Starting phenix.real_space_refine on Fri Aug 2 15:41:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u3f_41860/08_2024/8u3f_41860.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u3f_41860/08_2024/8u3f_41860.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u3f_41860/08_2024/8u3f_41860.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u3f_41860/08_2024/8u3f_41860.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u3f_41860/08_2024/8u3f_41860.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u3f_41860/08_2024/8u3f_41860.cif" } resolution = 3.31 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= 0.002 sd= 0.073 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: 4 Type Number sf(0) Gaussians S 17 5.16 5 C 2274 2.51 5 N 534 2.21 5 O 585 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 39": "NH1" <-> "NH2" Residue "A PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 57": "NH1" <-> "NH2" Residue "A ASP 69": "OD1" <-> "OD2" Residue "A GLU 85": "OE1" <-> "OE2" Residue "A ASP 104": "OD1" <-> "OD2" Residue "A GLU 106": "OE1" <-> "OE2" Residue "A ARG 195": "NH1" <-> "NH2" Residue "A ARG 257": "NH1" <-> "NH2" Residue "A ARG 271": "NH1" <-> "NH2" Residue "A ARG 321": "NH1" <-> "NH2" Residue "A PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 353": "NH1" <-> "NH2" Residue "A ARG 364": "NH1" <-> "NH2" Residue "A ARG 365": "NH1" <-> "NH2" Residue "A PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 481": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 3410 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3410 Classifications: {'peptide': 437} Link IDs: {'PTRANS': 19, 'TRANS': 417} Chain breaks: 2 Time building chain proxies: 2.90, per 1000 atoms: 0.85 Number of scatterers: 3410 At special positions: 0 Unit cell: (58.1, 64.74, 86.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 17 16.00 O 585 8.00 N 534 7.00 C 2274 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 83 " - pdb=" SG CYS A 387 " distance=2.03 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: 1.59 Conformation dependent library (CDL) restraints added in 654.1 milliseconds 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 796 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 0 sheets defined 82.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 37 through 58 Processing helix chain 'A' and resid 59 through 64 Processing helix chain 'A' and resid 104 through 114 Processing helix chain 'A' and resid 115 through 120 Processing helix chain 'A' and resid 122 through 134 Processing helix chain 'A' and resid 134 through 151 removed outlier: 4.555A pdb=" N LEU A 138 " --> pdb=" O GLY A 134 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU A 151 " --> pdb=" O ALA A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 160 removed outlier: 3.635A pdb=" N ASP A 158 " --> pdb=" O PRO A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 176 Processing helix chain 'A' and resid 177 through 187 Processing helix chain 'A' and resid 191 through 193 No H-bonds generated for 'chain 'A' and resid 191 through 193' Processing helix chain 'A' and resid 194 through 204 removed outlier: 3.506A pdb=" N SER A 200 " --> pdb=" O SER A 196 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TYR A 203 " --> pdb=" O LEU A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 224 Proline residue: A 215 - end of helix removed outlier: 3.712A pdb=" N GLY A 218 " --> pdb=" O LEU A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 248 removed outlier: 3.648A pdb=" N TRP A 246 " --> pdb=" O LEU A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 270 Processing helix chain 'A' and resid 281 through 287 Processing helix chain 'A' and resid 288 through 311 removed outlier: 3.743A pdb=" N ILE A 294 " --> pdb=" O PRO A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 319 Processing helix chain 'A' and resid 332 through 356 Processing helix chain 'A' and resid 359 through 384 Proline residue: A 375 - end of helix removed outlier: 3.614A pdb=" N GLY A 383 " --> pdb=" O LEU A 379 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N PHE A 384 " --> pdb=" O VAL A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 403 Processing helix chain 'A' and resid 404 through 409 Processing helix chain 'A' and resid 412 through 418 removed outlier: 3.636A pdb=" N ASP A 416 " --> pdb=" O ILE A 412 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA A 418 " --> pdb=" O HIS A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 434 removed outlier: 3.712A pdb=" N PHE A 432 " --> pdb=" O ILE A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 448 Proline residue: A 441 - end of helix Processing helix chain 'A' and resid 452 through 478 Processing helix chain 'A' and resid 483 through 487 239 hydrogen bonds defined for protein. 