REVERT: A 276 MET cc_start: 0.4925 (mtp) cc_final: 0.4451 (ttm) REVERT: A 290 LYS cc_start: 0.6505 (OUTLIER) cc_final: 0.4888 (tppt) REVERT: A 310 PHE cc_start: 0.8506 (p90) cc_final: 0.7509 (p90) outliers start: 7 outliers final: 2 residues processed: 26 average time/residue: 1.0019 time to fit residues: 27.4725 Evaluate side-chains 23 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 20 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 290 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 20 optimal weight: 9.9990 chunk 3 optimal weight: 30.0000 chunk 33 optimal weight: 0.0060 chunk 38 optimal weight: 0.8980 chunk 40 optimal weight: 6.9990 chunk 37 optimal weight: 30.0000 chunk 39 optimal weight: 20.0000 chunk 23 optimal weight: 20.0000 chunk 17 optimal weight: 50.0000 chunk 31 optimal weight: 5.9990 chunk 12 optimal weight: 20.0000 overall best weight: 4.7802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 352 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5983 moved from start: 0.5586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3673 Z= 0.158 Angle : 0.589 10.678 5008 Z= 0.293 Chirality : 0.046 0.161 569 Planarity : 0.005 0.055 613 Dihedral : 11.414 73.565 590 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.07 % Allowed : 17.69 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.20 (0.38), residues: 440 helix: 0.94 (0.52), residues: 97 sheet: 0.20 (0.56), residues: 90 loop : -0.66 (0.35), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 58 HIS 0.004 0.001 HIS A 364 PHE 0.013 0.001 PHE A 340 TYR 0.008 0.001 TYR A 162 ARG 0.002 0.000 ARG A 37 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 21 time to evaluate : 0.529 Fit side-chains revert: symmetry clash REVERT: A 49 MET cc_start: -0.1996 (mmt) cc_final: -0.2773 (mmm) REVERT: A 165 LYS cc_start: 0.7531 (mmpt) cc_final: 0.7233 (pmtt) REVERT: A 276 MET cc_start: 0.5037 (mtp) cc_final: 0.4562 (ttm) REVERT: A 290 LYS cc_start: 0.6500 (OUTLIER) cc_final: 0.4885 (tppt) REVERT: A 310 PHE cc_start: 0.8461 (p90) cc_final: 0.7456 (p90) outliers start: 4 outliers final: 3 residues processed: 24 average time/residue: 1.0548 time to fit residues: 26.6758 Evaluate side-chains 24 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 20 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 290 LYS Chi-restraints excluded: chain A residue 303 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 35 optimal weight: 40.0000 chunk 37 optimal weight: 40.0000 chunk 39 optimal weight: 30.0000 chunk 25 optimal weight: 20.0000 chunk 41 optimal weight: 8.9990 chunk 19 optimal weight: 30.0000 chunk 29 optimal weight: 0.9990 chunk 43 optimal weight: 9.9990 chunk 40 optimal weight: 20.0000 chunk 34 optimal weight: 5.9990 chunk 3 optimal weight: 9.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6000 moved from start: 0.5800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3673 Z= 0.190 Angle : 0.594 10.726 5008 Z= 0.298 Chirality : 0.045 0.134 569 Planarity : 0.005 0.058 613 Dihedral : 10.997 73.534 590 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.88 % Allowed : 17.43 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.24 (0.38), residues: 440 helix: 0.93 (0.52), residues: 97 sheet: 0.11 (0.54), residues: 95 loop : -0.68 (0.36), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 58 HIS 0.005 0.001 HIS A 26 PHE 0.031 0.002 PHE A 211 TYR 0.009 0.001 TYR A 162 ARG 0.003 0.001 ARG A 266 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 21 time to evaluate : 0.449 Fit side-chains revert: symmetry clash REVERT: A 82 THR cc_start: 0.6695 (p) cc_final: 0.5857 (t) REVERT: A 165 LYS cc_start: 0.7508 (mmpt) cc_final: 0.7224 (pmtt) REVERT: A 276 MET cc_start: 0.5104 (mtp) cc_final: 0.4625 (ttm) REVERT: A 290 LYS cc_start: 0.6594 (OUTLIER) cc_final: 0.4955 (tppt) REVERT: A 310 PHE cc_start: 0.8477 (p90) cc_final: 0.7479 (p90) outliers start: 7 outliers final: 4 residues processed: 27 