Starting phenix.real_space_refine on Fri Aug 2 14:33:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qcy_18337/08_2024/8qcy_18337.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qcy_18337/08_2024/8qcy_18337.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/8qcy_18337/08_2024/8qcy_18337.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qcy_18337/08_2024/8qcy_18337.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qcy_18337/08_2024/8qcy_18337.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qcy_18337/08_2024/8qcy_18337.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= 0.008 sd= 0.189 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 19 5.16 5 C 2176 2.51 5 N 520 2.21 5 O 558 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 241": "OE1" <-> "OE2" Residue "A ASP 244": "OD1" <-> "OD2" Residue "A GLU 274": "OE1" <-> "OE2" Residue "A GLU 342": "OE1" <-> "OE2" Residue "A GLU 343": "OE1" <-> "OE2" Residue "A PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 472": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 3273 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3273 Classifications: {'peptide': 421} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 405} Chain breaks: 1 Time building chain proxies: 2.57, per 1000 atoms: 0.79 Number of scatterers: 3273 At special positions: 0 Unit cell: (82.512, 53.862, 64.176, 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 19 16.00 O 558 8.00 N 520 7.00 C 2176 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.34 Conformation dependent library (CDL) restraints added in 588.2 milliseconds 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 770 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 0 sheets defined 91.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 82 through 108 removed outlier: 4.462A pdb=" N ALA A 86 " --> pdb=" O ARG A 82 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N TYR A 105 " --> pdb=" O GLN A 101 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N GLY A 106 " --> pdb=" O TRP A 102 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE A 108 " --> pdb=" O GLN A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 117 removed outlier: 3.663A pdb=" N HIS A 114 " --> pdb=" O ASN A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 149 removed outlier: 3.605A pdb=" N ILE A 123 " --> pdb=" O SER A 119 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N SER A 127 " --> pdb=" O ILE A 123 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N TYR A 130 " --> pdb=" O LEU A 126 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N MET A 131 " --> pdb=" O SER A 127 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU A 132 " --> pdb=" O MET A 128 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ILE A 135 " --> pdb=" O MET A 131 " (cutoff:3.500A) Proline residue: A 136 - end of helix removed outlier: 4.848A pdb=" N LEU A 139 " --> pdb=" O ILE A 135 " (cutoff:3.500A) Proline residue: A 140 - end of helix removed outlier: 4.380A pdb=" N GLU A 146 " --> pdb=" O ALA A 142 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS A 147 " --> pdb=" O TRP A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 167 removed outlier: 3.905A pdb=" N ILE A 153 " --> pdb=" O GLY A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 171 Processing helix chain 'A' and resid 176 through 193 removed outlier: 3.745A pdb=" N THR A 180 " --> pdb=" O LEU A 176 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL A 192 " --> pdb=" O SER A 188 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N PHE A 193 " --> pdb=" O VAL A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 206 Processing helix chain 'A' and resid 210 through 232 removed outlier: 3.578A pdb=" N CYS A 215 " --> pdb=" O VAL A 211 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE A 226 " --> pdb=" O ASN A 222 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU A 231 " --> pdb=" O ALA A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 237 Processing helix chain 'A' and resid 242 through 271 removed outlier: 3.545A pdb=" N TYR A 248 " --> pdb=" O ASP A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 291 removed outlier: 3.546A pdb=" N ALA A 289 " --> pdb=" O SER A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 307 Processing helix chain 'A' and resid 307 through 339 removed outlier: 4.859A pdb=" N ASN A 332 " --> pdb=" O