Starting phenix.real_space_refine on Mon Sep 23 16:37:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b6z_15893/09_2024/8b6z_15893.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b6z_15893/09_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_15893/09_2024/8b6z_15893.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b6z_15893/09_2024/8b6z_15893.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b6z_15893/09_2024/8b6z_15893.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b6z_15893/09_2024/8b6z_15893.cif" } 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. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 3.82, per 1000 atoms: 1.07 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.93 Conformation dependent library (CDL) restraints added in 373.4 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: 1.37 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: 1.14 Time building geometry restraints manager: 0.96 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: 0.00 - 1.47: 4915 1.47 - 2.93: 71 2.93 - 4.40: 20 4.40 - 5.86: 1 5.86 - 7.33: 1 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 3.040 nonbonded pdb=" O ALA A 231 " pdb=" OG1 THR A 234 " model vdw 2.388 3.040 nonbonded pdb=" O VAL A 277 " pdb=" OG SER A 329 " model vdw 2.390 3.040 nonbonded pdb=" OH TYR A 29 " pdb=" NE1 TRP A 58 " model vdw 2.391 3.120 nonbonded pdb=" OE2 GLU A 68 " pdb=" N ARG A 96 " model vdw 2.413 3.120 ... (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 Time spend for trying shortcut: 0.00 ========== 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: 10.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 15.830 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.010 ------------------------------------------------------------------------------- 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 : 0.426 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: 1.3362 time to fit residues: 96.2689 Evaluate side-chains 34 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.423 ------------------------------------------------------------------------------- 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: 40.0000 chunk 33 optimal weight: 10.0000 chunk 18 optimal weight: 20.0000 chunk 11 optimal weight: 50.0000 chunk 22 optimal weight: 50.0000 chunk 17 optimal weight: 30.0000 chunk 34 optimal weight: 9.9990 chunk 13 optimal weight: 50.0000 chunk 20 optimal weight: 20.0000 chunk 25 optimal weight: 9.9990 chunk 39 optimal weight: 20.0000 overall best weight: 13.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 349 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5947 moved from start: 0.3392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 3673 Z= 0.341 Angle : 0.761 11.936 5008 Z= 0.391 Chirality : 0.050 0.164 569 Planarity : 0.005 0.044 613 Dihedral : 11.968 72.927 590 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.68 % Allowed : 12.87 % Favored : 84.45 % 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 (0.38), residues: 440 helix: 0.41 (0.52), residues: 95 sheet: 0.02 (0.48), residues: 110 loop : -0.74 (0.39), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 196 HIS 0.009 0.002 HIS A 295 PHE 0.008 0.001 PHE A 211 TYR 0.017 0.002 TYR A 183 ARG 0.007 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 39 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 29 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 THR cc_start: 0.7133 (p) cc_final: 0.6129 (t) REVERT: A 290 LYS cc_start: 0.6651 (OUTLIER) cc_final: 0.5700 (tppt) REVERT: A 294 MET cc_start: 0.5125 (tpt) cc_final: 0.4885 (tmm) outliers start: 10 outliers final: 2 residues processed: 37 average time/residue: 1.5637 time to fit residues: 59.6065 Evaluate side-chains 27 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 24 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 MET Chi-restraints excluded: chain A residue 290 LYS Chi-restraints excluded: chain A residue 330 