Starting phenix.real_space_refine on Wed Nov 13 23:11:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gh0_40027/11_2024/8gh0_40027.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gh0_40027/11_2024/8gh0_40027.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gh0_40027/11_2024/8gh0_40027.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gh0_40027/11_2024/8gh0_40027.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gh0_40027/11_2024/8gh0_40027.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gh0_40027/11_2024/8gh0_40027.cif" } resolution = 4.0 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= 0.016 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 9 5.16 5 C 1287 2.51 5 N 326 2.21 5 O 332 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 1954 Number of models: 1 Model: "" Number of chains: 2 Chain: "R" Number of atoms: 1939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 1939 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 96} Link IDs: {'PTRANS': 7, 'TRANS': 273} Chain breaks: 1 Unresolved non-hydrogen bonds: 329 Unresolved non-hydrogen angles: 420 Unresolved non-hydrogen dihedrals: 265 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 6, 'TRP:plan': 2, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 153 Chain: "R" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'G1I': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.48, per 1000 atoms: 1.27 Number of scatterers: 1954 At special positions: 0 Unit cell: (55.5328, 85.0346, 65.0775, 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 9 16.00 O 332 8.00 N 326 7.00 C 1287 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 106 " - pdb=" SG CYS R 191 " distance=2.04 Simple disulfide: pdb=" SG CYS R 184 " - pdb=" SG CYS R 190 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 0.50 Conformation dependent library (CDL) restraints added in 268.4 milliseconds 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 538 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 0 sheets defined 87.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'R' and resid 37 through 61 removed outlier: 3.699A pdb=" N PHE R 61 " --> pdb=" O ALA R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 66 through 96 removed outlier: 4.021A pdb=" N PHE R 71 " --> pdb=" O VAL R 67 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N VAL R 87 " --> pdb=" O GLY R 83 " (cutoff:3.500A) Proline residue: R 88 - end of helix removed outlier: 3.588A pdb=" N ALA R 92 " --> pdb=" O PRO R 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 102 through 137 removed outlier: 3.637A pdb=" N VAL R 114 " --> pdb=" O THR R 110 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER R 137 " --> pdb=" O PHE R 133 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 145 removed outlier: 3.728A pdb=" N GLN R 142 " --> pdb=" O PRO R 138 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N SER R 143 " --> pdb=" O PHE R 139 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU R 145 " --> pdb=" O TYR R 141 " (cutoff:3.500A) Processing helix chain 'R' and resid 146 through 166 removed outlier: 3.905A pdb=" N ARG R 151 " --> pdb=" O LYS R 147 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL R 152 " --> pdb=" O ASN R 148 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE R 153 " --> pdb=" O LYS R 149 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE R 154 " --> pdb=" O ALA R 150 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL R 160 " --> pdb=" O MET R 156 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR R 164 " --> pdb=" O VAL R 160 " (cutoff:3.500A) Processing helix chain 'R' and resid 166 through 171 Processing helix chain 'R' and resid 172 through 175 Processing helix chain 'R' and resid 181 through 186 Processing helix chain 'R' and resid 196 through 208 removed outlier: 3.693A pdb=" N ALA R 200 " --> pdb=" O ASN R 196 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE R 201 " --> pdb=" O GLN R 197 " (cutoff:3.500A) Processing helix chain 'R' and resid 208 through 237 removed outlier: 3.992A pdb=" N PHE R 217 " --> pdb=" O VAL R 213 " (cutoff:3.500A) Processing helix chain 'R' and resid 270 through 299 removed outlier: 4.225A pdb=" N ILE R 278 " --> pdb=" O THR R 274 " (cutoff:3.500A) Proline residue: R 288 - end of helix removed outlier: 3.515A pdb=" N VAL R 292 " --> pdb=" O PRO R 288 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE R 294 " --> pdb=" O PHE R 290 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N VAL R 297 " --> pdb=" O ASN R 293 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 317 Processing helix chain 'R' and resid 317 through 327 Proline residue: R 323 - end of helix Processing helix chain 'R' and resid 329 through 339 161 hydrogen bonds defined for protein. 