Starting phenix.real_space_refine on Thu Jul 18 19:09:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qcy_18337/07_2024/8qcy_18337.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qcy_18337/07_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_18337/07_2024/8qcy_18337.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qcy_18337/07_2024/8qcy_18337.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qcy_18337/07_2024/8qcy_18337.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qcy_18337/07_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-5388/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: 2.61, per 1000 atoms: 0.80 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: 1.43 Conformation dependent library (CDL) restraints added in 588.7 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: 0.31 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: 0.88 Time building geometry restraints manager: 1.56 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 2.520 nonbonded pdb=" OG SER A 203 " pdb=" NE2 GLN A 284 " model vdw 2.256 2.520 nonbonded pdb=" OG SER A 107 " pdb=" O GLY A 229 " model vdw 2.300 2.440 nonbonded pdb=" O GLU A 435 " pdb=" OG SER A 439 " model vdw 2.309 2.440 nonbonded pdb=" O GLY A 450 " pdb=" OG1 THR A 454 " model vdw 2.327 2.440 ... (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: 0.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 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:13.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.620 ------------------------------------------------------------------------------- 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 : 0.373 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: 1.0255 time to fit residues: 60.4907 Evaluate side-chains 38 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.366 ------------------------------------------------------------------------------- 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: 5.9990 chunk 31 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 20 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 38 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 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 284 GLN A 459 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3355 Z= 0.220 Angle : 0.624 8.050 4569 Z= 0.317 Chirality : 0.042 0.157 542 Planarity : 0.004 0.031 553 Dihedral : 4.362 17.767 451 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.27 % Allowed : 8.52 % Favored : 89.20 % 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: 1.39 (0.27), residues: 346 sheet: None (None), residues: 0 loop : -0.73 (0.76), residues: 71 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 0.024 0.001 TYR A 94 ARG 0.001 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 55 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 47 time to evaluate : 0.361 Fit side-chains REVERT: A 96 MET cc_start: 0.8003 (OUTLIER) cc_final: 0.7575 (ptp) REVERT: A 255 TYR cc_start: 0.8294 (m-80) cc_final: 0.8060 (m-80) outliers start: 8 outliers final: 2 residues processed: 51 average time/residue: 0.6869 time to fit residues: 36.9273 Evaluate side-chains 44 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 41 time to evaluate : 0.362 ------------------------------------------------------------------------------- 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: 0.7980 chunk 25 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 38 optimal weight: 0.5980 chunk 41 optimal weight: 0.0980 chunk 34 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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: 0.7429 moved from start: 0.2282 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= 0.194 Angle : 0.586 8.394 4569 Z= 0.291 Chirality : 0.041 0.153 542 Planarity : 0.004 0.036 553 Dihedral : 4.251 17.132 451 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.84 % Allowed : 11.08 % Favored : 86.08 % 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: 1.67 (0.40), residues: 417 helix: 1.52 (0.27), residues: 352 sheet: None (None), residues: 0 loop : -0.99 (0.78), residues: 65 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 0.023 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 54 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 44 time to evaluate : 0.356 Fit side-chains REVERT: A 82 ARG cc_start: 0.7209 (OUTLIER) cc_final: 0.6935 (mtp85) REVERT: A 96 MET cc_start: 0.7988 (OUTLIER) cc_final: 0.7579 (ptp) REVERT: A 255 TYR cc_start: 0.8470 (m-80) cc_final: 0.8104 (m-80) outliers start: 10 outliers final: 3 residues processed: 50 average time/residue: 0.8094 time to fit residues: 42.2773 Evaluate side-chains 42 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 37 time to evaluate : 0.298 ------------------------------------------------------------------------------- 