SER A 328 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N ARG A 333 " --> pdb=" O THR A 329 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N HIS A 338 " --> pdb=" O MET A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 372 removed outlier: 3.670A pdb=" N VAL A 354 " --> pdb=" O GLY A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 396 Processing helix chain 'A' and resid 397 through 399 No H-bonds generated for 'chain 'A' and resid 397 through 399' Processing helix chain 'A' and resid 400 through 430 removed outlier: 3.852A pdb=" N VAL A 404 " --> pdb=" O HIS A 400 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE A 405 " --> pdb=" O LEU A 401 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ILE A 406 " --> pdb=" O TRP A 402 " (cutoff:3.500A) Proline residue: A 420 - end of helix Processing helix chain 'A' and resid 434 through 465 Processing helix chain 'A' and resid 465 through 486 removed outlier: 3.539A pdb=" N GLY A 469 " --> pdb=" O GLY A 465 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE A 486 " --> pdb=" O ALA A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 500 removed outlier: 3.748A pdb=" N LYS A 495 " --> pdb=" O LEU A 491 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N THR A 500 " --> pdb=" O ALA A 496 " (cutoff:3.500A) 266 hydrogen bonds defined for protein. 795 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: 0.95 Time building geometry restraints manager: 1.46 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: 975 1.34 - 1.46: 521 1.46 - 1.57: 1828 1.57 - 1.69: 0 1.69 - 1.81: 31 Bond restraints: 3355 Sorted by residual: bond pdb=" N ASN A 307 " pdb=" CA ASN A 307 " ideal model delta sigma weight residual 1.460 1.488 -0.028 1.28e-02 6.10e+03 4.80e+00 bond pdb=" C ASN A 307 " pdb=" O ASN A 307 " ideal model delta sigma weight residual 1.235 1.245 -0.010 1.15e-02 7.56e+03 7.37e-01 bond pdb=" CG LEU A 169 " pdb=" CD1 LEU A 169 " ideal model delta sigma weight residual 1.521 1.493 0.028 3.30e-02 9.18e+02 7.30e-01 bond pdb=" CG LEU A 169 " pdb=" CD2 LEU A 169 " ideal model delta sigma weight residual 1.521 1.493 0.028 3.30e-02 9.18e+02 6.95e-01 bond pdb=" C MET A 197 " pdb=" N PRO A 198 " ideal model delta sigma weight residual 1.334 1.347 -0.013 1.51e-02 4.39e+03 6.91e-01 ... (remaining 3350 not shown) Histogram of bond angle deviations from ideal: 98.69 - 105.75: 69 105.75 - 112.81: 1829 112.81 - 119.87: 1036 119.87 - 126.93: 1591 126.93 - 133.99: 44 Bond angle restraints: 4569 Sorted by residual: angle pdb=" N MET A 197 " pdb=" CA MET A 197 " pdb=" C MET A 197 " ideal model delta sigma weight residual 109.81 117.15 -7.34 2.21e+00 2.05e-01 1.10e+01 angle pdb=" N ILE A 103 " pdb=" CA ILE A 103 " pdb=" CB ILE A 103 " ideal model delta sigma weight residual 112.26 108.57 3.69 1.29e+00 6.01e-01 8.19e+00 angle pdb=" C TYR A 134 " pdb=" N ILE A 135 " pdb=" CA ILE A 135 " ideal model delta sigma weight residual 120.33 122.52 -2.19 8.00e-01 1.56e+00 7.48e+00 angle pdb=" CG1 ILE A 108 " pdb=" CB ILE A 108 " pdb=" CG2 ILE A 108 " ideal model delta sigma weight residual 110.70 103.41 7.29 3.00e+00 1.11e-01 5.90e+00 angle pdb=" N PRO A 233 " pdb=" CA PRO A 233 " pdb=" C PRO A 233 " ideal model delta sigma weight residual 110.70 113.63 -2.93 1.22e+00 6.72e-01 5.75e+00 ... (remaining 4564 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.61: 1803 17.61 - 35.22: 102 35.22 - 52.83: 22 52.83 - 70.44: 1 70.44 - 88.05: 2 Dihedral angle restraints: 1930 sinusoidal: 722 harmonic: 1208 Sorted by residual: dihedral pdb=" CA LEU A 169 " pdb=" C LEU A 169 " pdb=" N GLY A 170 " pdb=" CA GLY A 170 " ideal model delta harmonic sigma weight residual 180.00 161.96 18.04 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CA TYR A 94 " pdb=" C TYR A 94 " pdb=" N SER A 95 " pdb=" CA SER A 95 " ideal model delta harmonic sigma weight residual 180.00 162.58 17.42 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CA ILE A 270 " pdb=" C ILE A 270 " pdb=" N VAL A 271 " pdb=" CA VAL A 271 " ideal model delta harmonic sigma weight residual -180.00 -163.74 -16.26 0 5.00e+00 4.00e-02 1.06e+01 ... (remaining 1927 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 336 0.031 - 0.062: 145 0.062 - 0.093: 44 0.093 - 0.124: 15 0.124 - 0.155: 2 Chirality restraints: 542 Sorted by residual: chirality pdb=" CB ILE A 108 " pdb=" CA ILE A 108 " pdb=" CG1 ILE A 108 " pdb=" CG2 