Starting phenix.real_space_refine on Thu Dec 7 21:01:02 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8efp_28087/12_2023/8efp_28087.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8efp_28087/12_2023/8efp_28087.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8efp_28087/12_2023/8efp_28087.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8efp_28087/12_2023/8efp_28087.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8efp_28087/12_2023/8efp_28087.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8efp_28087/12_2023/8efp_28087.pdb" } resolution = 3.8 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= 0.009 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 13 5.16 5 C 2977 2.51 5 N 808 2.21 5 O 907 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 59": "OE1" <-> "OE2" Residue "B PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 101": "OE1" <-> "OE2" Residue "C GLU 15": "OE1" <-> "OE2" Residue "C GLU 83": "OE1" <-> "OE2" Residue "C TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 160": "OE1" <-> "OE2" Residue "C PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 266": "OE1" <-> "OE2" Residue "C ASP 270": "OD1" <-> "OD2" Residue "C GLU 289": "OE1" <-> "OE2" Residue "C GLU 342": "OE1" <-> "OE2" Residue "C GLU 351": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 4705 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 1976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1976 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 18, 'TRANS': 224} Chain: "C" Number of atoms: 2729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2729 Classifications: {'peptide': 351} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 11, 'TRANS': 339} Chain breaks: 2 Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 127 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 59 Time building chain proxies: 3.10, per 1000 atoms: 0.66 Number of scatterers: 4705 At special positions: 0 Unit cell: (76.176, 74.52, 113.436, 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 13 16.00 O 907 8.00 N 808 7.00 C 2977 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.15 Conformation dependent library (CDL) restraints added in 876.5 milliseconds 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1150 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 3 sheets defined 40.2% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'B' and resid 22 through 37 Processing helix chain 'B' and resid 43 through 56 Processing helix chain 'B' and resid 217 through 222 removed outlier: 3.524A pdb=" N PHE B 220 " --> pdb=" O PRO B 217 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N SER B 221 " --> pdb=" O GLU B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 249 Processing helix chain 'C' and resid 4 through 18 removed outlier: 3.527A pdb=" N ALA C 18 " --> pdb=" O LYS C 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 62 Processing helix chain 'C' and resid 68 through 77 removed outlier: 4.179A pdb=" N ASP C 74 " --> pdb=" O LEU C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 136 Processing helix chain 'C' and resid 143 through 150 removed outlier: 3.660A pdb=" N ARG C 147 " --> pdb=" O PRO C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 186 removed outlier: 4.258A pdb=" N HIS C 186 " --> pdb=" O ILE C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 262 Processing helix chain 'C' and resid 264 through 279 Processing helix chain 'C' and resid 281 through 299 Processing helix chain 'C' and resid 307 through 315 Processing helix chain 'C' and resid 322 through 339 Processing helix chain 'C' and resid 342 through 353 Processing helix chain 'C' and resid 354 through 369 Processing helix chain 'C' and resid 371 through 376 Processing helix chain 'C' and resid 383 through 404 Processing sheet with id=AA1, first strand: chain 'B' and resid 82 through 83 removed outlier: 6.594A pdb=" N LEU B 82 " --> pdb=" O ASN B 103 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LEU B 102 " --> pdb=" O SER B 123 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 161 through 163 removed outlier: 3.521A pdb=" N CYS B 183 " --> pdb=" O LEU B 162 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N