Starting phenix.real_space_refine on Fri Aug 2 12:54:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x5x_38074/08_2024/8x5x_38074.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x5x_38074/08_2024/8x5x_38074.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x5x_38074/08_2024/8x5x_38074.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x5x_38074/08_2024/8x5x_38074.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x5x_38074/08_2024/8x5x_38074.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x5x_38074/08_2024/8x5x_38074.cif" } resolution = 3.5 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= -0.000 sd= 0.052 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 1410 2.51 5 N 339 2.21 5 O 337 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 178": "OD1" <-> "OD2" Residue "B ASP 183": "OD1" <-> "OD2" Residue "B PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 475": "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: 2105 Number of models: 1 Model: "" Number of chains: 1 Chain: "B" Number of atoms: 2105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2105 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 8, 'TRANS': 247} Chain breaks: 4 Time building chain proxies: 2.21, per 1000 atoms: 1.05 Number of scatterers: 2105 At special positions: 0 Unit cell: (49.22, 70.62, 72.76, 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 337 8.00 N 339 7.00 C 1410 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 100 " - pdb=" SG CYS B 180 " distance=2.04 Simple disulfide: pdb=" SG CYS B 441 " - pdb=" SG CYS B 444 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.76 Conformation dependent library (CDL) restraints added in 355.8 milliseconds 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 496 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 0 sheets defined 85.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'B' and resid 29 through 55 removed outlier: 3.861A pdb=" N VAL B 33 " --> pdb=" O PRO B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 90 Proline residue: B 82 - end of helix removed outlier: 4.414A pdb=" N MET B 90 " --> pdb=" O LEU B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 131 Processing helix chain 'B' and resid 132 through 134 No H-bonds generated for 'chain 'B' and resid 132 through 134' Processing helix chain 'B' and resid 140 through 157 removed outlier: 3.887A pdb=" N SER B 145 " --> pdb=" O LYS B 141 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ALA B 146 " --> pdb=" O THR B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 164 removed outlier: 3.932A pdb=" N ILE B 162 " --> pdb=" O TRP B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 221 removed outlier: 5.167A pdb=" N LEU B 201 " --> pdb=" O ILE B 197 " (cutoff:3.500A) Proline residue: B 202 - end of helix Processing helix chain 'B' and resid 409 through 439 Proline residue: B 430 - end of helix Processing helix chain 'B' and resid 446 through 472 Proline residue: B 465 - end of helix Proline residue: B 469 - end of helix removed outlier: 3.797A pdb=" N ASN B 472 " --> pdb=" O TYR B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 481 removed outlier: 3.700A pdb=" N ARG B 481 " --> pdb=" O LYS B 477 " (cutoff:3.500A) 157 hydrogen bonds defined for protein. 471 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: 0.53 Time building geometry restraints manager: 0.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 608 1.35 - 1.47: 608 1.47 - 1.60: 917 1.60 - 1.72: 0 1.72 - 1.84: 29 Bond restraints: 2162 Sorted by residual: bond pdb=" C ILE B 429 " pdb=" N PRO B 430 " ideal model delta sigma weight residual 1.334 1.379 -0.045 2.34e-02 1.83e+03 3.68e+00 bond pdb=" CG1 ILE B 438 " pdb=" CD1 ILE B 438 " ideal model delta sigma weight residual 1.513 1.456 0.057 3.90e-02 6.57e+02 2.13e+00 bond pdb=" CG1 ILE B 115 " pdb=" CD1 ILE B 115 " ideal model delta sigma weight residual 1.513 1.459 0.054 3.90e-02 6.57e+02 1.91e+00 bond pdb=" CB CYS B 180 " pdb=" SG CYS B 180 " ideal model delta sigma weight residual 1.808 1.843 -0.035 3.30e-02 9.18e+02 1.15e+00 bond pdb=" N GLU B 181 " pdb=" CA GLU B 181 " ideal model delta sigma weight residual 1.468 1.455 0.013 1.24e-02 6.50e+03 1.12e+00 ... (remaining 2157 not