Starting phenix.real_space_refine on Wed Jan 17 14:13:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b6z_15893/01_2024/8b6z_15893.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b6z_15893/01_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_15893/01_2024/8b6z_15893.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b6z_15893/01_2024/8b6z_15893.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b6z_15893/01_2024/8b6z_15893.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b6z_15893/01_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-1.21-5211/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: 2.60, per 1000 atoms: 0.73 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: 1.84 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.07 Time building geometry restraints manager: 1.49 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: 2077 14.56 - 29.12: 95 29.12 - 43.68: 35 43.68 - 58.25: 14 58.25 - 72.81: 11 Dihedral angle restraints: 2232 sinusoidal: 973 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 2229 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: 7.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 24.110 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 15.510 Find NCS groups from input model: 0.090 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:12.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.210 ------------------------------------------------------------------------------- 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 : 11.871 72.808 1426 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 : 0.399 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: 1.3554 time to fit residues: 97.5058 Evaluate side-chains 34 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.388 ------------------------------------------------------------------------------- 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 311 ASN A 349 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5854 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3673 Z= 0.217 Angle : 0.687 12.905 5008 Z= 0.345 Chirality : 0.047 0.156 569 Planarity : 0.005 0.041 613 Dihedral : 11.320 73.880 586 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 5.72 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: -0.29 (0.39), residues: 440 helix: 0.66 (0.53), residues: 95 sheet: 0.15 (0.54), residues: 93 loop : -0.63 (0.37), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 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 : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 THR cc_start: 0.6789 (p) cc_final: 0.5959 (t) REVERT: A 276 MET cc_start: 0.4401 (mtp) cc_final: 0.3785 (ttm) outliers start: 7 outliers final: 2 residues processed: 39 average time/residue: 1.3639 time to fit residues: 55.0135 Evaluate side-chains 26 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 24 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 THR 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: 50.0000 chunk 33 optimal weight: 20.0000 chunk 27 optimal weight: 30.0000 chunk 11 optimal weight: 50.0000 chunk 40 optimal weight: 7.9990 chunk 43 optimal weight: 6.9990 chunk 35 optimal weight: 20.0000 chunk 39 optimal weight: 30.0000 chunk 13 optimal weight: 50.0000 chunk 32 optimal weight: 9.9990 overall best weight: 12.9994 ------------------------------------------------------------------------------- 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: 0.5992 moved from start: 0.4152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 3673 Z= 0.340 Angle : 0.744 14.281 5008 Z= 0.380 Chirality : 0.048 0.141 569 Planarity : 0.006 0.053 613 Dihedral : 11.363 73.302 586 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.68 % Allowed : 14.21 % 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: -0.51 (0.37), residues: 440 helix: 0.57 (0.51), residues: 95 sheet: 0.00 (0.53), residues: 95 loop : -0.80 (0.36), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 196 HIS 0.007 0.002 HIS A 349 PHE 0.031 0.003 PHE A 211 TYR 0.014 0.002 TYR A 183 ARG 0.004 0.001 ARG A 266 *********************** 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 34 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 24 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 THR cc_start: 0.7121 (p) cc_final: 0.6152 (t) REVERT: A 290 LYS cc_start: 0.6871 (OUTLIER) cc_final: 0.5609 (tppt) REVERT: A 310 PHE cc_start: 0.8534 (p90) cc_final: 0.7551 (p90) outliers start: 10 outliers final: 3 residues processed: 31 average time/residue: 1.2129 time to fit residues: 39.0711 Evaluate side-chains 25 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 21 time to evaluate : 0.416 ------------------------------------------------------------------------------- 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 330 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 39 optimal weight: 50.0000 chunk 30 optimal weight: 30.0000 chunk 20 optimal weight: 9.9990 chunk 4 optimal weight: 20.0000 chunk 19 optimal weight: 9.9990 chunk 26 optimal weight: 9.9990 chunk 40 optimal weight: 7.9990 chunk 42 optimal weight: 5.9990 chunk 38 optimal weight: 30.0000 chunk 11 optimal weight: 0.9990 chunk 35 optimal weight: 5.