LYS B 204 " --> pdb=" O ARG B 228 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ASN B 230 " --> pdb=" O LYS B 204 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N TYR B 206 " --> pdb=" O ASN B 230 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 22 through 24 removed outlier: 3.853A pdb=" N SER C 206 " --> pdb=" O LEU C 162 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLU C 160 " --> pdb=" O ARG C 208 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N LYS C 210 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N VAL C 158 " --> pdb=" O LYS C 210 " (cutoff:3.500A) 177 hydrogen bonds defined for protein. 522 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: 1.26 Time building geometry restraints manager: 2.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 959 1.33 - 1.45: 1038 1.45 - 1.57: 2773 1.57 - 1.69: 0 1.69 - 1.81: 20 Bond restraints: 4790 Sorted by residual: bond pdb=" N LEU C 263 " pdb=" CA LEU C 263 " ideal model delta sigma weight residual 1.456 1.499 -0.043 1.14e-02 7.69e+03 1.42e+01 bond pdb=" N ASP C 173 " pdb=" CA ASP C 173 " ideal model delta sigma weight residual 1.461 1.490 -0.029 9.70e-03 1.06e+04 9.06e+00 bond pdb=" N LYS C 177 " pdb=" CA LYS C 177 " ideal model delta sigma weight residual 1.453 1.490 -0.037 1.26e-02 6.30e+03 8.83e+00 bond pdb=" CA LYS C 177 " pdb=" C LYS C 177 " ideal model delta sigma weight residual 1.519 1.534 -0.016 5.30e-03 3.56e+04 8.82e+00 bond pdb=" N THR C 264 " pdb=" CA THR C 264 " ideal model delta sigma weight residual 1.454 1.494 -0.039 1.33e-02 5.65e+03 8.68e+00 ... (remaining 4785 not shown) Histogram of bond angle deviations from ideal: 89.70 - 98.69: 12 98.69 - 107.69: 227 107.69 - 116.68: 3118 116.68 - 125.68: 3075 125.68 - 134.67: 63 Bond angle restraints: 6495 Sorted by residual: angle pdb=" C PHE B 98 " pdb=" CA PHE B 98 " pdb=" CB PHE B 98 " ideal model delta sigma weight residual 113.37 93.25 20.12 1.61e+00 3.86e-01 1.56e+02 angle pdb=" N SER C 180 " pdb=" CA SER C 180 " pdb=" C SER C 180 " ideal model delta sigma weight residual 112.94 95.36 17.58 1.41e+00 5.03e-01 1.56e+02 angle pdb=" N PRO C 215 " pdb=" CA PRO C 215 " pdb=" C PRO C 215 " ideal model delta sigma weight residual 111.19 94.15 17.04 1.57e+00 4.06e-01 1.18e+02 angle pdb=" N GLN C 194 " pdb=" CA GLN C 194 " pdb=" C GLN C 194 " ideal model delta sigma weight residual 108.23 89.70 18.53 1.72e+00 3.38e-01 1.16e+02 angle pdb=" N ARG C 195 " pdb=" CA ARG C 195 " pdb=" C ARG C 195 " ideal model delta sigma weight residual 108.76 93.60 15.16 1.69e+00 3.50e-01 8.05e+01 ... (remaining 6490 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.18: 2474 18.18 - 36.37: 360 36.37 - 54.55: 101 54.55 - 72.73: 11 72.73 - 90.91: 8 Dihedral angle restraints: 2954 sinusoidal: 1197 harmonic: 1757 Sorted by residual: dihedral pdb=" C PHE B 98 " pdb=" N PHE B 98 " pdb=" CA PHE B 98 " pdb=" CB PHE B 98 " ideal model delta harmonic sigma weight residual -122.60 -97.68 -24.92 0 2.50e+00 1.60e-01 9.94e+01 dihedral pdb=" C VAL C 213 " pdb=" N VAL C 213 " pdb=" CA VAL C 213 " pdb=" CB VAL C 213 " ideal model delta harmonic sigma weight residual -122.00 -103.01 -18.99 0 2.50e+00 1.60e-01 5.77e+01 dihedral pdb=" C GLN C 194 " pdb=" N GLN C 194 " pdb=" CA GLN C 194 " pdb=" CB GLN C 194 " ideal model delta harmonic sigma weight residual -122.60 -104.35 -18.25 0 2.50e+00 1.60e-01 5.33e+01 ... (remaining 2951 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.147: 709 0.147 - 0.293: 30 0.293 - 0.440: 3 0.440 - 0.586: 0 0.586 - 0.733: 5 Chirality restraints: 747 Sorted by residual: chirality pdb=" CA VAL C 213 " pdb=" N VAL C 213 " pdb=" C VAL C 213 " pdb=" CB VAL C 213 " both_signs ideal model delta sigma weight residual False 2.44 3.17 -0.73 2.00e-01 2.50e+01 1.34e+01 chirality pdb=" CA TYR C 176 " pdb=" N TYR C 176 " pdb=" C TYR C 176 " pdb=" CB TYR C 176 " both_signs ideal model delta sigma weight residual False 2.51 1.82 0.69 2.00e-01 2.50e+01 1.18e+01 chirality pdb=" CA TRP C 179 " pdb=" N TRP C 179 " pdb=" C TRP C 179 " pdb=" CB TRP C 179 " both_signs ideal model delta sigma weight residual False 2.51 3.13 -0.62 2.00e-01 2.50e+01 9.68e+00 ... (remaining 744 not shown) Planarity restraints: 848 