shown) Histogram of bond angle deviations from ideal: 99.68 - 106.54: 55 106.54 - 113.39: 1187 113.39 - 120.25: 817 120.25 - 127.11: 842 127.11 - 133.96: 32 Bond angle restraints: 2933 Sorted by residual: angle pdb=" CA TRP B 455 " pdb=" CB TRP B 455 " pdb=" CG TRP B 455 " ideal model delta sigma weight residual 113.60 118.52 -4.92 1.90e+00 2.77e-01 6.69e+00 angle pdb=" CA LEU B 39 " pdb=" CB LEU B 39 " pdb=" CG LEU B 39 " ideal model delta sigma weight residual 116.30 124.28 -7.98 3.50e+00 8.16e-02 5.20e+00 angle pdb=" C THR B 478 " pdb=" N PHE B 479 " pdb=" CA PHE B 479 " ideal model delta sigma weight residual 121.58 117.23 4.35 1.95e+00 2.63e-01 4.97e+00 angle pdb=" C LEU B 426 " pdb=" N CYS B 427 " pdb=" CA CYS B 427 " ideal model delta sigma weight residual 122.65 119.13 3.52 1.60e+00 3.91e-01 4.85e+00 angle pdb=" N GLY B 96 " pdb=" CA GLY B 96 " pdb=" C GLY B 96 " ideal model delta sigma weight residual 113.18 108.34 4.84 2.37e+00 1.78e-01 4.16e+00 ... (remaining 2928 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.23: 1104 16.23 - 32.46: 119 32.46 - 48.69: 34 48.69 - 64.91: 3 64.91 - 81.14: 3 Dihedral angle restraints: 1263 sinusoidal: 504 harmonic: 759 Sorted by residual: dihedral pdb=" CB CYS B 441 " pdb=" SG CYS B 441 " pdb=" SG CYS B 444 " pdb=" CB CYS B 444 " ideal model delta sinusoidal sigma weight residual 93.00 174.14 -81.14 1 1.00e+01 1.00e-02 8.12e+01 dihedral pdb=" SG CYS B 441 " pdb=" CB CYS B 444 " pdb=" SG CYS B 444 " pdb=" CA CYS B 444 " ideal model delta sinusoidal sigma weight residual 79.00 8.82 70.18 1 2.00e+01 2.50e-03 1.59e+01 dihedral pdb=" CA CYS B 427 " pdb=" C CYS B 427 " pdb=" N TRP B 428 " pdb=" CA TRP B 428 " ideal model delta harmonic sigma weight residual 180.00 161.55 18.45 0 5.00e+00 4.00e-02 1.36e+01 ... (remaining 1260 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 208 0.032 - 0.065: 84 0.065 - 0.097: 36 0.097 - 0.129: 10 0.129 - 0.162: 2 Chirality restraints: 340 Sorted by residual: chirality pdb=" CG LEU B 74 " pdb=" CB LEU B 74 " pdb=" CD1 LEU B 74 " pdb=" CD2 LEU B 74 " both_signs ideal model delta sigma weight residual False -2.59 -2.75 0.16 2.00e-01 2.50e+01 6.54e-01 chirality pdb=" CB VAL B 79 " pdb=" CA VAL B 79 " pdb=" CG1 VAL B 79 " pdb=" CG2 VAL B 79 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.53e-01 chirality pdb=" CA ILE B 115 " pdb=" N ILE B 115 " pdb=" C ILE B 115 " pdb=" CB ILE B 115 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.94e-01 ... (remaining 337 not shown) Planarity restraints: 344 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 455 " -0.020 2.00e-02 2.50e+03 1.56e-02 6.06e+00 pdb=" CG TRP B 455 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 TRP B 455 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP B 455 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 455 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 455 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 455 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 455 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 455 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 455 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 428 " 0.016 2.00e-02 2.50e+03 1.25e-02 3.88e+00 pdb=" CG TRP B 428 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 TRP B 428 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP B 428 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 428 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 428 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 428 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 428 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 428 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 428 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 479 " 0.013 2.00e-02 2.50e+03 1.33e-02 3.09e+00 pdb=" CG PHE B 479 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 PHE B 479 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE B 479 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE B 479 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 479 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE B 479 " 0.000 2.00e-02 2.50e+03 ... (remaining 341 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.66: 