702 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.02 Time building geometry restraints manager: 1.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1002 1.34 - 1.46: 920 1.46 - 1.58: 1565 1.58 - 1.69: 0 1.69 - 1.81: 26 Bond restraints: 3513 Sorted by residual: bond pdb=" CA VAL A 280 " pdb=" CB VAL A 280 " ideal model delta sigma weight residual 1.537 1.525 0.013 1.29e-02 6.01e+03 9.50e-01 bond pdb=" N PRO A 84 " pdb=" CA PRO A 84 " ideal model delta sigma weight residual 1.469 1.476 -0.007 7.40e-03 1.83e+04 9.44e-01 bond pdb=" CA ASN A 323 " pdb=" C ASN A 323 " ideal model delta sigma weight residual 1.532 1.523 0.009 9.60e-03 1.09e+04 8.66e-01 bond pdb=" N GLY A 134 " pdb=" CA GLY A 134 " ideal model delta sigma weight residual 1.447 1.457 -0.011 1.18e-02 7.18e+03 8.22e-01 bond pdb=" CB VAL A 211 " pdb=" CG2 VAL A 211 " ideal model delta sigma weight residual 1.521 1.494 0.027 3.30e-02 9.18e+02 6.47e-01 ... (remaining 3508 not shown) Histogram of bond angle deviations from ideal: 99.75 - 106.61: 105 106.61 - 113.48: 1913 113.48 - 120.34: 1428 120.34 - 127.20: 1292 127.20 - 134.06: 53 Bond angle restraints: 4791 Sorted by residual: angle pdb=" N VAL A 177 " pdb=" CA VAL A 177 " pdb=" C VAL A 177 " ideal model delta sigma weight residual 109.34 113.83 -4.49 2.08e+00 2.31e-01 4.66e+00 angle pdb=" C LEU A 447 " pdb=" N THR A 448 " pdb=" CA THR A 448 " ideal model delta sigma weight residual 122.89 120.51 2.38 1.12e+00 7.97e-01 4.51e+00 angle pdb=" CA THR A 153 " pdb=" C THR A 153 " pdb=" N PRO A 154 " ideal model delta sigma weight residual 118.44 121.64 -3.20 1.59e+00 3.96e-01 4.05e+00 angle pdb=" N VAL A 58 " pdb=" CA VAL A 58 " pdb=" C VAL A 58 " ideal model delta sigma weight residual 109.34 113.48 -4.14 2.08e+00 2.31e-01 3.97e+00 angle pdb=" CA LEU A 289 " pdb=" C LEU A 289 " pdb=" N PRO A 290 " ideal model delta sigma weight residual 118.44 121.58 -3.14 1.59e+00 3.96e-01 3.91e+00 ... (remaining 4786 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.48: 1771 16.48 - 32.95: 182 32.95 - 49.43: 30 49.43 - 65.90: 3 65.90 - 82.38: 1 Dihedral angle restraints: 1987 sinusoidal: 737 harmonic: 1250 Sorted by residual: dihedral pdb=" CA ASN A 323 " pdb=" C ASN A 323 " pdb=" N VAL A 324 " pdb=" CA VAL A 324 " ideal model delta harmonic sigma weight residual 180.00 -156.33 -23.67 0 5.00e+00 4.00e-02 2.24e+01 dihedral pdb=" CA ASN A 323 " pdb=" CB ASN A 323 " pdb=" CG ASN A 323 " pdb=" OD1 ASN A 323 " ideal model delta sinusoidal sigma weight residual -90.00 -152.99 62.99 2 2.00e+01 2.50e-03 9.53e+00 dihedral pdb=" CG LYS A 278 " pdb=" CD LYS A 278 " pdb=" CE LYS A 278 " pdb=" NZ LYS A 278 " ideal model delta sinusoidal sigma weight residual -180.00 -136.68 -43.32 3 1.50e+01 4.44e-03 7.79e+00 ... (remaining 1984 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 356 0.037 - 0.073: 148 0.073 - 0.110: 33 0.110 - 0.146: 6 0.146 - 0.183: 1 Chirality restraints: 544 Sorted by residual: chirality pdb=" CA PHE A 305 " pdb=" N PHE A 305 " pdb=" C PHE A 305 " pdb=" CB PHE A 305 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.37e-01 chirality pdb=" CA PRO A 192 " pdb=" N PRO A 192 " pdb=" C PRO A 192 " pdb=" CB PRO A 192 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.50e-01 chirality pdb=" CA PRO A 375 " pdb=" N PRO A 375 " pdb=" C PRO A 375 " pdb=" CB PRO A 375 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.45e-01 ... (remaining 541 not shown) Planarity restraints: 581 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 305 " 0.014 2.00e-02 2.50e+03 1.40e-02 3.45e+00 pdb=" CG PHE A 305 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 PHE A 305 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE A 305 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 305 