480 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: 0.57 Time building geometry restraints manager: 0.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 596 1.34 - 1.46: 518 1.46 - 1.58: 878 1.58 - 1.71: 0 1.71 - 1.83: 12 Bond restraints: 2004 Sorted by residual: bond pdb=" CA HIS R 296 " pdb=" C HIS R 296 " ideal model delta sigma weight residual 1.524 1.486 0.038 1.27e-02 6.20e+03 9.02e+00 bond pdb=" CAC G1I R 501 " pdb=" CAD G1I R 501 " ideal model delta sigma weight residual 1.397 1.452 -0.055 2.00e-02 2.50e+03 7.54e+00 bond pdb=" CAD G1I R 501 " pdb=" CAE G1I R 501 " ideal model delta sigma weight residual 1.394 1.443 -0.049 2.00e-02 2.50e+03 5.99e+00 bond pdb=" CAI G1I R 501 " pdb=" CAJ G1I R 501 " ideal model delta sigma weight residual 1.523 1.570 -0.047 2.00e-02 2.50e+03 5.43e+00 bond pdb=" C HIS R 296 " pdb=" N VAL R 297 " ideal model delta sigma weight residual 1.335 1.306 0.028 1.26e-02 6.30e+03 5.07e+00 ... (remaining 1999 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.10: 2562 1.10 - 2.20: 151 2.20 - 3.30: 32 3.30 - 4.40: 6 4.40 - 5.50: 8 Bond angle restraints: 2759 Sorted by residual: angle pdb=" N THR R 189 " pdb=" CA THR R 189 " pdb=" C THR R 189 " ideal model delta sigma weight residual 111.28 113.69 -2.41 1.09e+00 8.42e-01 4.89e+00 angle pdb=" CA CYS R 191 " pdb=" CB CYS R 191 " pdb=" SG CYS R 191 " ideal model delta sigma weight residual 114.40 119.24 -4.84 2.30e+00 1.89e-01 4.43e+00 angle pdb=" N ASN R 322 " pdb=" CA ASN R 322 " pdb=" C ASN R 322 " ideal model delta sigma weight residual 112.75 115.56 -2.81 1.36e+00 5.41e-01 4.28e+00 angle pdb=" CA TRP R 109 " pdb=" CB TRP R 109 " pdb=" CG TRP R 109 " ideal model delta sigma weight residual 113.60 117.46 -3.86 1.90e+00 2.77e-01 4.12e+00 angle pdb=" C VAL R 295 " pdb=" N HIS R 296 " pdb=" CA HIS R 296 " ideal model delta sigma weight residual 120.44 117.81 2.63 1.30e+00 5.92e-01 4.10e+00 ... (remaining 2754 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.85: 1043 16.85 - 33.70: 77 33.70 - 50.54: 15 50.54 - 67.39: 2 67.39 - 84.24: 2 Dihedral angle restraints: 1139 sinusoidal: 314 harmonic: 825 Sorted by residual: dihedral pdb=" CA ALA R 59 " pdb=" C ALA R 59 " pdb=" N LYS R 60 " pdb=" CA LYS R 60 " ideal model delta harmonic sigma weight residual -180.00 -161.04 -18.96 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CA TRP R 99 " pdb=" C TRP R 99 " pdb=" N THR R 100 " pdb=" CA THR R 100 " ideal model delta harmonic sigma weight residual 180.00 161.56 18.44 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CA LEU R 302 " pdb=" C LEU R 302 " pdb=" N ILE R 303 " pdb=" CA ILE R 303 " ideal model delta harmonic sigma weight residual -180.00 -161.65 -18.35 0 5.00e+00 4.00e-02 1.35e+01 ... (remaining 1136 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 214 0.033 - 0.067: 93 0.067 - 0.100: 18 0.100 - 0.133: 9 0.133 - 0.167: 2 Chirality restraints: 336 Sorted by residual: chirality pdb=" CAJ G1I R 501 " pdb=" CAF G1I R 501 " pdb=" CAI G1I R 501 " pdb=" OAM G1I R 501 " both_signs ideal model delta sigma weight residual False 2.40 2.57 -0.17 2.00e-01 2.50e+01 6.95e-01 chirality pdb=" CA HIS R 296 " pdb=" N HIS R 296 " pdb=" C HIS R 296 " pdb=" CB HIS R 296 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.51e-01 chirality pdb=" CB VAL R 218 " pdb=" CA VAL R 218 " pdb=" CG1 VAL R 218 " pdb=" CG2 VAL R 218 " both_signs ideal model delta sigma weight residual False -2.63 -2.51 -0.12 2.00e-01 2.50e+01 3.46e-01 ... (remaining 333 not shown) Planarity restraints: 346 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU R 155 " -0.008 2.00e-02 