18 2.66 - 3.22: 2097 3.22 - 3.78: 3431 3.78 - 4.34: 4203 4.34 - 4.90: 6642 Nonbonded interactions: 16391 Sorted by model distance: nonbonded pdb=" OD1 ASN B 63 " pdb=" OH TYR B 468 " model vdw 2.094 3.040 nonbonded pdb=" OH TYR B 65 " pdb=" OG1 THR B 147 " model vdw 2.143 3.040 nonbonded pdb=" OG1 THR B 41 " pdb=" OG1 THR B 462 " model vdw 2.277 3.040 nonbonded pdb=" O TYR B 458 " pdb=" OG SER B 461 " model vdw 2.364 3.040 nonbonded pdb=" ND2 ASN B 45 " pdb=" OD2 ASP B 73 " model vdw 2.406 3.120 ... (remaining 16386 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.970 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: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 11.540 Find NCS groups from input model: 0.020 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5295 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 0.057 2162 Z= 0.261 Angle : 0.775 7.979 2933 Z= 0.392 Chirality : 0.044 0.162 340 Planarity : 0.005 0.037 344 Dihedral : 14.147 79.862 761 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 0.43 % Allowed : 0.43 % Favored : 99.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.56), residues: 246 helix: 1.40 (0.37), residues: 200 sheet: None (None), residues: 0 loop : -2.56 (0.94), residues: 46 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP B 455 HIS 0.003 0.001 HIS B 450 PHE 0.031 0.002 PHE B 479 TYR 0.014 0.002 TYR B 185 ARG 0.002 0.000 ARG B 97 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 54 time to evaluate : 0.246 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 54 average time/residue: 0.1171 time to fit residues: 7.5880 Evaluate side-chains 41 residues out of total 232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 21 optimal weight: 0.0070 chunk 18 optimal weight: 4.9990 chunk 10 optimal weight: 6.9990 chunk 6 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 7 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 chunk 14 optimal weight: 0.0970 chunk 22 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 ASN ** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5416 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 2162 Z= 0.211 Angle : 0.724 7.601 2933 Z= 0.351 Chirality : 0.042 0.135 340 Planarity : 0.004 0.043 344 Dihedral : 4.942 18.212 275 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.72 % Allowed : 10.78 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.55), residues: 246 helix: 1.37 (0.36), residues: 201 sheet: None (None), residues: 0 loop : -2.54 (0.96), residues: 45 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 455 HIS 0.002 0.001 HIS B 59 PHE 0.025 0.002 PHE B 479 TYR 0.012 0.002 TYR B 126 ARG 0.001 0.000 ARG B 53 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 45 time to evaluate : 0.316 Fit side-chains revert: symmetry clash REVERT: B 185 TYR cc_start: 0.2526 (m-10) cc_final: 0.2187 (m-80) REVERT: B 461 SER cc_start: 0.7712 (p) cc_final: 0.7438 (t) outliers start: 4 outliers final: 4 residues processed: 47 average time/residue: 0.0951 time to fit residues: 5.7517 Evaluate side-chains 42 residues out of total 232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 38 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 197 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 6 optimal weight: 0.1980 chunk 22 optimal weight: 0.0770 chunk 24 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 2 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5459 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 2162 Z= 0.197 Angle : 0.687 7.368 2933 Z= 0.333 Chirality : 0.041 0.121 340 Planarity : 0.004 0.049 344 Dihedral : 4.733 16.878 275 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.88 % Allowed : 13.79 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.55), residues: 246 helix: 1.44 (0.37), residues: 201 sheet: None (None), residues: 0 loop : -2.13 (0.93), residues: 45 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 455 HIS 0.005 0.001 HIS B 167 PHE 0.023 0.001 PHE B 479 TYR 0.015 0.002 TYR B 468 ARG 0.001 0.000 ARG B 97 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 40 time to evaluate : 0.245 Fit side-chains revert: symmetry clash REVERT: B 185 TYR cc_start: 0.2375 (m-10) cc_final: 0.2023 (m-80) REVERT: B 451 MET cc_start: 0.6204 (tpp) cc_final: 0.5935 (mmt) outliers start: 9 outliers final: 7 residues processed: 45 average time/residue: 0.0905 time to fit residues: 5.2909 Evaluate side-chains 43 residues out of total 232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 36 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 204 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 22 optimal weight: 0.1980 chunk 24 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 21 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 13 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 17 optimal weight: 0.9990 chunk 9 optimal weight: 6.9990 chunk 16 optimal weight: 0.7980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 45 ASN ** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5518 moved from start: 0.2958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 2162 Z= 0.214 Angle : 0.712 7.361 2933 Z= 0.344 Chirality : 0.042 0.152 340 Planarity : 0.004 0.046 344 Dihedral : 4.688 16.303 275 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.45 % Allowed : 19.40 % Favored : 77.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.54), residues: 246 helix: 1.33 (0.37), residues: 201 sheet: None (None), residues: 0 loop : -2.15 (0.91), residues: 45 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 455 HIS 0.002 0.001 HIS B 167 PHE 0.029 0.002 PHE B 479 TYR 0.008 0.001 TYR B 468 ARG 0.001 0.000 ARG B 97 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 42 time to evaluate : 0.272 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 6 residues processed: 46 average time/residue: 0.1012 time to fit residues: 5.8570 Evaluate side-chains 41 residues out of total 232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 35 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 204 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 0 optimal weight: 7.9990 chunk 12 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 14 optimal weight: 0.0470 chunk 5 optimal weight: 0.7980 chunk 24 optimal weight: 0.0070 chunk 20 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 overall best weight: 0.4896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5509 moved from start: 0.3238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 2162 Z= 0.186 Angle : 0.672 7.162 2933 Z= 0.324 Chirality : 0.041 0.151 340 Planarity : 0.004 0.047 344 Dihedral : 4.530 15.294 275 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 4.31 % Allowed : 20.69 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.54), residues: 246 helix: 1.46 (0.37), residues: 201 sheet: None (None), residues: 0 loop : -2.13 (0.89), residues: 45 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 455 HIS 0.002 0.001 HIS B 167 PHE 0.026 0.002 PHE B 479 TYR 0.011 0.002 TYR B 468 ARG 0.001 0.000 ARG B 97 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 36 time to evaluate : 0.245 Fit side-chains revert: symmetry clash REVERT: B 450 HIS cc_start: 0.6723 (OUTLIER) cc_final: 0.5874 (t-90) outliers start: 10 outliers final: 5 residues processed: 42 average time/residue: 0.0962 time to fit residues: 5.1882 Evaluate side-chains 41 residues out of total 232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 35 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 450 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 2 optimal weight: 0.0170 chunk 8 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 24 optimal weight: 8.9990 chunk 15 optimal weight: 0.2980 chunk 14 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5540 moved from start: 0.3527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 2162 Z= 0.195 Angle : 0.679 7.184 2933 Z= 0.326 Chirality : 0.040 0.149 340 Planarity : 0.004 0.046 344 Dihedral : 4.550 15.425 275 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.88 % Allowed : 22.84 % Favored : 73.