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 22 optimal weight: 50.0000 chunk 12 optimal weight: 0.0970 chunk 33 optimal weight: 9.9990 chunk 27 optimal weight: 10.0000 chunk 11 optimal weight: 0.9980 chunk 40 optimal weight: 8.9990 chunk 43 optimal weight: 9.9990 chunk 35 optimal weight: 10.0000 chunk 39 optimal weight: 30.0000 chunk 13 optimal weight: 40.0000 chunk 32 optimal weight: 5.9990 overall best weight: 5.2184 ------------------------------------------------------------------------------- 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: 0.5923 moved from start: 0.3896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3673 Z= 0.210 Angle : 0.668 13.011 5008 Z= 0.339 Chirality : 0.046 0.143 569 Planarity : 0.005 0.048 613 Dihedral : 11.827 73.439 590 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.88 % Allowed : 15.82 % 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: -0.41 (0.38), residues: 440 helix: 0.52 (0.52), residues: 95 sheet: 0.02 (0.52), residues: 102 loop : -0.68 (0.37), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 196 HIS 0.006 0.001 HIS A 349 PHE 0.029 0.003 PHE A 211 TYR 0.011 0.002 TYR A 183 ARG 0.003 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: 7 poor density : 24 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 MET cc_start: -0.2216 (mmt) cc_final: -0.2598 (mmm) REVERT: A 82 THR cc_start: 0.7039 (p) cc_final: 0.6035 (t) REVERT: A 208 MET cc_start: 0.7428 (ppp) cc_final: 0.7227 (tmm) REVERT: A 310 PHE cc_start: 0.8436 (p90) cc_final: 0.7462 (p90) outliers start: 7 outliers final: 0 residues processed: 28 average time/residue: 1.1423 time to fit residues: 33.4424 Evaluate side-chains 21 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 39 optimal weight: 1.9990 chunk 30 optimal weight: 8.9990 chunk 20 optimal weight: 40.0000 chunk 4 optimal weight: 50.0000 chunk 19 optimal weight: 10.0000 chunk 26 optimal weight: 20.0000 chunk 40 optimal weight: 8.9990 chunk 42 optimal weight: 9.9990 chunk 38 optimal weight: 20.0000 chunk 11 optimal weight: 40.0000 chunk 35 optimal weight: 6.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- 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: 0.5970 moved from start: 0.4442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3673 Z= 0.224 Angle : 0.648 10.991 5008 Z= 0.327 Chirality : 0.047 0.141 569 Planarity : 0.005 0.053 613 Dihedral : 11.722 73.548 590 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.61 % Allowed : 15.82 % Favored : 82.57 % 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: -0.47 (0.38), residues: 440 helix: 0.59 (0.51), residues: 95 sheet: -0.03 (0.56), residues: 86 loop : -0.73 (0.36), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 196 HIS 0.005 0.001 HIS A 364 PHE 0.020 0.002 PHE A 211 TYR 0.012 0.002 TYR A 183 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 28 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 22 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 THR cc_start: 0.7137 (p) cc_final: 0.6091 (t) REVERT: A 155 MET cc_start: 0.5139 (mtm) cc_final: 0.4591 (pmm) REVERT: A 165 LYS cc_start: 0.7613 (mmpt) cc_final: 0.7412 (mmpt) REVERT: A 276 MET cc_start: 0.4833 (mtp) cc_final: 0.4259 (ttm) REVERT: A 310 PHE cc_start: 0.8489 (p90) cc_final: 0.7543 (p90) outliers start: 6 outliers final: 0 residues processed: 27 average time/residue: 1.2746 time to fit residues: 35.8277 Evaluate side-chains 19 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 60.0000 chunk 31 optimal weight: 7.9990 chunk 17 optimal weight: 50.0000 chunk 36 optimal weight: 30.0000 chunk 29 optimal weight: 4.9990 chunk 21 optimal weight: 8.9990 chunk 38 optimal weight: 0.9980 chunk 10 optimal weight: 20.0000 chunk 14 optimal weight: 40.0000 chunk 8 optimal weight: 9.9990 overall best weight: 6.