Starting phenix.real_space_refine on Mon May 6 13:30:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x5x_38074/05_2024/8x5x_38074.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x5x_38074/05_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_38074/05_2024/8x5x_38074.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x5x_38074/05_2024/8x5x_38074.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x5x_38074/05_2024/8x5x_38074.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x5x_38074/05_2024/8x5x_38074.pdb" } 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-5322/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: 1.71, per 1000 atoms: 0.81 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: 0.88 Conformation dependent library (CDL) restraints added in 352.6 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: 0.17 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: 0.97 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 2.440 nonbonded pdb=" OH TYR B 65 " pdb=" OG1 THR B 147 " model vdw 2.143 2.440 nonbonded pdb=" OG1 THR B 41 " pdb=" OG1 THR B 462 " model vdw 2.277 2.440 nonbonded pdb=" O TYR B 458 " pdb=" OG SER B 461 " model vdw 2.364 2.440 nonbonded pdb=" ND2 ASN B 45 " pdb=" OD2 ASP B 73 " model vdw 2.406 2.520 ... (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: 1.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.520 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.000 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.000 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: 0.010 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.720 ------------------------------------------------------------------------------- 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 : 0.217 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 54 average time/residue: 0.1255 time to fit residues: 8.0997 Evaluate side-chains 41 residues out of total 232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.247 ------------------------------------------------------------------------------- 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: 8.9990 chunk 18 optimal weight: 5.9990 chunk 10 optimal weight: 0.4980 chunk 6 optimal weight: 0.2980 chunk 12 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 14 optimal weight: 0.2980 chunk 22 optimal weight: 0.7980 chunk 15 optimal weight: 3.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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: 0.5420 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 2162 Z= 0.204 Angle : 0.701 7.474 2933 Z= 0.342 Chirality : 0.042 0.128 340 Planarity : 0.004 0.043 344 Dihedral : 4.928 18.583 275 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.72 % Allowed : 11.21 % Favored : 87.07 % 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: 1.22 (0.56), residues: 246 helix: 1.53 (0.37), 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 97 *********************** 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 45 residues out of total 232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 41 time to evaluate : 0.267 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 4 residues processed: 43 average time/residue: 0.0963 time to fit residues: 5.3556 Evaluate side-chains 41 residues out of total 232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 37 time to evaluate : 0.240 ------------------------------------------------------------------------------- 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: 0.6980 chunk 22 optimal weight: 0.4980 chunk 24 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 2 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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: 0.5499 moved from start: 0.2571 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= 0.199 Angle : 0.675 7.318 2933 Z= 0.330 Chirality : 0.040 0.124 340 Planarity : 0.004 0.048 344 Dihedral : 4.656 15.966 275 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.88 % Allowed : 15.09 % Favored : 81.03 % 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: 1.38 (0.55), residues: 246 helix: 1.58 (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 0.025 0.001 TRP B 455 HIS 0.006 0.002 HIS B 167 PHE 0.024 0.001 PHE B 479 TYR 0.013 0.002 TYR B 468 ARG 0.001 0.000 ARG B 176 *********************** 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 : 0.242 Fit side-chains revert: symmetry clash REVERT: B 185 TYR cc_start: 0.2420 (m-10) cc_final: 0.2071 (m-80) outliers start: 9 outliers final: 7 residues processed: 44 average time/residue: 0.0939 time to fit residues: 5.3217 Evaluate side-chains 42 residues out of total 232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 35 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 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: 0.9980 chunk 24 optimal weight: 0.0270 chunk 11 optimal weight: 1.9990 chunk 21 optimal weight: 0.0870 chunk 6 optimal weight: 0.1980 chunk 20 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 17 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 overall best weight: 0.4616 ------------------------------------------------------------------------------- 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: 0.5475 moved from start: 0.2929 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 7.027 2933 Z= 0.330 Chirality : 0.040 0.148 340 Planarity : 0.004 0.047 344 Dihedral : 4.528 15.274 275 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % 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: 1.24 (0.56), residues: 246 helix: 1.46 (0.37), residues: 201 sheet: None (None), residues: 0 loop : -2.10 (0.95), residues: 45 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 455 HIS 0.002 0.001 HIS B 59 PHE 0.028 0.002 PHE B 479 TYR 0.014 0.002 TYR B 458 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 51 residues out of total 232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 41 time to evaluate : 0.225 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 5 residues processed: 45 average time/residue: 0.0867 time to fit residues: 5.0335 Evaluate side-chains 40 residues out of total 232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 35 time to evaluate : 0.228 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 21 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 24 optimal weight: 0.0670 chunk 20 optimal weight: 0.9980 chunk 11 optimal weight: 6.9990 overall best weight: 0.8120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 446 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: 0.5564 moved from start: 0.