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.55), residues: 246 helix: 1.60 (0.37), residues: 196 sheet: None (None), residues: 0 loop : -2.71 (0.86), residues: 50 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 455 HIS 0.002 0.001 HIS B 167 PHE 0.024 0.001 PHE B 479 TYR 0.007 0.001 TYR B 468 ARG 0.001 0.000 ARG B 97 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 38 time to evaluate : 0.218 Fit side-chains REVERT: B 450 HIS cc_start: 0.6648 (OUTLIER) cc_final: 0.6137 (t-90) outliers start: 9 outliers final: 5 residues processed: 44 average time/residue: 0.0842 time to fit residues: 4.7751 Evaluate side-chains 41 residues out of total 232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 35 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 450 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 14 optimal weight: 0.0070 chunk 9 optimal weight: 8.9990 chunk 7 optimal weight: 0.8980 chunk 4 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 18 optimal weight: 0.2980 chunk 21 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5546 moved from start: 0.3691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 2162 Z= 0.186 Angle : 0.676 7.052 2933 Z= 0.324 Chirality : 0.040 0.136 340 Planarity : 0.004 0.047 344 Dihedral : 4.605 15.714 275 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.02 % Allowed : 24.14 % Favored : 72.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.55), residues: 246 helix: 1.58 (0.37), residues: 196 sheet: None (None), residues: 0 loop : -2.45 (0.86), residues: 50 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 455 HIS 0.002 0.001 HIS B 59 PHE 0.023 0.001 PHE B 479 TYR 0.008 0.001 TYR B 185 ARG 0.001 0.000 ARG B 97 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 36 time to evaluate : 0.223 Fit side-chains REVERT: B 93 TRP cc_start: 0.5036 (OUTLIER) cc_final: 0.4673 (m-10) REVERT: B 450 HIS cc_start: 0.6671 (OUTLIER) cc_final: 0.6253 (t-90) outliers start: 7 outliers final: 5 residues processed: 41 average time/residue: 0.0921 time to fit residues: 4.8693 Evaluate side-chains 40 residues out of total 232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 33 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 93 TRP Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 450 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 21 optimal weight: 0.4980 chunk 22 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 13 optimal weight: 5.9990 chunk 9 optimal weight: 8.9990 chunk 17 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 16 optimal weight: 0.1980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5580 moved from start: 0.3976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 2162 Z= 0.202 Angle : 0.735 8.882 2933 Z= 0.350 Chirality : 0.041 0.136 340 Planarity : 0.004 0.047 344 Dihedral : 4.735 16.014 275 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 4.31 % Allowed : 23.71 % Favored : 71.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.54), residues: 246 helix: 1.37 (0.37), residues: 201 sheet: None (None), residues: 0 loop : -2.36 (0.89), residues: 45 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 455 HIS 0.002 0.001 HIS B 167 PHE 0.024 0.002 PHE B 479 TYR 0.010 0.001 TYR B 468 ARG 0.002 0.000 ARG B 97 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 35 time to evaluate : 0.236 Fit side-chains REVERT: B 93 TRP cc_start: 0.5105 (OUTLIER) cc_final: 0.4437 (m-10) REVERT: B 450 HIS cc_start: 0.6650 (OUTLIER) cc_final: 0.6334 (t-90) REVERT: B 461 SER cc_start: 0.7838 (t) cc_final: 0.7623 (p) outliers start: 10 outliers final: 6 residues processed: 42 average time/residue: 0.0996 time to fit residues: 5.2864 Evaluate side-chains 40 residues out of total 232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 32 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 93 TRP Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 435 PHE Chi-restraints excluded: chain B residue 450 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 24 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 2 optimal weight: 10.0000 chunk 15 optimal weight: 0.9980 chunk 12 optimal weight: 0.1980 chunk 21 optimal weight: 0.8980 chunk 6 optimal weight: 0.2980 chunk 18 optimal weight: 0.0170 chunk 5 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 overall best weight: 0.4018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5568 moved from start: 0.4216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 2162 Z= 0.188 Angle : 0.722 10.494 2933 Z= 0.339 Chirality : 0.041 0.192 340 Planarity : 0.004 0.048 344 Dihedral : 4.683 16.426 275 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.88 % Allowed : 24.14 % Favored : 71.