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 ASN ** 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: 0.5976 moved from start: 0.4834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 3673 Z= 0.201 Angle : 0.620 9.058 5008 Z= 0.312 Chirality : 0.045 0.139 569 Planarity : 0.005 0.056 613 Dihedral : 11.704 73.543 590 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.23 % Allowed : 2.27 % Favored : 97.50 % Rotamer: Outliers : 1.61 % Allowed : 16.09 % 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: -0.36 (0.38), residues: 440 helix: 0.77 (0.52), residues: 95 sheet: -0.10 (0.56), residues: 92 loop : -0.65 (0.36), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 210 HIS 0.004 0.001 HIS A 364 PHE 0.027 0.002 PHE A 211 TYR 0.009 0.001 TYR A 357 ARG 0.003 0.000 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: 6 poor density : 22 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 THR cc_start: 0.7147 (p) cc_final: 0.6124 (t) REVERT: A 155 MET cc_start: 0.5062 (OUTLIER) cc_final: 0.4440 (pmm) REVERT: A 276 MET cc_start: 0.4883 (mtp) cc_final: 0.4300 (ttm) REVERT: A 310 PHE cc_start: 0.8527 (p90) cc_final: 0.7624 (p90) outliers start: 6 outliers final: 0 residues processed: 26 average time/residue: 1.2372 time to fit residues: 33.5996 Evaluate side-chains 22 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 21 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 30.0000 chunk 10 optimal weight: 10.0000 chunk 42 optimal weight: 9.9990 chunk 35 optimal weight: 6.9990 chunk 19 optimal weight: 40.0000 chunk 3 optimal weight: 50.0000 chunk 14 optimal weight: 9.9990 chunk 22 optimal weight: 20.0000 chunk 41 optimal weight: 4.9990 chunk 4 optimal weight: 50.0000 chunk 31 optimal weight: 20.0000 overall best weight: 8.3992 ------------------------------------------------------------------------------- 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: 0.6015 moved from start: 0.5316 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= 0.218 Angle : 0.624 8.676 5008 Z= 0.317 Chirality : 0.046 0.138 569 Planarity : 0.005 0.061 613 Dihedral : 11.675 73.530 590 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.07 % Allowed : 17.16 % 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: -0.19 (0.38), residues: 440 helix: 0.92 (0.52), residues: 95 sheet: 0.19 (0.53), residues: 97 loop : -0.65 (0.37), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 210 HIS 0.006 0.001 HIS A 295 PHE 0.037 0.002 PHE A 211 TYR 0.010 0.002 TYR A 162 ARG 0.002 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 25 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 21 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 THR cc_start: 0.7256 (p) cc_final: 0.6111 (t) REVERT: A 155 MET cc_start: 0.5047 (OUTLIER) cc_final: 0.4541 (pmm) REVERT: A 165 LYS cc_start: 0.7531 (mmpt) cc_final: 0.7087 (pmtt) REVERT: A 276 MET cc_start: 0.4747 (mtp) cc_final: 0.4210 (ttm) REVERT: A 310 PHE cc_start: 0.8461 (p90) cc_final: 0.7414 (p90) outliers start: 4 outliers final: 1 residues processed: 24 average time/residue: 1.3069 time to fit residues: 32.7231 Evaluate side-chains 22 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 20 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 330 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 9.9990 chunk 35 optimal weight: 40.0000 chunk 23 optimal weight: 9.9990 chunk 42 optimal weight: 10.0000 chunk 26 optimal weight: 7.9990 chunk 25 optimal weight: 20.0000 chunk 19 optimal weight: 50.0000 chunk 16 optimal weight: 20.0000 chunk 12 optimal weight: 20.0000 chunk 8 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- 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: 0.6004 moved from start: 0.5587 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= 0.197 Angle : 0.616 8.174 5008 Z= 0.315 Chirality : 0.046 0.138 569 Planarity : 0.005 0.059 613 Dihedral : 11.511 73.514 590 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.54 % Allowed : 18.23 % 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: -0.34 (0.38), residues: 440 helix: 0.81 (0.52), residues: 95 sheet: -0.04 (0.55), residues: 