average time/residue: 1.1122 time to fit residues: 31.5260 Evaluate side-chains 23 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 18 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 290 LYS Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 330 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 26 optimal weight: 7.9990 chunk 21 optimal weight: 0.9980 chunk 27 optimal weight: 10.0000 chunk 37 optimal weight: 0.9990 chunk 10 optimal weight: 40.0000 chunk 32 optimal weight: 30.0000 chunk 5 optimal weight: 50.0000 chunk 9 optimal weight: 20.0000 chunk 34 optimal weight: 40.0000 chunk 14 optimal weight: 50.0000 chunk 35 optimal weight: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5984 moved from start: 0.5940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 3673 Z= 0.156 Angle : 0.579 10.455 5008 Z= 0.287 Chirality : 0.045 0.134 569 Planarity : 0.005 0.057 613 Dihedral : 10.905 73.529 590 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.80 % Allowed : 17.96 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.10 (0.38), residues: 440 helix: 1.00 (0.52), residues: 97 sheet: 0.42 (0.57), residues: 83 loop : -0.64 (0.36), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 58 HIS 0.004 0.001 HIS A 364 PHE 0.013 0.001 PHE A 340 TYR 0.007 0.001 TYR A 162 ARG 0.002 0.000 ARG A 37 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 20 time to evaluate : 0.392 Fit side-chains revert: symmetry clash REVERT: A 49 MET cc_start: -0.1749 (mmt) cc_final: -0.2132 (mpt) REVERT: A 82 THR cc_start: 0.6547 (p) cc_final: 0.5534 (t) REVERT: A 165 LYS cc_start: 0.7454 (mmpt) cc_final: 0.7197 (pmtt) REVERT: A 290 LYS cc_start: 0.6453 (OUTLIER) cc_final: 0.4657 (tppt) REVERT: A 310 PHE cc_start: 0.8490 (p90) cc_final: 0.7499 (p90) outliers start: 3 outliers final: 2 residues processed: 23 average time/residue: 1.1236 time to fit residues: 27.1411 Evaluate side-chains 23 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 20 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 290 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 4 optimal weight: 40.0000 chunk 6 optimal weight: 30.0000 chunk 30 optimal weight: 10.0000 chunk 1 optimal weight: 20.0000 chunk 25 optimal weight: 10.0000 chunk 40 optimal weight: 1.9990 chunk 23 optimal weight: 7.9990 chunk 29 optimal weight: 8.9990 chunk 27 optimal weight: 20.0000 chunk 26 optimal weight: 7.9990 chunk 17 optimal weight: 30.0000 overall best weight: 7.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.101816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.085896 restraints weight = 13768.889| |-----------------------------------------------------------------------------| r_work (start): 0.3872 rms_B_bonded: 4.57 r_work: 0.3695 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3660 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3660 r_free = 0.3660 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1041 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3649 r_free = 0.3649 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1056 | |-----------------------------------------------------------------------------| r_final: 0.3649 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.6173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3673 Z= 0.195 Angle : 0.606 11.001 5008 Z= 0.300 Chirality : 0.045 0.134 569 Planarity : 0.005 0.058 613 Dihedral : 10.952 73.615 590 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.07 % Allowed : 17.69 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.18 (0.38), residues: 440 helix: 0.96 (0.52), residues: 98 sheet: 0.23 (0.55), residues: 92 loop : -0.68 (0.36), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 58 HIS 0.005 0.001 HIS A 26 PHE 0.013 0.002 PHE A 340 TYR 0.009 0.001 TYR A 162 ARG 0.005 0.001 ARG A 273 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1591.37 seconds wall clock time: 29 minutes 10.60 seconds (1750.60 seconds total)