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 158 SER Chi-restraints excluded: chain A residue 188 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 0.1980 chunk 18 optimal weight: 0.4980 chunk 25 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 chunk 40 optimal weight: 0.0270 chunk 20 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 overall best weight: 0.4038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN A 497 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.2674 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= 0.168 Angle : 0.557 8.840 4569 Z= 0.275 Chirality : 0.040 0.151 542 Planarity : 0.004 0.036 553 Dihedral : 4.158 18.007 451 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.41 % Allowed : 13.92 % Favored : 82.67 % 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: 2.03 (0.40), residues: 417 helix: 1.74 (0.27), residues: 356 sheet: None (None), residues: 0 loop : -0.91 (0.80), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 125 HIS 0.001 0.000 HIS A 249 PHE 0.019 0.001 PHE A 472 TYR 0.022 0.001 TYR A 94 ARG 0.001 0.000 ARG A 493 *********************** 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 52 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 40 time to evaluate : 0.272 Fit side-chains REVERT: A 96 MET cc_start: 0.7990 (OUTLIER) cc_final: 0.7575 (ptp) REVERT: A 255 TYR cc_start: 0.8488 (m-80) cc_final: 0.8106 (m-80) REVERT: A 305 PHE cc_start: 0.7639 (m-80) cc_final: 0.7367 (m-80) REVERT: A 334 MET cc_start: 0.8411 (mtm) cc_final: 0.8068 (mtm) REVERT: A 376 GLU cc_start: 0.7731 (mp0) cc_final: 0.7470 (mp0) outliers start: 12 outliers final: 3 residues processed: 47 average time/residue: 0.7929 time to fit residues: 39.0063 Evaluate side-chains 40 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 36 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 439 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 4.9990 chunk 16 optimal weight: 0.0980 chunk 34 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 20 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 13 optimal weight: 0.4980 chunk 8 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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: 0.7404 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3355 Z= 0.173 Angle : 0.572 8.951 4569 Z= 0.277 Chirality : 0.041 0.162 542 Planarity : 0.004 0.038 553 Dihedral : 4.182 18.382 451 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.56 % Allowed : 14.77 % Favored : 82.67 % 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: 2.15 (0.40), residues: 417 helix: 1.91 (0.27), residues: 351 sheet: None (None), residues: 0 loop : -1.25 (0.76), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 125 HIS 0.001 0.000 HIS A 249 PHE 0.019 0.001 PHE A 472 TYR 0.023 0.001 TYR A 94 ARG 0.001 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 49 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 40 time to evaluate : 0.341 Fit side-chains REVERT: A 82 ARG cc_start: 0.7294 (OUTLIER) cc_final: 0.7007 (mtp85) REVERT: A 96 MET cc_start: 0.8007 (OUTLIER) cc_final: 0.7571 (ptp) REVERT: A 113 MET cc_start: 0.6180 (mtm) cc_final: 0.5767 (mmm) REVERT: A 255 TYR cc_start: 0.8591 (m-80) cc_final: 0.8210 (m-80) REVERT: A 305 PHE cc_start: 0.7577 (m-80) cc_final: 0.7337 (m-80) REVERT: A 334 MET cc_start: 0.8362 (mtm) cc_final: 0.8043 (mtm) REVERT: A 376 GLU cc_start: 0.7806 (mp0) cc_final: 0.7509 (mp0) outliers start: 9 outliers final: 3 residues processed: 45 average time/residue: 0.7331 time to fit residues: 34.6191 Evaluate side-chains 40 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 35 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 137 LEU Chi-restraints excluded: chain A residue 172 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: 0.9980 chunk 40 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 21 optimal weight: 7.9990 chunk 39 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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: 0.7430 moved from start: 0.2795 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= 0.201 Angle : 0.561 9.168 4569 Z= 0.276 Chirality : 0.041 0.161 542 Planarity : 0.004 0.039 553 Dihedral : 4.192 19.072 451 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.12 % Allowed : 14.77 % 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: 2.18 (0.40), residues: 417 helix: 1.96 (0.26), residues: 351 sheet: None (None), residues: 0 loop : -1.38 (0.74), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 125 HIS 0.002 0.001 HIS A 249 PHE 0.017 0.001 PHE A 472 TYR 0.025 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 49 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 38 time to evaluate : 0.385 Fit side-chains REVERT: A 82 ARG cc_start: 0.7311 (OUTLIER) cc_final: 0.7018 (mtp85) REVERT: A 96 MET cc_start: 0.8017 (OUTLIER) cc_final: 0.7556 (ptp) REVERT: A 113 MET cc_start: 0.6209 (mtm) cc_final: 0.5758 (mmm) REVERT: A 255 TYR cc_start: 0.8688 (m-80) cc_final: 0.8359 (m-80) REVERT: A 305 PHE cc_start: 0.7597 (m-80) cc_final: 0.7339 (m-80) REVERT: A 334 MET cc_start: 0.8312 (mtm) cc_final: 0.7972 (mtm) REVERT: A 376 GLU cc_start: 0.7848 (mp0) cc_final: 0.7534 (mp0) REVERT: A 401 LEU cc_start: 0.7878 (OUTLIER) cc_final: 0.7667 (tt) REVERT: A 433 GLU cc_start: 0.7462 (OUTLIER) cc_final: 0.6133 (mp0) outliers start: 11 outliers final: 3 residues processed: 44 average time/residue: 0.8723 time to fit residues: 40.1442 Evaluate side-chains 40 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 33 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 137 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain A residue 439 SER 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: 3.9990 chunk 40 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 7 optimal weight: 0.4980 chunk 27 optimal weight: 2.9990 chunk 20 optimal weight: 0.0470 overall best weight: 0.6280 ------------------------------------------------------------------------------- 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: 0.7413 moved from start: 0.2892 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= 0.181 Angle : 0.580 10.080 4569 Z= 0.279 Chirality : 0.041 0.181 542 Planarity : 0.004 0.039 553 Dihedral : 4.190 18.609 451 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 3.41 % Allowed : 15.62 % Favored : 80.97 % 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: 2.27 (0.40), residues: 417 helix: 1.96 (0.26), residues: 356 sheet: None (None), residues: 0 loop : -1.23 (0.75), residues: 61 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 0.015 0.001 PHE A 472 TYR 0.023 0.001 TYR A 94 ARG 0.001 0.000 ARG A 84 *********************** 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 54 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 42 time to evaluate : 0.360 Fit side-chains REVERT: A 82 ARG cc_start: 0.7282 (OUTLIER) cc_final: 0.6969 (mtp85) REVERT: A 255 TYR cc_start: 0.8737 (m-80) cc_final: 0.8372 (m-80) REVERT: A 305 PHE cc_start: 0.7532 (m-80) cc_final: 0.7276 (m-80) REVERT: A 334 MET cc_start: 0.8260 (mtm) cc_final: 0.7947 (mtm) REVERT: A 376 GLU cc_start: 0.7870 (mp0) cc_final: 0.7553 (mp0) REVERT: A 433 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.6111 (mp0) outliers start: 12 outliers final: 4 residues processed: 49 average time/residue: 0.9250 time to fit residues: 47.2307 Evaluate side-chains 42 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 36 time to evaluate : 0.353 ------------------------------------------------------------------------------- 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 172 LEU Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain A residue 439 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 16 optimal weight: 0.0000 chunk 29 optimal weight: 0.6980 chunk 11 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 overall best weight: 0.6184 ------------------------------------------------------------------------------- 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: 0.7408 moved from start: 0.2960 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= 0.190 Angle : 0.606 9.409 4569 Z= 0.294 Chirality : 0.041 0.166 542 Planarity : 0.004 0.039 553 Dihedral : 4.196 18.548 451 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.56 % Allowed : 18.47 % 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: 2.33 (0.40), residues: 417 helix: 2.00 (0.26), residues: 354 sheet: None (None), residues: 0 loop : -1.10 (0.77), 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 0.015 0.001 PHE A 472 TYR 0.023 0.001 TYR A 94 ARG 0.001 0.000 ARG A 493 *********************** 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 47 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 38 time to evaluate : 0.360 Fit side-chains REVERT: A 82 ARG cc_start: 0.7263 (OUTLIER) cc_final: 0.6949 (mtp85) REVERT: A 113 MET cc_start: 0.6249 (mtm) cc_final: 0.5852 (mmm) REVERT: A 255 TYR cc_start: 0.8756 (m-80) cc_final: 0.8383 (m-80) REVERT: A 305 PHE cc_start: 0.7546 (m-80) cc_final: 0.7008 (m-80) REVERT: A 334 MET cc_start: 0.8209 (mtm) cc_final: 0.7948 (mtm) REVERT: A 376 GLU cc_start: 0.7875 (mp0) cc_final: 0.7554 (mp0) outliers start: 9 outliers final: 4 residues processed: 42 average time/residue: 0.7008 time to fit residues: 31.1163 Evaluate side-chains 40 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 35 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ARG Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 439 SER 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: 0.5980 chunk 37 