90 loop : -0.67 (0.36), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 58 HIS 0.004 0.001 HIS A 295 PHE 0.012 0.002 PHE A 340 TYR 0.009 0.001 TYR A 162 ARG 0.002 0.000 ARG A 37 *********************** 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 22 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 20 time to evaluate : 0.460 Fit side-chains revert: symmetry clash REVERT: A 49 MET cc_start: -0.1766 (mmt) cc_final: -0.3569 (tpp) REVERT: A 82 THR cc_start: 0.7258 (p) cc_final: 0.6141 (t) REVERT: A 155 MET cc_start: 0.4905 (OUTLIER) cc_final: 0.4386 (pmm) REVERT: A 165 LYS cc_start: 0.7467 (mmpt) cc_final: 0.7067 (pmtt) REVERT: A 276 MET cc_start: 0.4826 (mtp) cc_final: 0.4278 (ttm) REVERT: A 310 PHE cc_start: 0.8437 (p90) cc_final: 0.7422 (p90) outliers start: 2 outliers final: 1 residues processed: 21 average time/residue: 1.1318 time to fit residues: 25.0160 Evaluate side-chains 22 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 20 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 303 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 20 optimal weight: 0.7980 chunk 3 optimal weight: 30.0000 chunk 33 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 40 optimal weight: 7.9990 chunk 37 optimal weight: 50.0000 chunk 39 optimal weight: 30.0000 chunk 23 optimal weight: 5.9990 chunk 17 optimal weight: 50.0000 chunk 31 optimal weight: 30.0000 chunk 12 optimal weight: 50.0000 overall best weight: 4.9588 ------------------------------------------------------------------------------- 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: 0.5982 moved from start: 0.5764 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= 0.166 Angle : 0.596 9.105 5008 Z= 0.301 Chirality : 0.045 0.142 569 Planarity : 0.005 0.056 613 Dihedral : 10.929 73.508 590 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % 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: -0.24 (0.38), residues: 440 helix: 0.83 (0.53), residues: 97 sheet: 0.37 (0.60), residues: 78 loop : -0.70 (0.35), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 210 HIS 0.004 0.001 HIS A 364 PHE 0.013 0.001 PHE A 340 TYR 0.009 0.001 TYR A 162 ARG 0.003 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 24 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 21 time to evaluate : 0.329 Fit side-chains revert: symmetry clash REVERT: A 82 THR cc_start: 0.7213 (p) cc_final: 0.6121 (t) REVERT: A 155 MET cc_start: 0.4930 (OUTLIER) cc_final: 0.4711 (mpp) REVERT: A 165 LYS cc_start: 0.7428 (mmpt) cc_final: 0.7110 (pmtt) REVERT: A 310 PHE cc_start: 0.8455 (p90) cc_final: 0.7447 (p90) outliers start: 3 outliers final: 0 residues processed: 23 average time/residue: 0.7996 time to fit residues: 19.3212 Evaluate side-chains 21 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 20 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 MET 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: 40.0000 chunk 25 optimal weight: 30.0000 chunk 41 optimal weight: 0.0870 chunk 19 optimal weight: 7.9990 chunk 29 optimal weight: 40.0000 chunk 43 optimal weight: 40.0000 chunk 40 optimal weight: 8.9990 chunk 34 optimal weight: 7.9990 chunk 3 optimal weight: 30.0000 overall best weight: 11.0168 ------------------------------------------------------------------------------- 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: 0.6037 moved from start: 0.6106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3673 Z= 0.264 Angle : 0.661 8.749 5008 Z= 0.335 Chirality : 0.046 0.137 569 Planarity : 0.006 0.061 613 Dihedral : 11.189 73.575 590 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 0.54 % Allowed : 18.77 % 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: -0.28 (0.39), residues: 440 helix: 0.78 (0.53), residues: 97 sheet: 0.29 (0.54), residues: 96 loop : -0.76 (0.37), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 58 HIS 0.008 0.002 HIS A 295 PHE 0.013 0.002 PHE A 340 TYR 0.013 0.002 TYR A 162 ARG 0.002 