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5975 moved from start: 0.4541 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= 0.194 Angle : 0.639 10.433 5008 Z= 0.321 Chirality : 0.045 0.139 569 Planarity : 0.005 0.054 613 Dihedral : 11.263 73.512 586 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.07 % Allowed : 16.09 % Favored : 82.84 % 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: -0.61 (0.37), residues: 440 helix: 0.39 (0.50), residues: 97 sheet: 0.07 (0.57), residues: 86 loop : -0.88 (0.34), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 58 HIS 0.004 0.001 HIS A 364 PHE 0.029 0.002 PHE A 211 TYR 0.010 0.002 TYR A 357 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 26 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 22 time to evaluate : 0.370 Fit side-chains revert: symmetry clash REVERT: A 49 MET cc_start: -0.2071 (mmt) cc_final: -0.2930 (mmm) REVERT: A 82 THR cc_start: 0.7089 (p) cc_final: 0.6148 (t) REVERT: A 155 MET cc_start: 0.5070 (mtm) cc_final: 0.4262 (pmm) REVERT: A 290 LYS cc_start: 0.6722 (OUTLIER) cc_final: 0.5297 (tppt) REVERT: A 310 PHE cc_start: 0.8522 (p90) cc_final: 0.7602 (p90) outliers start: 4 outliers final: 0 residues processed: 25 average time/residue: 1.3019 time to fit residues: 33.8976 Evaluate side-chains 20 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 19 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 40.0000 chunk 0 optimal weight: 70.0000 chunk 31 optimal weight: 20.0000 chunk 17 optimal weight: 50.0000 chunk 36 optimal weight: 30.0000 chunk 29 optimal weight: 0.0050 chunk 21 optimal weight: 0.6980 chunk 38 optimal weight: 40.0000 chunk 10 optimal weight: 9.9990 chunk 14 optimal weight: 50.0000 chunk 8 optimal weight: 9.9990 overall best weight: 8.1402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6011 moved from start: 0.5103 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= 0.217 Angle : 0.628 9.302 5008 Z= 0.317 Chirality : 0.045 0.135 569 Planarity : 0.006 0.059 613 Dihedral : 11.122 73.556 586 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.95 % Allowed : 14.75 % 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: -0.30 (0.38), residues: 440 helix: 0.68 (0.52), residues: 97 sheet: 0.25 (0.52), residues: 103 loop : -0.75 (0.36), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 58 HIS 0.004 0.001 HIS A 364 PHE 0.038 0.002 PHE A 211 TYR 0.009 0.001 TYR A 162 ARG 0.003 0.001 ARG A 321 *********************** 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 31 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 20 time to evaluate : 0.468 Fit side-chains revert: symmetry clash REVERT: A 82 THR cc_start: 0.7301 (p) cc_final: 0.6321 (t) REVERT: A 155 MET cc_start: 0.4968 (OUTLIER) cc_final: 0.4654 (pmm) REVERT: A 165 LYS cc_start: 0.7415 (mmpt) cc_final: 0.6900 (pmtt) REVERT: A 290 LYS cc_start: 0.6693 (OUTLIER) cc_final: 0.5229 (tppt) REVERT: A 310 PHE cc_start: 0.8480 (p90) cc_final: 0.7542 (p90) outliers start: 11 outliers final: 2 residues processed: 28 average time/residue: 1.0760 time to fit residues: 31.7051 Evaluate side-chains 24 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 20 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 155 MET 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: 5.9990 chunk 10 optimal weight: 0.8980 chunk 42 optimal weight: 7.9990 chunk 35 optimal weight: 6.9990 chunk 19 optimal weight: 20.0000 chunk 3 optimal weight: 7.9990 chunk 14 optimal weight: 5.9990 chunk 22 optimal weight: 20.0000 chunk 41 optimal weight: 4.9990 chunk 4 optimal weight: 50.0000 chunk 31 optimal weight: 30.0000 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5988 moved from start: 0.5287 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= 0.161 Angle : 0.569 8.465 5008 Z= 0.288 Chirality : 0.045 0.137 569 Planarity : 0.005 0.057 613 Dihedral : 10.928 73.540 586 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.61 % Allowed : 16.62 % Favored : 81.77 % 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: -0.26 (0.38), residues: 440 helix: 0.81 (0.52), residues: 97 sheet: 0.33 (0.53), residues: 97 loop : -0.76 (0.35), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 58 HIS 0.004 0.001 HIS A 364 PHE 0.029 0.002 PHE A 211 TYR 0.007 0.001 TYR A 357 ARG 0.002 0.000 ARG A 37 *********************** 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 26 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 20 time to evaluate : 0.422 Fit side-chains revert: symmetry clash