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 2162 Z= 0.228 Angle : 0.671 7.148 2933 Z= 0.329 Chirality : 0.040 0.139 340 Planarity : 0.004 0.046 344 Dihedral : 4.584 15.614 275 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 4.31 % Allowed : 21.98 % Favored : 73.71 % 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: 1.34 (0.56), residues: 246 helix: 1.51 (0.37), residues: 201 sheet: None (None), residues: 0 loop : -1.96 (0.98), residues: 45 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 455 HIS 0.006 0.002 HIS B 450 PHE 0.026 0.002 PHE B 479 TYR 0.015 0.002 TYR B 458 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 49 residues out of total 232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 39 time to evaluate : 0.238 Fit side-chains revert: symmetry clash REVERT: B 450 HIS cc_start: 0.6540 (OUTLIER) cc_final: 0.5775 (t-90) outliers start: 10 outliers final: 7 residues processed: 46 average time/residue: 0.0992 time to fit residues: 5.8158 Evaluate side-chains 43 residues out of total 232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 35 time to evaluate : 0.256 ------------------------------------------------------------------------------- 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 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: 5.9990 chunk 8 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 13 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 20 optimal weight: 0.5980 chunk 24 optimal weight: 7.9990 chunk 15 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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: 0.5606 moved from start: 0.3626 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= 0.203 Angle : 0.680 7.192 2933 Z= 0.331 Chirality : 0.040 0.120 340 Planarity : 0.004 0.046 344 Dihedral : 4.619 15.905 275 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.88 % Allowed : 23.71 % Favored : 72.41 % 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 (0.56), residues: 246 helix: 1.48 (0.37), residues: 200 sheet: None (None), residues: 0 loop : -2.14 (0.97), residues: 46 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 0.024 0.001 PHE B 479 TYR 0.015 0.001 TYR B 458 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 46 residues out of total 232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 37 time to evaluate : 0.286 Fit side-chains REVERT: B 90 MET cc_start: 0.2785 (ppp) cc_final: 0.2570 (ppp) REVERT: B 102 PHE cc_start: 0.5294 (m-80) cc_final: 0.5029 (m-80) REVERT: B 165 TRP cc_start: 0.4999 (t-100) cc_final: 0.4328 (t-100) REVERT: B 183 ASP cc_start: 0.4548 (t0) cc_final: 0.4297 (t0) REVERT: B 193 MET cc_start: 0.6299 (ttm) cc_final: 0.6053 (ttm) REVERT: B 450 HIS cc_start: 0.6627 (OUTLIER) cc_final: 0.6119 (t-90) outliers start: 9 outliers final: 6 residues processed: 43 average time/residue: 0.0938 time to fit residues: 5.0767 Evaluate side-chains 43 residues out of total 232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 36 time to evaluate : 0.210 ------------------------------------------------------------------------------- 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 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: 2.9990 chunk 9 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 2 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 21 optimal weight: 0.0470 chunk 23 optimal weight: 0.9980 overall best weight: 0.6678 ------------------------------------------------------------------------------- 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: 0.5608 moved from start: 0.3856 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= 0.193 Angle : 0.658 7.167 2933 Z= 0.321 Chirality : 0.039 0.122 340 Planarity : 0.004 0.047 344 Dihedral : 4.646 16.203 275 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 3.45 % Allowed : 25.00 % Favored : 71.55 % 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: 1.28 (0.55), residues: 246 helix: 1.54 (0.37), residues: 201 sheet: None (None), residues: 0 loop : -2.30 (0.93), 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 0.023 0.001 PHE B 479 TYR 0.014 0.001 TYR B 458 ARG 0.002 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: 8 poor density : 35 time to evaluate : 0.253 Fit side-chains REVERT: B 102 PHE cc_start: 0.5303 (m-80) cc_final: 0.5051 (m-80) REVERT: B 126 TYR cc_start: 0.5232 (OUTLIER) cc_final: 0.4755 (t80) REVERT: B 450 HIS cc_start: 0.6667 (OUTLIER) cc_final: 0.6169 (t-90) outliers start: 8 outliers final: 6 residues processed: 40 average time/residue: 0.0894 time to fit residues: 4.6623 Evaluate side-chains 41 residues out of total 232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 33 time to evaluate : 0.257 ------------------------------------------------------------------------------- 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 126 TYR 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: 1.9990 chunk 22 optimal weight: 0.6980 chunk 23 optimal weight: 3.9990 chunk 13 optimal weight: 0.0000 chunk 9 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 6 optimal weight: 0.0270 chunk 20 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 overall best weight: 0.5042 ------------------------------------------------------------------------------- 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: 0.5602 moved from start: 0.4132 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= 0.183 Angle : 0.669 6.910 2933 Z= 0.322 Chirality : 0.040 0.142 340 Planarity : 0.004 0.048 344 Dihedral : 4.571 16.415 275 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 4.74 % Allowed : 24.14 % 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: 1.28 (0.56), residues: 246 helix: 1.54 (0.37), residues: 201 sheet: None (None), residues: 0 loop : -2.33 (0.93), residues: 45 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 455 HIS 0.002 0.001 HIS B 59 PHE 0.023 0.001 PHE B 479 TYR 0.013 0.001 TYR B 458 ARG 0.001 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: 11 poor density : 34 time to evaluate : 0.199 Fit side-chains REVERT: B 90 MET cc_start: 0.3281 (ppp) cc_final: 0.2884 (ppp) REVERT: B 102 PHE cc_start: 0.5286 (m-80) cc_final: 0.5021 (m-80) REVERT: B 126 TYR cc_start: 0.5223 (OUTLIER) cc_final: 0.4737 (t80) REVERT: B 450 HIS cc_start: 0.6530 (OUTLIER) cc_final: 0.6249 (t-90) outliers start: 11 outliers final: 7 residues processed: 42 average time/residue: 0.0957 time to fit residues: 5.0949 Evaluate side-chains 44 residues out of total 232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 35 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 79 VAL Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 126 TYR Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 197 ILE 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: 0.3980 chunk 22 optimal weight: 0.2980 chunk 19 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 6 optimal weight: 0.0870 chunk 18 optimal weight: 0.0980 chunk 5 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 overall best weight: 0.3358 ------------------------------------------------------------------------------- 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: 0.5590 moved from start: 0.4206 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= 0.180 Angle : 0.660 6.767 2933 Z= 0.315 Chirality : 0.039 0.134 340 Planarity : 0.004 0.053 344 Dihedral : 4.508 16.660 275 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 4.74 % Allowed : 23.28 % 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: 1.47 (0.56), residues: 246 helix: 1.69 (0.37), residues: 201 sheet: None (None), residues: 0 loop : -2.41 (0.94), residues: 45 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 0.023 0.001 PHE B 479 TYR 0.012 0.001 TYR B 458 ARG 0.001 0.000 ARG B 97 *********************** 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 45 residues out of total 232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 34 time to evaluate : 0.241 Fit side-chains REVERT: B 126 TYR cc_start: 0.5163 (OUTLIER) cc_final: 0.4739 (t80) outliers start: 11 outliers final: 8 residues processed: 41 average time/residue: 0.1023 time to fit residues: 5.2758 Evaluate side-chains 40 residues out of total 232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 31 time to evaluate : 0.237 ------------------------------------------------------------------------------- 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 126 TYR Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 435 PHE Chi-restraints excluded: chain B residue 442 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 20 optimal weight: 0.9980 chunk 2 optimal weight: 4.9990 chunk 3 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 14 optimal weight: 0.0170 chunk 22 optimal weight: 4.9990 chunk 13 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 overall best weight: 0.9220 ------------------------------------------------------------------------------- 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: 0.5685 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 0.040 2162 Z= 0.217 Angle : 0.731 8.395 2933 Z= 0.351 Chirality : 0.041 0.123 340 Planarity : 0.005 0.045 344 Dihedral : 4.723 17.093 275 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 4.31 % Allowed : 25.86 % Favored : 69.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.55), residues: 246 helix: 1.56 (0.37), residues: 201 sheet: None (None), residues: 0 loop : -2.56 (0.91), residues: 45 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 455 HIS 0.003 0.001 HIS B 167 PHE 0.026 0.002 PHE B 475 TYR 0.016 0.002 TYR B 458 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 42 residues out of total 232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 32 time to evaluate : 0.254 Fit side-chains REVERT: B 93 TRP cc_start: 0.5177 (m-10) cc_final: 0.4574 (m-10) REVERT: B 126 TYR cc_start: 0.5423 (OUTLIER) cc_final: 0.4916 (t80) REVERT: B 450 HIS cc_start: 0.6374 (OUTLIER) cc_final: 0.5790 (t-90) outliers start: 10 outliers final: 8 residues processed: 39 average time/residue: 0.1069 time to fit residues: 5.2773 Evaluate side-chains 41 residues out of total 232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 31 time to evaluate : 0.250 ------------------------------------------------------------------------------- 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 126 TYR Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 165 TRP Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 435 PHE Chi-restraints excluded: chain B residue 442 LYS 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: 3.9990 chunk 24 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 4 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- 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 = 0.4569 r_free = 0.4569 target = 0.185453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.172325 restraints weight = 4911.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.175096 restraints weight = 2854.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.176905 restraints weight = 1939.541| |-----------------------------------------------------------------------------| r_work (final): 0.4465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5734 moved from start: 0.4695 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 : 0.740 11.255 2933 Z= 0.351 Chirality : 0.041 0.124 340 Planarity : 0.004 0.047 344 Dihedral : 4.766 17.094 275 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 4.31 % Allowed : 26.72 % Favored : 68.97 % 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: 1.17 (0.55), residues: 246 helix: 1.52 (0.37), residues: 201 sheet: None (None), residues: 0 loop : -2.70 (0.88), residues: 45 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 455 HIS 0.004 0.001 HIS B 167 PHE 0.025 0.002 PHE B 475 TYR 0.014 0.001 TYR B 458 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: 904.61 seconds wall clock time: 17 minutes 13.30 seconds (1033.30 seconds total)