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 95 " -0.024 2.00e-02 2.50e+03 4.63e-02 2.14e+01 pdb=" C LEU B 95 " 0.080 2.00e-02 2.50e+03 pdb=" O LEU B 95 " -0.029 2.00e-02 2.50e+03 pdb=" N PRO B 96 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 37 " -0.013 2.00e-02 2.50e+03 2.68e-02 7.18e+00 pdb=" C ASN B 37 " 0.046 2.00e-02 2.50e+03 pdb=" O ASN B 37 " -0.018 2.00e-02 2.50e+03 pdb=" N SER B 38 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 398 " -0.011 2.00e-02 2.50e+03 2.19e-02 4.80e+00 pdb=" C ILE C 398 " 0.038 2.00e-02 2.50e+03 pdb=" O ILE C 398 " -0.014 2.00e-02 2.50e+03 pdb=" N LEU C 399 " -0.013 2.00e-02 2.50e+03 ... (remaining 845 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 64 2.51 - 3.10: 3894 3.10 - 3.70: 7797 3.70 - 4.30: 10845 4.30 - 4.90: 16554 Nonbonded interactions: 39154 Sorted by model distance: nonbonded pdb=" O TRP C 179 " pdb=" CG TRP C 179 " model vdw 1.908 3.260 nonbonded pdb=" O TRP C 179 " pdb=" CD2 TRP C 179 " model vdw 2.113 3.260 nonbonded pdb=" N VAL C 213 " pdb=" O VAL C 213 " model vdw 2.191 2.496 nonbonded pdb=" OG1 THR C 151 " pdb=" NH1 ARG C 152 " model vdw 2.219 2.520 nonbonded pdb=" O LYS C 359 " pdb=" N VAL C 362 " model vdw 2.258 2.520 ... (remaining 39149 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: 0.790 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: 3.640 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 17.850 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 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:3.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6341 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 : 0.006 0.052 4790 Z= 0.385 Angle : 1.460 20.115 6495 Z= 0.886 Chirality : 0.085 0.733 747 Planarity : 0.007 0.067 848 Dihedral : 18.607 90.911 1804 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 33.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.31 % Favored : 86.69 % Rotamer: Outliers : 3.07 % Allowed : 31.03 % Favored : 65.90 % Cbeta Deviations : 1.22 % 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: -4.26 (0.29), residues: 586 helix: -2.31 (0.31), residues: 203 sheet: -3.30 (0.61), residues: 49 loop : -3.21 (0.30), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP B 34 HIS 0.006 0.001 HIS B 26 PHE 0.021 0.003 PHE B 98 TYR 0.027 0.002 TYR C 129 ARG 0.008 0.001 ARG C 124 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 64 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 4 residues processed: 77 average time/residue: 0.1903 time to fit residues: 18.5326 Evaluate side-chains 50 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 46 time to evaluate : 0.602 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1628 time to fit residues: 1.5962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 49 optimal weight: 8.9990 chunk 44 optimal weight: 7.9990 chunk 24 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 30 optimal weight: 7.9990 chunk 23 optimal weight: 0.9980 chunk 46 optimal weight: 6.9990 chunk 17 optimal weight: 4.9990 chunk 28 optimal weight: 0.1980 chunk 34 optimal weight: 7.9990 chunk 53 optimal weight: 10.0000 overall best weight: 1.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 24 ASN ** B 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 ASN ** B 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 GLN B 257 GLN ** C 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6524 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 4790 Z= 0.281 Angle : 0.882 12.037 6495 Z= 0.440 Chirality : 0.046 0.175 747 Planarity : 0.006 0.068 848 Dihedral : 6.899 26.575 637 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 30.