REVERT: A 82 THR cc_start: 0.7232 (p) cc_final: 0.6251 (t) REVERT: A 155 MET cc_start: 0.4976 (OUTLIER) cc_final: 0.4771 (mpp) REVERT: A 165 LYS cc_start: 0.7456 (mmpt) cc_final: 0.6968 (ptpp) REVERT: A 310 PHE cc_start: 0.8488 (p90) cc_final: 0.7466 (p90) outliers start: 6 outliers final: 2 residues processed: 24 average time/residue: 0.9946 time to fit residues: 25.2996 Evaluate side-chains 23 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 20 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 222 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 8.9990 chunk 35 optimal weight: 40.0000 chunk 23 optimal weight: 9.9990 chunk 42 optimal weight: 8.9990 chunk 26 optimal weight: 6.9990 chunk 25 optimal weight: 6.9990 chunk 19 optimal weight: 30.0000 chunk 16 optimal weight: 50.0000 chunk 12 optimal weight: 50.0000 chunk 8 optimal weight: 9.9990 chunk 28 optimal weight: 30.0000 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6015 moved from start: 0.5633 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= 0.214 Angle : 0.619 9.538 5008 Z= 0.311 Chirality : 0.046 0.171 569 Planarity : 0.005 0.058 613 Dihedral : 10.771 73.481 586 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.88 % Allowed : 17.69 % Favored : 80.43 % 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: -0.38 (0.38), residues: 440 helix: 0.89 (0.52), residues: 97 sheet: 0.18 (0.56), residues: 90 loop : -0.87 (0.35), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 58 HIS 0.004 0.001 HIS A 26 PHE 0.013 0.002 PHE A 340 TYR 0.009 0.001 TYR A 162 ARG 0.002 0.001 ARG A 266 *********************** 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 : 0.467 Fit side-chains revert: symmetry clash REVERT: A 49 MET cc_start: -0.1853 (mmt) cc_final: -0.3452 (tpp) REVERT: A 165 LYS cc_start: 0.7404 (mmpt) cc_final: 0.7030 (pmtt) REVERT: A 276 MET cc_start: 0.4993 (mtp) cc_final: 0.4370 (ttm) REVERT: A 290 LYS cc_start: 0.6556 (OUTLIER) cc_final: 0.5125 (tppt) REVERT: A 310 PHE cc_start: 0.8457 (p90) cc_final: 0.7421 (p90) outliers start: 7 outliers final: 4 residues processed: 26 average time/residue: 1.2073 time to fit residues: 32.8386 Evaluate side-chains 26 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 21 time to evaluate : 0.426 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 20 optimal weight: 30.0000 chunk 3 optimal weight: 10.0000 chunk 33 optimal weight: 0.0980 chunk 38 optimal weight: 0.6980 chunk 40 optimal weight: 20.0000 chunk 37 optimal weight: 20.0000 chunk 39 optimal weight: 8.9990 chunk 23 optimal weight: 7.9990 chunk 17 optimal weight: 50.0000 chunk 31 optimal weight: 20.0000 chunk 12 optimal weight: 20.0000 overall best weight: 5.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6000 moved from start: 0.5775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3673 Z= 0.168 Angle : 0.600 9.448 5008 Z= 0.300 Chirality : 0.045 0.141 569 Planarity : 0.005 0.057 613 Dihedral : 10.754 73.548 586 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.07 % Allowed : 18.77 % Favored : 80.16 % 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: -0.43 (0.38), residues: 440 helix: 0.93 (0.52), residues: 97 sheet: 0.18 (0.58), residues: 87 loop : -0.95 (0.35), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 58 HIS 0.004 0.001 HIS A 26 PHE 0.030 0.002 PHE A 211 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 : 0.418 Fit side-chains revert: symmetry clash REVERT: A 82 THR cc_start: 0.6680 (p) cc_final: 0.5745 (t) REVERT: A 155 MET cc_start: 0.4932 (mpp) cc_final: 0.4691 (mpt) REVERT: A 165 LYS cc_start: 0.7447 (mmpt) cc_final: 0.7114 (pmtt) REVERT: A 290 LYS cc_start: 0.6495 (OUTLIER) cc_final: 0.4822 (tppt) REVERT: A 310 PHE cc_start: 0.8503 (p90) cc_final: 0.7505 (p90) outliers start: 4 outliers final: 3 residues processed: 25 average time/residue: 1.1488 time to fit residues: 30.1210 Evaluate side-chains 25 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 21 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 35 optimal weight: 3.9990 chunk 37 optimal weight: 50.0000 chunk 39 optimal weight: 10.0000 chunk 25 optimal weight: 30.0000 chunk 41 optimal weight: 8.9990 chunk 19 optimal weight: 10.0000 chunk 29 optimal weight: 40.0000 chunk 43 optimal weight: 30.0000 chunk 40 optimal weight: 7.9990 chunk 34 optimal weight: 7.9990 chunk 3 optimal weight: 10.0000 overall best weight: 7.