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 305 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE A 305 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 289 " -0.030 5.00e-02 4.00e+02 4.56e-02 3.33e+00 pdb=" N PRO A 290 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO A 290 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 290 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 162 " -0.026 5.00e-02 4.00e+02 3.86e-02 2.38e+00 pdb=" N PRO A 163 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 163 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 163 " -0.022 5.00e-02 4.00e+02 ... (remaining 578 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 911 2.79 - 3.32: 3343 3.32 - 3.85: 5797 3.85 - 4.37: 6821 4.37 - 4.90: 11982 Nonbonded interactions: 28854 Sorted by model distance: nonbonded pdb=" NH2 ARG A 57 " pdb=" OE2 GLU A 175 " model vdw 2.265 3.120 nonbonded pdb=" OH TYR A 101 " pdb=" OD1 ASP A 158 " model vdw 2.286 3.040 nonbonded pdb=" O PRO A 192 " pdb=" NH2 ARG A 353 " model vdw 2.314 3.120 nonbonded pdb=" OG SER A 37 " pdb=" OE2 GLU A 262 " model vdw 2.352 3.040 nonbonded pdb=" O ALA A 444 " pdb=" OG1 THR A 448 " model vdw 2.358 3.040 ... (remaining 28849 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.420 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: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.810 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 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 : 0.005 0.038 3513 Z= 0.299 Angle : 0.625 5.254 4791 Z= 0.369 Chirality : 0.041 0.183 544 Planarity : 0.005 0.046 581 Dihedral : 12.988 82.377 1188 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.37), residues: 431 helix: -0.90 (0.26), residues: 323 sheet: None (None), residues: 0 loop : -0.82 (0.64), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 240 HIS 0.006 0.001 HIS A 298 PHE 0.032 0.002 PHE A 305 TYR 0.011 0.001 TYR A 306 ARG 0.003 0.000 ARG A 353 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.373 Fit side-chains REVERT: A 256 LYS cc_start: 0.5750 (mmtt) cc_final: 0.4278 (tttp) outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.1728 time to fit residues: 9.0278 Evaluate side-chains 38 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 36 optimal weight: 0.0010 chunk 32 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 chunk 21 optimal weight: 0.3980 chunk 17 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 13 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 39 optimal weight: 8.9990 overall best weight: 0.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 323 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.0947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3513 Z= 0.181 Angle : 0.544 5.323 4791 Z= 0.289 Chirality : 0.040 0.114 544 Planarity : 0.005 0.044 581 Dihedral : 4.248 20.132 463 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.55 % Allowed : 9.70 % Favored : 89.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.40), residues: 431 helix: 0.61 (0.29), residues: 319 sheet: None (None), residues: 0 loop : -1.12 (0.59), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 244 HIS 0.003 0.001 HIS A 298 PHE 0.011 0.001 PHE A 305 TYR 0.012 0.001 TYR A 306 ARG 0.001 0.000 ARG A 364 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 35 time to evaluate : 0.366 Fit side-chains REVERT: A 256 LYS cc_start: 0.5660 (mmtt) cc_final: 0.4139 (tttp) outliers start: 2 outliers final: 0 residues processed: 35 average time/residue: 0.1881 time to fit residues: 8.2571 Evaluate side-chains 32 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 21 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 chunk 32 optimal weight: 0.5980 chunk 26 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 13 optimal weight: 0.3980 chunk 31 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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: 0.8225 moved from start: 0.1240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3513 Z= 0.204 Angle : 0.539 5.215 4791 Z= 0.280 Chirality : 0.040 0.115 544 Planarity : 0.005 0.042 581 Dihedral : 4.216 22.013 463 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.11 % Allowed : 11.63 % Favored : 87.