2.50e+03 1.54e-02 2.37e+00 pdb=" C LEU R 155 " 0.027 2.00e-02 2.50e+03 pdb=" O LEU R 155 " -0.010 2.00e-02 2.50e+03 pdb=" N MET R 156 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE R 277 " -0.008 2.00e-02 2.50e+03 1.52e-02 2.32e+00 pdb=" C ILE R 277 " 0.026 2.00e-02 2.50e+03 pdb=" O ILE R 277 " -0.010 2.00e-02 2.50e+03 pdb=" N ILE R 278 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP R 99 " 0.008 2.00e-02 2.50e+03 7.37e-03 1.36e+00 pdb=" CG TRP R 99 " -0.019 2.00e-02 2.50e+03 pdb=" CD1 TRP R 99 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TRP R 99 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP R 99 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP R 99 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP R 99 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 99 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 99 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP R 99 " -0.000 2.00e-02 2.50e+03 ... (remaining 343 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.88: 760 2.88 - 3.38: 2097 3.38 - 3.89: 3039 3.89 - 4.39: 2998 4.39 - 4.90: 5005 Nonbonded interactions: 13899 Sorted by model distance: nonbonded pdb=" OD1 ASP R 130 " pdb=" N ARG R 131 " model vdw 2.374 3.120 nonbonded pdb=" O ASN R 318 " pdb=" OD1 ASN R 318 " model vdw 2.516 3.040 nonbonded pdb=" O ILE R 58 " pdb=" NE2 GLN R 65 " model vdw 2.556 3.120 nonbonded pdb=" O HIS R 296 " pdb=" O GLN R 299 " model vdw 2.558 3.040 nonbonded pdb=" O ILE R 127 " pdb=" OD1 ASP R 130 " model vdw 2.579 3.040 ... (remaining 13894 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.810 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: 0.020 Set scattering table: 0.020 Process input model: 11.050 Find NCS groups from input model: 0.040 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:3.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 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 0.055 2004 Z= 0.283 Angle : 0.651 5.502 2759 Z= 0.375 Chirality : 0.041 0.167 336 Planarity : 0.004 0.027 346 Dihedral : 13.375 84.238 595 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 0.89 (0.51), residues: 277 helix: 1.34 (0.38), residues: 202 sheet: None (None), residues: 0 loop : -1.47 (0.62), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP R 99 HIS 0.004 0.002 HIS R 178 PHE 0.016 0.002 PHE R 108 TYR 0.007 0.001 TYR R 132 ARG 0.008 0.001 ARG R 228 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.220 Fit side-chains REVERT: R 190 CYS cc_start: 0.6395 (t) cc_final: 0.5772 (t) REVERT: R 215 MET cc_start: 0.7844 (mmm) cc_final: 0.7401 (mtt) outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.1033 time to fit residues: 5.2387 Evaluate side-chains 27 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 23 optimal weight: 0.6980 chunk 21 optimal weight: 0.0870 chunk 11 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 chunk 14 optimal weight: 0.0570 chunk 8 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 overall best weight: 0.4076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 296 HIS R 312 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2004 Z= 0.188 Angle : 0.566 5.264 2759 Z= 0.319 Chirality : 0.041 0.147 336 Planarity : 0.004 0.027 346 Dihedral : 5.262 18.661 307 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.32 % Allowed : 17.76 % Favored : 80.92 % 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: 2.01 (0.53), residues: 277 helix: 1.92 (0.37), residues: 212 sheet: None (None), residues: 0 loop : -0.60 (0.87), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP R 158 HIS 0.014 0.003 HIS R 296 PHE 0.009 0.001 PHE R 108 TYR 0.013 0.001 TYR R 141 ARG 0.002 0.001 ARG R 228 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 36 time to evaluate : 0.188 Fit side-chains revert: symmetry clash REVERT: R 131 ARG cc_start: 0.8603 (mmm-85) cc_final: 0.8372 (mmm-85) outliers start: 2 outliers final: 2 residues processed: 36 average time/residue: 0.1150 time to fit residues: 5.1310 Evaluate side-chains 31 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 29 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 272 LEU Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 