ILE A 108 " both_signs ideal model delta sigma weight residual False 2.64 2.80 -0.15 2.00e-01 2.50e+01 5.97e-01 chirality pdb=" CA MET A 197 " pdb=" N MET A 197 " pdb=" C MET A 197 " pdb=" CB MET A 197 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.97e-01 chirality pdb=" CA LEU A 169 " pdb=" N LEU A 169 " pdb=" C LEU A 169 " pdb=" CB LEU A 169 " both_signs ideal model delta sigma weight residual False 2.51 2.40 0.11 2.00e-01 2.50e+01 3.25e-01 ... (remaining 539 not shown) Planarity restraints: 553 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 130 " 0.016 2.00e-02 2.50e+03 1.72e-02 5.94e+00 pdb=" CG TYR A 130 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TYR A 130 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR A 130 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR A 130 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR A 130 " 0.010 2.00e-02 2.50e+03 pdb=" CZ TYR A 130 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 130 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 232 " -0.023 5.00e-02 4.00e+02 3.43e-02 1.88e+00 pdb=" N PRO A 233 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 233 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 233 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 431 " 0.021 5.00e-02 4.00e+02 3.18e-02 1.62e+00 pdb=" N PRO A 432 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO A 432 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 432 " 0.016 5.00e-02 4.00e+02 ... (remaining 550 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 758 2.78 - 3.31: 3431 3.31 - 3.84: 5463 3.84 - 4.37: 6729 4.37 - 4.90: 11431 Nonbonded interactions: 27812 Sorted by model distance: nonbonded pdb=" O LEU A 429 " pdb=" NH2 ARG A 492 " model vdw 2.245 3.120 nonbonded pdb=" OG SER A 203 " pdb=" NE2 GLN A 284 " model vdw 2.256 3.120 nonbonded pdb=" OG SER A 107 " pdb=" O GLY A 229 " model vdw 2.300 3.040 nonbonded pdb=" O GLU A 435 " pdb=" OG SER A 439 " model vdw 2.309 3.040 nonbonded pdb=" O GLY A 450 " pdb=" OG1 THR A 454 " model vdw 2.327 3.040 ... (remaining 27807 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.210 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: 0.030 Process input model: 13.920 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 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 : 0.004 0.036 3355 Z= 0.230 Angle : 0.582 7.336 4569 Z= 0.316 Chirality : 0.040 0.155 542 Planarity : 0.004 0.034 553 Dihedral : 11.881 88.055 1160 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.40 (0.40), residues: 417 helix: 0.61 (0.27), residues: 341 sheet: None (None), residues: 0 loop : -0.88 (0.71), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 125 HIS 0.001 0.000 HIS A 338 PHE 0.016 0.002 PHE A 272 TYR 0.041 0.002 TYR A 130 ARG 0.002 0.000 ARG A 84 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 0.350 Fit side-chains REVERT: A 245 GLU cc_start: 0.6516 (tp30) cc_final: 0.5975 (mm-30) REVERT: A 332 ASN cc_start: 0.7568 (m-40) cc_final: 0.7212 (t0) REVERT: A 342 GLU cc_start: 0.8014 (mm-30) cc_final: 0.7492 (mm-30) outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 1.0510 time to fit residues: 61.9960 Evaluate side-chains 38 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 20 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 38 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 284 GLN A 459 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3355 Z= 0.228 Angle : 0.633 8.328 4569 Z= 0.323 Chirality : 0.042 0.168 542 Planarity : 0.005 0.030 553 Dihedral : 4.324 17.115 451 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.56 % Allowed : 8.81 % Favored : 88.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.51 (0.40), residues: 417 helix: 1.38 (0.26), residues: 347 sheet: None (None), residues: 0 loop : -0.71 (0.77), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 125 HIS 0.001 0.000 HIS A 338 PHE 0.019 0.002 PHE A 472 TYR 0.022 0.001 TYR A 94 ARG 0.002 0.000 ARG A 333 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 45 time to evaluate : 0.360 Fit side-chains REVERT: A 96 MET cc_start: 0.8011 (OUTLIER) cc_final: 0.7575 (ptp) REVERT: A 255 TYR cc_start: 0.8279 (m-80) cc_final: 0.8068 (m-80) REVERT: A 376 GLU cc_start: 0.7723 (mp0) cc_final: 0.7523 (mp0) outliers start: 9 outliers final: 2 residues processed: 49 average time/residue: 0.7064 time to fit residues: 36.4340 Evaluate side-chains 42 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 39 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 172 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 19 optimal weight: 0.0010 overall best weight: 0.