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.80 % Favored : 87.20 % Rotamer: Outliers : 4.21 % Allowed : 29.69 % Favored : 66.09 % 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: -3.83 (0.31), residues: 586 helix: -1.75 (0.32), residues: 206 sheet: -3.64 (0.50), residues: 66 loop : -2.90 (0.33), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.004 TRP C 179 HIS 0.005 0.001 HIS B 26 PHE 0.015 0.002 PHE B 192 TYR 0.022 0.001 TYR B 27 ARG 0.007 0.001 ARG C 33 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 52 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 13 residues processed: 69 average time/residue: 0.1525 time to fit residues: 13.9427 Evaluate side-chains 60 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 47 time to evaluate : 0.567 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1156 time to fit residues: 2.7574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 29 optimal weight: 6.9990 chunk 16 optimal weight: 0.8980 chunk 44 optimal weight: 6.9990 chunk 36 optimal weight: 7.9990 chunk 14 optimal weight: 2.9990 chunk 53 optimal weight: 0.0870 chunk 57 optimal weight: 6.9990 chunk 47 optimal weight: 20.0000 chunk 18 optimal weight: 0.9980 chunk 43 optimal weight: 9.9990 chunk 40 optimal weight: 8.9990 overall best weight: 2.3962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 53 GLN ** B 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 78 HIS B 87 ASN ** B 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 257 GLN ** C 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6632 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 4790 Z= 0.298 Angle : 0.784 7.972 6495 Z= 0.407 Chirality : 0.043 0.173 747 Planarity : 0.005 0.069 848 Dihedral : 6.395 23.988 637 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 31.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.80 % Favored : 87.20 % Rotamer: Outliers : 2.68 % Allowed : 31.03 % Favored : 66.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.43 (0.32), residues: 586 helix: -1.31 (0.32), residues: 214 sheet: -3.21 (0.58), residues: 56 loop : -2.87 (0.33), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 34 HIS 0.007 0.002 HIS B 78 PHE 0.022 0.003 PHE B 48 TYR 0.013 0.002 TYR B 27 ARG 0.004 0.001 ARG B 44 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 50 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 6 residues processed: 62 average time/residue: 0.1409 time to fit residues: 12.0295 Evaluate side-chains 48 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 42 time to evaluate : 0.599 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0629 time to fit residues: 1.3845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 27 optimal weight: 0.9980 chunk 5 optimal weight: 20.0000 chunk 25 optimal weight: 6.9990 chunk 36 optimal weight: 8.9990 chunk 53 optimal weight: 0.7980 chunk 57 optimal weight: 5.9990 chunk 28 optimal weight: 20.0000 chunk 51 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 286 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6669 moved from start: 0.3773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 4790 Z= 0.261 Angle : 0.810 10.313 6495 Z= 0.397 Chirality : 0.044 0.166 747 Planarity : 0.005 0.066 848 Dihedral : 6.190 23.086 637 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 27.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.95 % Favored : 88.05 % Rotamer: Outliers : 2.11 % Allowed : 30.84 % Favored : 67.05 % 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: -3.31 (0.32), residues: 586 helix: -1.12 (0.32), residues: 217 sheet: -3.24 (0.59), residues: 54 loop : -2.87 (0.33), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 34 HIS 0.003 0.001 HIS B 209 PHE 0.012 0.002 PHE B 192 TYR 0.011 0.001 TYR B 27 ARG 0.004 0.000 ARG B 108 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 46 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 6 residues processed: 54 average time/residue: 0.1308 time to fit residues: 10.0754 Evaluate side-chains 42 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 36 time to evaluate : 0.562 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0498 time to fit residues: 1.2865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 0 optimal weight: 10.0000 chunk 42 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 39 optimal weight: 10.0000 chunk 29 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 19 optimal weight: 0.2980 chunk 11 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 286 GLN ** C 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6669 moved from start: 0.4317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 4790 Z= 0.243 Angle : 0.786 13.587 6495 Z= 0.380 Chirality : 0.044 0.136 747 Planarity : 0.004 0.054 848 Dihedral : 5.970 21.496 637 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 25.