22 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 2 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 27 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 296 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2004 Z= 0.220 Angle : 0.568 5.357 2759 Z= 0.319 Chirality : 0.041 0.165 336 Planarity : 0.004 0.028 346 Dihedral : 5.194 18.367 307 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Rotamer: Outliers : 3.95 % Allowed : 15.79 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.52), residues: 277 helix: 1.89 (0.36), residues: 212 sheet: None (None), residues: 0 loop : -0.76 (0.83), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP R 109 HIS 0.015 0.003 HIS R 296 PHE 0.010 0.001 PHE R 282 TYR 0.010 0.001 TYR R 141 ARG 0.002 0.000 ARG R 228 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 31 time to evaluate : 0.239 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 33 average time/residue: 0.1198 time to fit residues: 4.7839 Evaluate side-chains 33 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 29 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 120 SER Chi-restraints excluded: chain R residue 158 TRP Chi-restraints excluded: chain R residue 272 LEU Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 7 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 20 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 18 optimal weight: 0.5980 chunk 13 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 296 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2004 Z= 0.214 Angle : 0.555 5.369 2759 Z= 0.311 Chirality : 0.041 0.161 336 Planarity : 0.003 0.027 346 Dihedral : 5.139 18.160 307 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 5.26 % Allowed : 18.42 % Favored : 76.32 % 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: 1.83 (0.52), residues: 277 helix: 1.88 (0.36), residues: 213 sheet: None (None), residues: 0 loop : -1.06 (0.79), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 109 HIS 0.014 0.003 HIS R 296 PHE 0.010 0.001 PHE R 282 TYR 0.007 0.001 TYR R 199 ARG 0.001 0.000 ARG R 131 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 33 time to evaluate : 0.222 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 7 residues processed: 38 average time/residue: 0.1059 time to fit residues: 4.8807 Evaluate side-chains 37 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 30 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 87 VAL Chi-restraints excluded: chain R residue 120 SER Chi-restraints excluded: chain R residue 158 TRP Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 272 LEU Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 9 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 2 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 296 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2004 Z= 0.218 Angle : 0.556 5.391 2759 Z= 0.312 Chirality : 0.041 0.167 336 Planarity : 0.004 0.027 346 Dihedral : 5.123 18.071 307 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 8.55 % Allowed : 19.08 % Favored : 72.37 % 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: 1.75 (0.52), residues: 277 helix: 1.81 (0.36), residues: 213 sheet: None (None), residues: 0 loop : -1.06 (0.79), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP R 99 HIS 0.012 0.003 HIS R 296 PHE 0.011 0.001 PHE R 282 TYR 0.007 0.001 TYR R 199 ARG 0.001 0.000 ARG R 228 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 33 time to evaluate : 0.212 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 66 THR cc_start: 0.8787 (m) cc_final: 0.8583 (m) REVERT: R 272 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8817 (tp) outliers start: 13 outliers final: 8 residues processed: 40 average time/residue: 0.0966 time to fit residues: 4.7551 Evaluate side-chains 41 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 32 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 87 VAL Chi-restraints excluded: chain R residue 99 TRP Chi-restraints excluded: chain R residue 120 SER Chi-restraints excluded: chain R residue 158 TRP Chi-restraints excluded: chain R residue 164 THR Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 272 