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3355 Z= 0.208 Angle : 0.593 8.544 4569 Z= 0.295 Chirality : 0.041 0.166 542 Planarity : 0.004 0.036 553 Dihedral : 4.280 16.950 451 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.84 % Allowed : 11.65 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.40), residues: 417 helix: 1.54 (0.26), residues: 349 sheet: None (None), residues: 0 loop : -0.90 (0.75), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 125 HIS 0.001 0.000 HIS A 338 PHE 0.020 0.002 PHE A 472 TYR 0.025 0.001 TYR A 94 ARG 0.001 0.000 ARG A 84 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 43 time to evaluate : 0.365 Fit side-chains REVERT: A 96 MET cc_start: 0.8002 (OUTLIER) cc_final: 0.7574 (ptp) REVERT: A 255 TYR cc_start: 0.8477 (m-80) cc_final: 0.8180 (m-80) REVERT: A 327 LEU cc_start: 0.6713 (tp) cc_final: 0.6494 (mt) REVERT: A 376 GLU cc_start: 0.7753 (mp0) cc_final: 0.7469 (mp0) outliers start: 10 outliers final: 3 residues processed: 48 average time/residue: 0.7630 time to fit residues: 38.4717 Evaluate side-chains 43 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 39 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain A residue 290 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 0.2980 chunk 18 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 40 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3355 Z= 0.213 Angle : 0.589 8.892 4569 Z= 0.294 Chirality : 0.041 0.188 542 Planarity : 0.004 0.037 553 Dihedral : 4.256 18.245 451 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.69 % Allowed : 13.92 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.40), residues: 417 helix: 1.60 (0.26), residues: 353 sheet: None (None), residues: 0 loop : -0.99 (0.76), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 125 HIS 0.001 0.000 HIS A 338 PHE 0.023 0.002 PHE A 472 TYR 0.024 0.001 TYR A 94 ARG 0.001 0.000 ARG A 84 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 44 time to evaluate : 0.332 Fit side-chains REVERT: A 82 ARG cc_start: 0.7250 (OUTLIER) cc_final: 0.6949 (mtp85) REVERT: A 96 MET cc_start: 0.8011 (OUTLIER) cc_final: 0.7575 (ptp) REVERT: A 255 TYR cc_start: 0.8586 (m-80) cc_final: 0.8253 (m-80) REVERT: A 382 TYR cc_start: 0.8693 (t80) cc_final: 0.8453 (t80) outliers start: 13 outliers final: 5 residues processed: 50 average time/residue: 0.8581 time to fit residues: 44.7834 Evaluate side-chains 46 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 39 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ARG Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 471 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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: 0.7463 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3355 Z= 0.237 Angle : 0.606 9.351 4569 Z= 0.301 Chirality : 0.043 0.194 542 Planarity : 0.004 0.040 553 Dihedral : 4.318 18.515 451 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.84 % Allowed : 15.06 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.84 (0.40), residues: 417 helix: 1.65 (0.26), residues: 353 sheet: None (None), residues: 0 loop : -1.14 (0.74), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 125 HIS 0.001 0.000 HIS A 338 PHE 0.023 0.002 PHE A 472 TYR 0.025 0.001 TYR A 94 ARG 0.002 0.000 ARG A 282 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 38 time to evaluate : 0.360 Fit side-chains REVERT: A 82 ARG cc_start: 0.7304 (OUTLIER) cc_final: 0.7002 (mtp85) REVERT: A 113 MET cc_start: 0.6406 (mtm) cc_final: 0.6034 (mmm) REVERT: A 376 GLU cc_start: 0.7804 (mp0) cc_final: 0.7588 (mp0) outliers start: 10 outliers final: 6 residues processed: 42 average time/residue: 0.8789 time to fit residues: 38.5995 Evaluate side-chains 42 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 35 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ARG Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 471 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 0.5980 chunk 40 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 chunk 18 optimal weight: 5.9990 chunk 3 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 21 