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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: 0.7421 moved from start: 0.3035 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= 0.206 Angle : 0.599 9.732 4569 Z= 0.293 Chirality : 0.041 0.161 542 Planarity : 0.004 0.039 553 Dihedral : 4.228 18.586 451 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.99 % Allowed : 20.45 % Favored : 77.56 % 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: 2.22 (0.40), residues: 417 helix: 1.92 (0.26), residues: 355 sheet: None (None), residues: 0 loop : -1.15 (0.76), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 337 HIS 0.002 0.000 HIS A 249 PHE 0.015 0.001 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 45 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 38 time to evaluate : 0.353 Fit side-chains REVERT: A 82 ARG cc_start: 0.7273 (OUTLIER) cc_final: 0.6961 (mtp85) REVERT: A 113 MET cc_start: 0.6191 (mtm) cc_final: 0.5792 (mmm) REVERT: A 255 TYR cc_start: 0.8748 (m-80) cc_final: 0.8442 (m-80) REVERT: A 305 PHE cc_start: 0.7565 (m-80) cc_final: 0.7329 (m-80) REVERT: A 334 MET cc_start: 0.8215 (mtm) cc_final: 0.8007 (mtm) REVERT: A 376 GLU cc_start: 0.7892 (mp0) cc_final: 0.7565 (mp0) outliers start: 7 outliers final: 3 residues processed: 43 average time/residue: 0.7694 time to fit residues: 34.8248 Evaluate side-chains 40 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 36 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ARG Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 439 SER 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: 0.3980 chunk 26 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 30 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 13 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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: 0.7416 moved from start: 0.3066 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= 0.199 Angle : 0.612 10.963 4569 Z= 0.297 Chirality : 0.041 0.155 542 Planarity : 0.004 0.039 553 Dihedral : 4.243 18.400 451 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.14 % Allowed : 21.59 % 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: 2.29 (0.40), residues: 417 helix: 1.98 (0.26), residues: 354 sheet: None (None), residues: 0 loop : -1.16 (0.74), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 337 HIS 0.002 0.000 HIS A 249 PHE 0.014 0.001 PHE A 472 TYR 0.023 0.001 TYR A 94 ARG 0.001 0.000 ARG A 84 ********************** 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 41 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 37 time to evaluate : 0.363 Fit side-chains REVERT: A 82 ARG cc_start: 0.7271 (OUTLIER) cc_final: 0.6959 (mtp85) REVERT: A 113 MET cc_start: 0.6172 (mtm) cc_final: 0.5773 (mmm) REVERT: A 255 TYR cc_start: 0.8745 (m-80) cc_final: 0.8438 (m-80) REVERT: A 305 PHE cc_start: 0.7533 (m-80) cc_final: 0.6966 (m-80) REVERT: A 358 MET cc_start: 0.8046 (mtp) cc_final: 0.7815 (mtp) REVERT: A 376 GLU cc_start: 0.7899 (mp0) cc_final: 0.7562 (mp0) outliers start: 4 outliers final: 2 residues processed: 40 average time/residue: 0.7931 time to fit residues: 33.4157 Evaluate side-chains 38 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 35 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ARG Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 439 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 0.6980 chunk 1 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 22 optimal weight: 0.0370 chunk 28 optimal weight: 0.8980 chunk 26 optimal weight: 6.9990 chunk 25 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 41 optimal weight: 0.0980 overall best weight: 0.4858 ------------------------------------------------------------------------------- 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 = 0.3568 r_free = 0.3568 target = 0.131412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.112038 restraints weight = 4237.715| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 2.27 r_work: 0.3222 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7012 moved from start: 0.3184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3355 Z= 0.178 Angle : 0.584 9.834 4569 Z= 0.287 Chirality : 0.040 0.151 542 Planarity : 0.004 0.039 553 Dihedral : 4.205 18.017 451 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.99 % Allowed : 21.02 % Favored : 76.99 % 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: 2.36 (0.40), residues: 417 helix: 2.03 (0.26), residues: 354 sheet: None (None), residues: 0 loop : -1.18 (0.72), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 337 HIS 0.002 0.000 HIS A 249 PHE 0.013 0.001 PHE A 472 TYR 0.022 0.001 TYR A 94 ARG 0.001 0.000 ARG A 84 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1365.28 seconds wall clock time: 26 minutes 7.20 seconds (1567.20 seconds total)