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.40), residues: 431 helix: 1.18 (0.29), residues: 318 sheet: None (None), residues: 0 loop : -1.06 (0.58), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 244 HIS 0.004 0.001 HIS A 298 PHE 0.016 0.001 PHE A 322 TYR 0.012 0.001 TYR A 306 ARG 0.001 0.000 ARG A 364 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 35 time to evaluate : 0.384 Fit side-chains REVERT: A 256 LYS cc_start: 0.5707 (mmtt) cc_final: 0.4237 (tttp) REVERT: A 317 LYS cc_start: 0.8351 (tppt) cc_final: 0.8118 (tppt) outliers start: 4 outliers final: 2 residues processed: 38 average time/residue: 0.2033 time to fit residues: 9.3883 Evaluate side-chains 35 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 33 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 385 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 38 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 4 optimal weight: 0.0050 chunk 18 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 37 optimal weight: 0.3980 chunk 11 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 overall best weight: 0.8598 ------------------------------------------------------------------------------- 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: 0.8246 moved from start: 0.1354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3513 Z= 0.239 Angle : 0.548 5.244 4791 Z= 0.285 Chirality : 0.041 0.116 544 Planarity : 0.005 0.042 581 Dihedral : 4.219 21.873 463 Min Nonbonded Distance : 2.653 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.94 % Allowed : 13.30 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.41), residues: 431 helix: 1.34 (0.29), residues: 319 sheet: None (None), residues: 0 loop : -0.92 (0.59), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 244 HIS 0.005 0.001 HIS A 298 PHE 0.025 0.001 PHE A 322 TYR 0.011 0.001 TYR A 306 ARG 0.001 0.000 ARG A 364 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 34 time to evaluate : 0.307 Fit side-chains REVERT: A 256 LYS cc_start: 0.5685 (mmtt) cc_final: 0.4162 (tttp) outliers start: 7 outliers final: 6 residues processed: 38 average time/residue: 0.1631 time to fit residues: 7.8616 Evaluate side-chains 39 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 33 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 385 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 23 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 30 optimal weight: 0.0570 chunk 17 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 28 optimal weight: 0.0570 chunk 21 optimal weight: 0.5980 chunk 37 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 overall best weight: 0.4216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 413 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 3513 Z= 0.155 Angle : 0.509 5.203 4791 Z= 0.264 Chirality : 0.039 0.112 544 Planarity : 0.005 0.043 581 Dihedral : 4.124 22.050 463 Min Nonbonded Distance : 2.652 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.66 % Allowed : 13.57 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.41), residues: 431 helix: 1.67 (0.29), residues: 319 sheet: None (None), residues: 0 loop : -0.74 (0.61), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 244 HIS 0.004 0.001 HIS A 298 PHE 0.027 0.001 PHE A 322 TYR 0.011 0.001 TYR A 306 ARG 0.001 0.000 ARG A 57 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 30 time to evaluate : 0.341 Fit side-chains REVERT: A 256 LYS cc_start: 0.5629 (mmtt) cc_final: 0.4109 (tttp) REVERT: A 257 ARG cc_start: 0.8121 (mtm110) cc_final: 0.7876 (ttm110) outliers start: 6 outliers final: 5 residues processed: 35 average time/residue: 0.1707 time to fit residues: 7.4946 Evaluate side-chains 33 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 28 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 CYS Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 385 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 24 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 41 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 3 optimal weight: 10.0000 chunk 13 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 413 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3513 Z= 0.203 Angle : 0.526 5.214 4791 Z= 0.273 Chirality : 0.040 0.117 544 Planarity : 0.005 0.043 581 Dihedral : 4.130 