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 23 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3355 Z= 0.192 Angle : 0.566 8.842 4569 Z= 0.280 Chirality : 0.041 0.173 542 Planarity : 0.004 0.038 553 Dihedral : 4.226 18.139 451 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.84 % Allowed : 15.62 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 2.06 (0.40), residues: 417 helix: 1.82 (0.26), residues: 354 sheet: None (None), residues: 0 loop : -1.25 (0.74), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 125 HIS 0.001 0.000 HIS A 338 PHE 0.022 0.002 PHE A 472 TYR 0.022 0.001 TYR A 94 ARG 0.001 0.000 ARG A 84 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 44 time to evaluate : 0.381 Fit side-chains REVERT: A 82 ARG cc_start: 0.7236 (OUTLIER) cc_final: 0.6933 (mtp85) REVERT: A 96 MET cc_start: 0.7975 (OUTLIER) cc_final: 0.7597 (ptp) REVERT: A 255 TYR cc_start: 0.8551 (m-80) cc_final: 0.8330 (m-80) REVERT: A 376 GLU cc_start: 0.7844 (mp0) cc_final: 0.7495 (mp0) REVERT: A 401 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7625 (tt) REVERT: A 433 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.6306 (mp0) outliers start: 10 outliers final: 5 residues processed: 48 average time/residue: 0.9154 time to fit residues: 45.8676 Evaluate side-chains 44 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 35 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ARG Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 433 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 40 optimal weight: 0.3980 chunk 25 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 18 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 497 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3355 Z= 0.193 Angle : 0.601 10.416 4569 Z= 0.289 Chirality : 0.042 0.186 542 Planarity : 0.004 0.040 553 Dihedral : 4.219 17.768 451 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.41 % Allowed : 16.19 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 2.16 (0.40), residues: 417 helix: 1.90 (0.26), residues: 354 sheet: None (None), residues: 0 loop : -1.28 (0.74), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 125 HIS 0.001 0.000 HIS A 249 PHE 0.023 0.002 PHE A 472 TYR 0.023 0.001 TYR A 94 ARG 0.001 0.000 ARG A 151 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 39 time to evaluate : 0.374 Fit side-chains REVERT: A 82 ARG cc_start: 0.7241 (OUTLIER) cc_final: 0.6947 (mtp85) REVERT: A 96 MET cc_start: 0.7957 (OUTLIER) cc_final: 0.7614 (ptp) REVERT: A 113 MET cc_start: 0.6253 (mtm) cc_final: 0.5768 (mmm) REVERT: A 255 TYR cc_start: 0.8636 (m-80) cc_final: 0.8331 (m-80) REVERT: A 376 GLU cc_start: 0.7920 (mp0) cc_final: 0.7562 (mp0) REVERT: A 433 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.6295 (mp0) outliers start: 12 outliers final: 6 residues processed: 45 average time/residue: 0.9093 time to fit residues: 42.6908 Evaluate side-chains 45 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 36 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ARG Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain A residue 471 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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: 0.7445 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3355 Z= 0.207 Angle : 0.610 9.660 4569 Z= 0.295 Chirality : 0.042 0.178 542 Planarity : 0.004 0.039 553 Dihedral : 4.239 17.720 451 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.12 % Allowed : 16.76 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 2.12 (0.40), residues: 417 helix: 1.88 (0.26), residues: 354 sheet: None (None), residues: 0 loop : -1.31 (0.74), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 125 HIS 0.002 0.000 HIS A 249 PHE 0.023 0.002 PHE A 472 TYR 0.024 0.001 TYR A 94 ARG 0.001 0.000 ARG A 84 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 40 time to evaluate : 0.329 Fit side-chains REVERT: A 82 ARG cc_start: 0.7219 (OUTLIER) cc_final: 0.6917 (mtp85) REVERT: A 113 MET cc_start: 0.6295 (mtm) cc_final: 0.5785 (mmm) REVERT: A 332 ASN cc_start: 0.7216 (m-40) cc_final: 0.6864 (t0) REVERT: A 376 GLU cc_start: 0.7935 (mp0) cc_final: 0.7621 (mp0) REVERT: A 433 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.6273 (mp0) outliers start: 11 outliers final: 7 residues processed: 46 average time/residue: 0.7245 time to fit residues: 35.0773 Evaluate side-chains 48 