LEU Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 26 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 15 optimal weight: 7.9990 chunk 19 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 10 optimal weight: 0.0370 chunk 8 optimal weight: 0.6980 chunk 5 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 269 HIS R 296 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2004 Z= 0.200 Angle : 0.543 5.383 2759 Z= 0.304 Chirality : 0.041 0.170 336 Planarity : 0.003 0.026 346 Dihedral : 5.051 17.678 307 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 6.58 % Allowed : 24.34 % Favored : 69.08 % 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: 1.79 (0.52), residues: 277 helix: 1.80 (0.36), residues: 214 sheet: None (None), residues: 0 loop : -0.95 (0.81), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP R 99 HIS 0.010 0.003 HIS R 296 PHE 0.011 0.001 PHE R 282 TYR 0.007 0.001 TYR R 199 ARG 0.001 0.000 ARG R 228 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 32 time to evaluate : 0.219 Fit side-chains revert: symmetry clash REVERT: R 272 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8828 (tp) outliers start: 10 outliers final: 9 residues processed: 38 average time/residue: 0.1188 time to fit residues: 5.4836 Evaluate side-chains 41 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 31 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 87 VAL Chi-restraints excluded: chain R residue 99 TRP Chi-restraints excluded: chain R residue 120 SER Chi-restraints excluded: chain R residue 158 TRP Chi-restraints excluded: chain R residue 164 THR Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 272 LEU Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 18 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 21 optimal weight: 0.0980 chunk 24 optimal weight: 0.6980 chunk 25 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 296 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2004 Z= 0.181 Angle : 0.523 5.380 2759 Z= 0.294 Chirality : 0.040 0.172 336 Planarity : 0.003 0.026 346 Dihedral : 4.945 17.345 307 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 5.92 % Allowed : 27.63 % Favored : 66.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.52), residues: 277 helix: 1.86 (0.36), residues: 214 sheet: None (None), residues: 0 loop : -1.08 (0.80), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 109 HIS 0.009 0.002 HIS R 296 PHE 0.012 0.001 PHE R 282 TYR 0.007 0.001 TYR R 199 ARG 0.001 0.000 ARG R 228 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 32 time to evaluate : 0.214 Fit side-chains outliers start: 9 outliers final: 8 residues processed: 37 average time/residue: 0.1175 time to fit residues: 5.2640 Evaluate side-chains 38 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 30 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 99 TRP Chi-restraints excluded: chain R residue 120 SER Chi-restraints excluded: chain R residue 158 TRP Chi-restraints excluded: chain R residue 164 THR Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 22 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 16 optimal weight: 0.0270 chunk 26 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 13 optimal weight: 0.4980 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 296 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2004 Z= 0.189 Angle : 0.554 7.026 2759 Z= 0.311 Chirality : 0.041 0.172 336 Planarity : 0.003 0.026 346 Dihedral : 4.941 18.979 307 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 7.89 % Allowed : 25.66 % Favored : 66.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.52), residues: 277 helix: 1.87 (0.36), residues: 214 sheet: None (None), residues: 0 loop : -0.99 (0.78), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP R 109 HIS 0.011 0.003 HIS R 296 PHE 0.012 0.001 PHE R 282 TYR 0.007 0.001 TYR R 199 ARG 0.002 0.000 ARG R 228 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 33 time to evaluate : 0.216 Fit side-chains outliers start: 12 outliers final: 10 residues processed: 40 average time/residue: 0.1116 time to fit residues: 5.4304 Evaluate side-chains 41 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 31 