22.077 463 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.22 % Allowed : 14.13 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.41), residues: 431 helix: 1.70 (0.29), residues: 319 sheet: None (None), residues: 0 loop : -0.61 (0.62), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 244 HIS 0.003 0.001 HIS A 298 PHE 0.021 0.001 PHE A 322 TYR 0.010 0.001 TYR A 306 ARG 0.001 0.000 ARG A 364 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 29 time to evaluate : 0.396 Fit side-chains REVERT: A 256 LYS cc_start: 0.5686 (mmtt) cc_final: 0.4108 (tttp) REVERT: A 257 ARG cc_start: 0.8122 (mtm110) cc_final: 0.7718 (ttm110) outliers start: 8 outliers final: 6 residues processed: 35 average time/residue: 0.1506 time to fit residues: 6.9040 Evaluate side-chains 34 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 28 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 CYS Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 385 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 30 optimal weight: 0.0170 chunk 23 optimal weight: 0.5980 chunk 35 optimal weight: 3.9990 chunk 41 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 overall best weight: 0.5218 ------------------------------------------------------------------------------- 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: 0.8200 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3513 Z= 0.172 Angle : 0.513 5.202 4791 Z= 0.266 Chirality : 0.039 0.112 544 Planarity : 0.005 0.043 581 Dihedral : 4.088 22.445 463 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.94 % Allowed : 14.96 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.41), residues: 431 helix: 1.83 (0.29), residues: 319 sheet: None (None), residues: 0 loop : -0.60 (0.61), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 240 HIS 0.003 0.001 HIS A 298 PHE 0.034 0.001 PHE A 322 TYR 0.010 0.001 TYR A 306 ARG 0.001 0.000 ARG A 353 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 29 time to evaluate : 0.326 Fit side-chains REVERT: A 256 LYS cc_start: 0.5680 (mmtt) cc_final: 0.4105 (tttp) REVERT: A 257 ARG cc_start: 0.8102 (mtm110) cc_final: 0.7716 (ttm110) REVERT: A 305 PHE cc_start: 0.7074 (OUTLIER) cc_final: 0.6570 (t80) outliers start: 7 outliers final: 6 residues processed: 34 average time/residue: 0.1573 time to fit residues: 7.0246 Evaluate side-chains 35 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 28 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 CYS Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 224 MET Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 385 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 28 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 3 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 36 optimal weight: 0.0770 chunk 38 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 30 optimal weight: 0.5980 overall best weight: 0.4938 ------------------------------------------------------------------------------- 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: 0.8194 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3513 Z= 0.167 Angle : 0.509 5.189 4791 Z= 0.263 Chirality : 0.039 0.122 544 Planarity : 0.005 0.043 581 Dihedral : 4.059 22.170 463 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.49 % Allowed : 14.40 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.41), residues: 431 helix: 1.91 (0.29), residues: 319 sheet: None (None), residues: 0 loop : -0.54 (0.62), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 244 HIS 0.003 0.001 HIS A 298 PHE 0.028 0.001 PHE A 322 TYR 0.010 0.001 TYR A 306 ARG 0.001 0.000 ARG A 364 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 30 time to evaluate : 0.387 Fit side-chains REVERT: A 256 LYS cc_start: 0.5696 (mmtt) cc_final: 0.4117 (tttp) REVERT: A 257 ARG cc_start: 0.8091 (mtm110) cc_final: 0.7713 (ttm110) REVERT: A 305 PHE cc_start: 0.7067 (OUTLIER) cc_final: 0.6577 (t80) outliers start: 9 outliers final: 6 residues processed: 35 average time/residue: 0.1609 time to fit residues: 7.2923 Evaluate side-chains 34 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 27 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 CYS Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 224 MET Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 