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6018 moved from start: 0.5955 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= 0.200 Angle : 0.613 10.289 5008 Z= 0.307 Chirality : 0.045 0.134 569 Planarity : 0.005 0.060 613 Dihedral : 10.776 73.504 586 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.07 % Allowed : 18.50 % Favored : 80.43 % 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: -0.44 (0.38), residues: 440 helix: 0.92 (0.53), residues: 97 sheet: 0.11 (0.57), residues: 89 loop : -0.93 (0.36), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 58 HIS 0.004 0.001 HIS A 364 PHE 0.012 0.002 PHE A 340 TYR 0.009 0.001 TYR A 162 ARG 0.002 0.000 ARG A 423 *********************** 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 25 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 21 time to evaluate : 0.407 Fit side-chains revert: symmetry clash REVERT: A 82 THR cc_start: 0.6567 (p) cc_final: 0.5523 (t) REVERT: A 165 LYS cc_start: 0.7513 (mmpt) cc_final: 0.7200 (pmtt) REVERT: A 290 LYS cc_start: 0.6588 (OUTLIER) cc_final: 0.4946 (tppt) REVERT: A 310 PHE cc_start: 0.8481 (p90) cc_final: 0.7480 (p90) outliers start: 4 outliers final: 4 residues processed: 25 average time/residue: 1.1343 time to fit residues: 29.7031 Evaluate side-chains 25 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 20 time to evaluate : 0.388 ------------------------------------------------------------------------------- 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: 8.9990 chunk 21 optimal weight: 30.0000 chunk 27 optimal weight: 6.9990 chunk 37 optimal weight: 40.0000 chunk 10 optimal weight: 30.0000 chunk 32 optimal weight: 7.9990 chunk 5 optimal weight: 7.9990 chunk 9 optimal weight: 7.9990 chunk 34 optimal weight: 40.0000 chunk 14 optimal weight: 9.9990 chunk 35 optimal weight: 5.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6019 moved from start: 0.6225 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= 0.194 Angle : 0.628 12.412 5008 Z= 0.311 Chirality : 0.045 0.134 569 Planarity : 0.005 0.060 613 Dihedral : 10.811 73.503 586 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.07 % Allowed : 18.50 % Favored : 80.43 % 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: -0.49 (0.38), residues: 440 helix: 0.90 (0.52), residues: 97 sheet: -0.01 (0.56), residues: 89 loop : -0.93 (0.36), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 58 HIS 0.004 0.001 HIS A 26 PHE 0.013 0.001 PHE A 340 TYR 0.008 0.001 TYR A 162 ARG 0.002 0.000 ARG A 67 ********************** 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 24 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 20 time to evaluate : 0.469 Fit side-chains revert: symmetry clash REVERT: A 82 THR cc_start: 0.6691 (p) cc_final: 0.5585 (t) REVERT: A 165 LYS cc_start: 0.7490 (mmpt) cc_final: 0.7205 (pmtt) REVERT: A 290 LYS cc_start: 0.6600 (OUTLIER) cc_final: 0.4807 (tppt) REVERT: A 310 PHE cc_start: 0.8457 (p90) cc_final: 0.7461 (p90) outliers start: 4 outliers final: 3 residues processed: 24 average time/residue: 1.1761 time to fit residues: 29.5713 Evaluate side-chains 23 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 19 time to evaluate : 0.320 ------------------------------------------------------------------------------- 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 330 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 4 optimal weight: 50.0000 chunk 6 optimal weight: 40.0000 chunk 30 optimal weight: 0.2980 chunk 1 optimal weight: 9.9990 chunk 25 optimal weight: 30.0000 chunk 40 optimal weight: 7.9990 chunk 23 optimal weight: 0.7980 chunk 29 optimal weight: 7.9990 chunk 27 optimal weight: 8.9990 chunk 26 optimal weight: 8.9990 chunk 17 optimal weight: 9.9990 overall best weight: 5.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.101980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.083998 restraints weight = 13713.807| |-----------------------------------------------------------------------------| r_work (start): 0.3804 rms_B_bonded: 2.52 r_work: 0.3738 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3674 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3650 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3650 r_free = 0.3650 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1041 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3639 r_free = 0.3639 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1056 | |-----------------------------------------------------------------------------| r_final: 0.3639 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.6335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3673 Z= 0.165 Angle : 0.609 10.051 5008 Z= 0.299 Chirality : 0.045 0.133 569 Planarity : 0.005 0.058 613 Dihedral : 10.740 73.516 586 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 1.07 % Allowed : 18.50 % Favored : 80.43 % 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: -0.29 (0.38), residues: 440 helix: 0.96 (0.53), residues: 97 sheet: 0.46 (0.61), residues: 75 loop : -0.84 (0.36), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 58 HIS 0.004 0.001 HIS A 364 PHE 0.014 0.001 PHE A 340 TYR 0.006 0.001 TYR A 162 ARG 0.002 0.000 ARG A 423 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1663.07 seconds wall clock time: 30 minutes 50.02 seconds (1850.02 seconds total)