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 99 TRP Chi-restraints excluded: chain R residue 120 SER Chi-restraints excluded: chain R residue 139 PHE Chi-restraints excluded: chain R residue 158 TRP Chi-restraints excluded: chain R residue 164 THR Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 17 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 3 optimal weight: 0.4980 chunk 22 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 296 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2004 Z= 0.204 Angle : 0.559 6.298 2759 Z= 0.315 Chirality : 0.041 0.172 336 Planarity : 0.003 0.026 346 Dihedral : 4.952 19.227 307 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 7.24 % Allowed : 26.97 % Favored : 65.79 % 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: 1.82 (0.52), residues: 277 helix: 1.85 (0.36), residues: 214 sheet: None (None), residues: 0 loop : -1.02 (0.78), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 109 HIS 0.010 0.003 HIS R 296 PHE 0.012 0.001 PHE R 282 TYR 0.007 0.001 TYR R 199 ARG 0.002 0.000 ARG R 228 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 31 time to evaluate : 0.219 Fit side-chains outliers start: 11 outliers final: 10 residues processed: 38 average time/residue: 0.1181 time to fit residues: 5.4622 Evaluate side-chains 40 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 30 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 99 TRP Chi-restraints excluded: chain R residue 120 SER Chi-restraints excluded: chain R residue 139 PHE Chi-restraints excluded: chain R residue 158 TRP Chi-restraints excluded: chain R residue 164 THR Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 16 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 14 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 296 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2004 Z= 0.212 Angle : 0.568 5.712 2759 Z= 0.321 Chirality : 0.042 0.171 336 Planarity : 0.003 0.026 346 Dihedral : 4.966 19.437 307 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 6.58 % Allowed : 28.29 % Favored : 65.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.52), residues: 277 helix: 1.85 (0.36), residues: 214 sheet: None (None), residues: 0 loop : -0.94 (0.80), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 109 HIS 0.011 0.003 HIS R 296 PHE 0.012 0.001 PHE R 282 TYR 0.007 0.001 TYR R 199 ARG 0.002 0.000 ARG R 228 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 29 time to evaluate : 0.236 Fit side-chains outliers start: 10 outliers final: 10 residues processed: 36 average time/residue: 0.1147 time to fit residues: 5.0001 Evaluate side-chains 39 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 29 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 99 TRP Chi-restraints excluded: chain R residue 120 SER Chi-restraints excluded: chain R residue 139 PHE Chi-restraints excluded: chain R residue 158 TRP Chi-restraints excluded: chain R residue 164 THR Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 3 optimal weight: 0.0030 chunk 5 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 7 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 296 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.135249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.121879 restraints weight = 4007.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.124284 restraints weight = 2191.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.125965 restraints weight = 1405.414| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2004 Z= 0.187 Angle : 0.546 5.457 2759 Z= 0.308 Chirality : 0.041 0.172 336 Planarity : 0.003 0.026 346 Dihedral : 4.859 19.235 307 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 7.24 % Allowed : 28.29 % Favored : 64.47 % 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: 1.91 (0.52), residues: 277 helix: 1.89 (0.36), residues: 214 sheet: None (None), residues: 0 loop : -0.90 (0.81), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 109 HIS 0.010 0.003 HIS R 296 PHE 0.012 0.001 PHE R 282 TYR 0.007 0.001 TYR R 199 ARG 0.002 0.000 ARG R 228 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 886.94 seconds wall clock time: 21 minutes 7.22 seconds (1267.22 seconds total)