385 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 11 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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: 0.8215 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3513 Z= 0.204 Angle : 0.529 5.201 4791 Z= 0.274 Chirality : 0.040 0.113 544 Planarity : 0.005 0.043 581 Dihedral : 4.081 22.370 463 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.77 % Allowed : 14.40 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.41), residues: 431 helix: 1.83 (0.29), residues: 319 sheet: None (None), residues: 0 loop : -0.51 (0.62), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 244 HIS 0.003 0.001 HIS A 298 PHE 0.027 0.001 PHE A 322 TYR 0.009 0.001 TYR A 306 ARG 0.001 0.000 ARG A 353 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 30 time to evaluate : 0.373 Fit side-chains REVERT: A 256 LYS cc_start: 0.5733 (mmtt) cc_final: 0.4164 (tttp) REVERT: A 257 ARG cc_start: 0.8095 (mtm110) cc_final: 0.7727 (ttm110) REVERT: A 305 PHE cc_start: 0.7115 (OUTLIER) cc_final: 0.6600 (t80) outliers start: 10 outliers final: 7 residues processed: 35 average time/residue: 0.1577 time to fit residues: 7.3258 Evaluate side-chains 36 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 28 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 CYS Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 224 MET Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 385 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 34 optimal weight: 3.9990 chunk 3 optimal weight: 0.0870 chunk 26 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 9 optimal weight: 0.5980 chunk 14 optimal weight: 0.9980 overall best weight: 0.6758 ------------------------------------------------------------------------------- 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: 0.8210 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3513 Z= 0.206 Angle : 0.531 5.201 4791 Z= 0.275 Chirality : 0.040 0.114 544 Planarity : 0.005 0.044 581 Dihedral : 4.083 22.275 463 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.49 % Allowed : 15.24 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.41), residues: 431 helix: 1.85 (0.29), residues: 319 sheet: None (None), residues: 0 loop : -0.45 (0.62), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 244 HIS 0.003 0.001 HIS A 298 PHE 0.026 0.001 PHE A 322 TYR 0.010 0.001 TYR A 306 ARG 0.001 0.000 ARG A 364 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 30 time to evaluate : 0.375 Fit side-chains REVERT: A 256 LYS cc_start: 0.5729 (mmtt) cc_final: 0.4145 (tttp) REVERT: A 257 ARG cc_start: 0.8098 (mtm110) cc_final: 0.7736 (ttm110) REVERT: A 305 PHE cc_start: 0.7107 (OUTLIER) cc_final: 0.6572 (t80) outliers start: 9 outliers final: 7 residues processed: 35 average time/residue: 0.1490 time to fit residues: 6.7620 Evaluate side-chains 38 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 30 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 CYS Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 224 MET Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 385 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 35 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 6 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 24 optimal weight: 0.5980 chunk 39 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.3600 r_free = 0.3600 target = 0.139601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.105104 restraints weight = 3874.303| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 1.85 r_work: 0.3004 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3513 Z= 0.225 Angle : 0.538 5.211 4791 Z= 0.280 Chirality : 0.041 0.115 544 Planarity : 0.005 0.044 581 Dihedral : 4.114 22.376 463 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.22 % Allowed : 15.51 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.41), residues: 431 helix: 1.82 (0.29), residues: 319 sheet: None (None), residues: 0 loop : -0.40 (0.63), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 244 HIS 0.003 0.001 HIS A 298 PHE 0.025 0.001 PHE A 322 TYR 0.009 0.001 TYR A 306 ARG 0.001 0.000 ARG A 364 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1144.75 seconds wall clock time: 21 minutes 22.20 seconds (1282.20 seconds total)