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 39 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ARG Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain A residue 471 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 18 optimal weight: 4.9990 chunk 27 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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: 0.7451 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3355 Z= 0.220 Angle : 0.610 9.503 4569 Z= 0.296 Chirality : 0.042 0.174 542 Planarity : 0.004 0.038 553 Dihedral : 4.251 18.467 451 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.12 % Allowed : 17.90 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 2.09 (0.40), residues: 417 helix: 1.85 (0.26), residues: 354 sheet: None (None), residues: 0 loop : -1.29 (0.74), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 125 HIS 0.001 0.001 HIS A 249 PHE 0.023 0.002 PHE A 472 TYR 0.025 0.001 TYR A 94 ARG 0.001 0.000 ARG A 84 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 43 time to evaluate : 0.305 Fit side-chains REVERT: A 82 ARG cc_start: 0.7224 (OUTLIER) cc_final: 0.6922 (mtp85) REVERT: A 255 TYR cc_start: 0.8573 (m-80) cc_final: 0.8336 (m-80) REVERT: A 332 ASN cc_start: 0.7266 (m-40) cc_final: 0.6850 (t0) REVERT: A 376 GLU cc_start: 0.7920 (mp0) cc_final: 0.7620 (mp0) REVERT: A 433 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.6290 (mp0) outliers start: 11 outliers final: 7 residues processed: 49 average time/residue: 0.7215 time to fit residues: 37.1877 Evaluate side-chains 48 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 39 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ARG Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain A residue 471 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 10 optimal weight: 0.6980 chunk 30 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 6 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 397 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3355 Z= 0.212 Angle : 0.625 12.255 4569 Z= 0.299 Chirality : 0.042 0.168 542 Planarity : 0.004 0.038 553 Dihedral : 4.237 18.231 451 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.84 % Allowed : 19.89 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 2.19 (0.40), residues: 417 helix: 1.92 (0.26), residues: 354 sheet: None (None), residues: 0 loop : -1.23 (0.75), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 337 HIS 0.001 0.000 HIS A 249 PHE 0.022 0.002 PHE A 472 TYR 0.023 0.001 TYR A 94 ARG 0.001 0.000 ARG A 493 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 42 time to evaluate : 0.380 Fit side-chains REVERT: A 82 ARG cc_start: 0.7266 (OUTLIER) cc_final: 0.6983 (mtp85) REVERT: A 96 MET cc_start: 0.7956 (OUTLIER) cc_final: 0.7596 (ptp) REVERT: A 332 ASN cc_start: 0.7190 (m-40) cc_final: 0.6893 (t0) REVERT: A 376 GLU cc_start: 0.7928 (mp0) cc_final: 0.7625 (mp0) REVERT: A 433 GLU cc_start: 0.7570 (OUTLIER) cc_final: 0.6273 (mp0) outliers start: 10 outliers final: 6 residues processed: 47 average time/residue: 0.8017 time to fit residues: 39.5482 Evaluate side-chains 48 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 39 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ARG Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain A residue 471 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 38 optimal weight: 0.4980 chunk 22 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3532 r_free = 0.3532 target = 0.128567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.108966 restraints weight = 4256.133| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.32 r_work: 0.3120 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6982 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3355 Z= 0.214 Angle : 0.607 10.032 4569 Z= 0.295 Chirality : 0.041 0.161 542 Planarity : 0.004 0.039 553 Dihedral : 4.238 18.047 451 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.56 % Allowed : 20.17 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 2.17 (0.40), residues: 417 helix: 1.91 (0.26), residues: 354 sheet: None (None), residues: 0 loop : -1.24 (0.74), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 337 HIS 0.001 0.000 HIS A 249 PHE 0.022 0.002 PHE A 472 TYR 0.024 0.001 TYR A 94 ARG 0.001 0.000 ARG A 493 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1337.71 seconds wall clock time: 24 minutes 19.58 seconds (1459.58 seconds total)