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 21 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 19 time to evaluate : 0.439 Fit side-chains revert: symmetry clash REVERT: A 82 THR cc_start: 0.7281 (p) cc_final: 0.6209 (t) REVERT: A 165 LYS cc_start: 0.7496 (mmpt) cc_final: 0.7145 (pmtt) REVERT: A 310 PHE cc_start: 0.8453 (p90) cc_final: 0.7468 (p90) outliers start: 2 outliers final: 0 residues processed: 19 average time/residue: 1.1537 time to fit residues: 23.1398 Evaluate side-chains 19 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 26 optimal weight: 6.9990 chunk 21 optimal weight: 30.0000 chunk 27 optimal weight: 7.9990 chunk 37 optimal weight: 40.0000 chunk 10 optimal weight: 40.0000 chunk 32 optimal weight: 20.0000 chunk 5 optimal weight: 10.0000 chunk 9 optimal weight: 9.9990 chunk 34 optimal weight: 3.9990 chunk 14 optimal weight: 10.0000 chunk 35 optimal weight: 20.0000 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: 0.6019 moved from start: 0.6306 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= 0.202 Angle : 0.639 11.603 5008 Z= 0.318 Chirality : 0.045 0.139 569 Planarity : 0.005 0.060 613 Dihedral : 11.138 73.440 590 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 0.27 % Allowed : 19.03 % 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: -0.16 (0.39), residues: 440 helix: 0.90 (0.53), residues: 97 sheet: 0.41 (0.56), residues: 94 loop : -0.70 (0.37), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 58 HIS 0.006 0.002 HIS A 26 PHE 0.014 0.001 PHE A 340 TYR 0.009 0.001 TYR A 357 ARG 0.003 0.001 ARG A 273 ********************** 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 20 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 19 time to evaluate : 0.381 Fit side-chains revert: symmetry clash REVERT: A 165 LYS cc_start: 0.7435 (mmpt) cc_final: 0.7142 (pmtt) REVERT: A 276 MET cc_start: 0.4770 (mtp) cc_final: 0.3655 (ttm) REVERT: A 310 PHE cc_start: 0.8437 (p90) cc_final: 0.7433 (p90) outliers start: 1 outliers final: 0 residues processed: 19 average time/residue: 1.1219 time to fit residues: 22.5042 Evaluate side-chains 19 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 1 optimal weight: 1.9990 chunk 25 optimal weight: 10.0000 chunk 40 optimal weight: 40.0000 chunk 23 optimal weight: 5.9990 chunk 29 optimal weight: 8.9990 chunk 27 optimal weight: 8.9990 chunk 26 optimal weight: 10.0000 chunk 17 optimal weight: 30.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- 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 = 0.4305 r_free = 0.4305 target = 0.101874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.083777 restraints weight = 13709.691| |-----------------------------------------------------------------------------| r_work (start): 0.3798 rms_B_bonded: 2.53 r_work: 0.3728 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3668 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3645 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3645 r_free = 0.3645 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 = 0.3634 r_free = 0.3634 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1057 | |-----------------------------------------------------------------------------| r_final: 0.3634 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.6415 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= 0.187 Angle : 0.628 11.181 5008 Z= 0.316 Chirality : 0.045 0.136 569 Planarity : 0.005 0.059 613 Dihedral : 11.108 73.530 590 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 0.00 % Allowed : 19.57 % 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: -0.19 (0.39), residues: 440 helix: 0.85 (0.54), residues: 97 sheet: 0.31 (0.56), residues: 92 loop : -0.66 (0.36), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 58 HIS 0.007 0.002 HIS A 26 PHE 0.026 0.002 PHE A 211 TYR 0.011 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: 1622.24 seconds wall clock time: 37 minutes 24.48 seconds (2244.48 seconds total)