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.55), residues: 246 helix: 1.39 (0.37), residues: 200 sheet: None (None), residues: 0 loop : -2.04 (0.98), residues: 46 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 455 HIS 0.003 0.001 HIS B 167 PHE 0.024 0.001 PHE B 479 TYR 0.011 0.001 TYR B 185 ARG 0.001 0.000 ARG B 53 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 33 time to evaluate : 0.247 Fit side-chains REVERT: B 93 TRP cc_start: 0.5181 (OUTLIER) cc_final: 0.4552 (m-10) REVERT: B 450 HIS cc_start: 0.6579 (OUTLIER) cc_final: 0.6282 (t-90) outliers start: 9 outliers final: 6 residues processed: 39 average time/residue: 0.1059 time to fit residues: 5.2332 Evaluate side-chains 39 residues out of total 232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 31 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 93 TRP Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 435 PHE Chi-restraints excluded: chain B residue 450 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 20 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 15 optimal weight: 0.7980 chunk 9 optimal weight: 5.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 130 GLN ** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5684 moved from start: 0.4471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 2162 Z= 0.221 Angle : 0.774 12.299 2933 Z= 0.366 Chirality : 0.043 0.195 340 Planarity : 0.004 0.045 344 Dihedral : 4.797 16.893 275 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 3.88 % Allowed : 25.00 % Favored : 71.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.55), residues: 246 helix: 1.26 (0.36), residues: 201 sheet: None (None), residues: 0 loop : -2.34 (0.94), residues: 45 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 165 HIS 0.003 0.001 HIS B 167 PHE 0.023 0.002 PHE B 479 TYR 0.009 0.001 TYR B 210 ARG 0.001 0.000 ARG B 97 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 31 time to evaluate : 0.241 Fit side-chains REVERT: B 93 TRP cc_start: 0.5363 (OUTLIER) cc_final: 0.4772 (m-10) REVERT: B 450 HIS cc_start: 0.6602 (OUTLIER) cc_final: 0.6264 (t-90) outliers start: 9 outliers final: 7 residues processed: 38 average time/residue: 0.0947 time to fit residues: 4.6621 Evaluate side-chains 39 residues out of total 232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 30 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 93 TRP Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 165 TRP Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 435 PHE Chi-restraints excluded: chain B residue 450 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 9 optimal weight: 4.9990 chunk 24 optimal weight: 0.0060 chunk 0 optimal weight: 7.9990 chunk 4 optimal weight: 0.9980 chunk 3 optimal weight: 0.5980 chunk 5 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 overall best weight: 0.8398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4582 r_free = 0.4582 target = 0.186839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.173519 restraints weight = 4951.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.176374 restraints weight = 2913.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.178407 restraints weight = 2004.104| |-----------------------------------------------------------------------------| r_work (final): 0.4484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5698 moved from start: 0.4624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 2162 Z= 0.210 Angle : 0.758 11.394 2933 Z= 0.357 Chirality : 0.043 0.190 340 Planarity : 0.004 0.046 344 Dihedral : 4.823 17.205 275 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 5.17 % Allowed : 24.14 % Favored : 70.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.55), residues: 246 helix: 1.30 (0.37), residues: 201 sheet: None (None), residues: 0 loop : -2.40 (0.93), residues: 45 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 455 HIS 0.003 0.001 HIS B 167 PHE 0.028 0.002 PHE B 475 TYR 0.009 0.001 TYR B 468 ARG 0.001 0.000 ARG B 97 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 921.41 seconds wall clock time: 17 minutes 44.96 seconds (1064.96 seconds total)