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.75 % Favored : 89.25 % Rotamer: Outliers : 1.92 % Allowed : 30.08 % Favored : 68.01 % 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: -3.12 (0.32), residues: 586 helix: -0.98 (0.33), residues: 217 sheet: -3.28 (0.59), residues: 54 loop : -2.71 (0.33), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 179 HIS 0.005 0.001 HIS C 302 PHE 0.010 0.002 PHE B 192 TYR 0.016 0.002 TYR C 393 ARG 0.002 0.000 ARG B 246 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 42 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 6 residues processed: 50 average time/residue: 0.1211 time to fit residues: 8.9551 Evaluate side-chains 45 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 39 time to evaluate : 0.570 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0567 time to fit residues: 1.3080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 14 optimal weight: 0.9980 chunk 57 optimal weight: 6.9990 chunk 47 optimal weight: 5.9990 chunk 26 optimal weight: 10.0000 chunk 4 optimal weight: 1.9990 chunk 18 optimal weight: 6.9990 chunk 29 optimal weight: 10.0000 chunk 55 optimal weight: 6.9990 chunk 6 optimal weight: 0.8980 chunk 32 optimal weight: 5.9990 chunk 41 optimal weight: 6.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6765 moved from start: 0.4938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 4790 Z= 0.322 Angle : 0.800 9.756 6495 Z= 0.397 Chirality : 0.045 0.137 747 Planarity : 0.005 0.051 848 Dihedral : 6.100 22.046 637 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 32.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.16 % Favored : 85.84 % Rotamer: Outliers : 1.53 % Allowed : 30.84 % Favored : 67.62 % 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: -3.04 (0.32), residues: 586 helix: -0.84 (0.33), residues: 211 sheet: -3.73 (0.55), residues: 53 loop : -2.60 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 179 HIS 0.006 0.001 HIS B 78 PHE 0.010 0.002 PHE C 47 TYR 0.010 0.002 TYR B 227 ARG 0.003 0.001 ARG C 291 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 40 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 47 average time/residue: 0.1203 time to fit residues: 8.4748 Evaluate side-chains 37 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 34 time to evaluate : 0.702 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0670 time to fit residues: 1.2320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 32 optimal weight: 0.8980 chunk 48 optimal weight: 0.0670 chunk 31 optimal weight: 9.9990 chunk 56 optimal weight: 0.0670 chunk 35 optimal weight: 7.9990 chunk 34 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 11 optimal weight: 0.3980 overall best weight: 0.4856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6618 moved from start: 0.5054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4790 Z= 0.207 Angle : 0.797 13.848 6495 Z= 0.376 Chirality : 0.043 0.138 747 Planarity : 0.004 0.042 848 Dihedral : 5.730 19.899 637 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 23.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.90 % Favored : 90.10 % Rotamer: Outliers : 1.15 % Allowed : 31.42 % Favored : 67.43 % 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: -2.84 (0.34), residues: 586 helix: -0.71 (0.34), residues: 211 sheet: -3.69 (0.52), residues: 66 loop : -2.34 (0.35), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 179 HIS 0.004 0.001 HIS B 209 PHE 0.008 0.001 PHE C 146 TYR 0.009 0.001 TYR B 27 ARG 0.006 0.000 ARG B 202 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 48 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 54 average time/residue: 0.1325 time to fit residues: 10.0430 Evaluate side-chains 45 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 42 time to evaluate : 0.504 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1713 time to fit residues: 1.3639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 11 optimal weight: 0.3980 chunk 36 optimal weight: 20.0000 chunk 38 optimal weight: 9.9990 chunk 28 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 chunk 44 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 54 optimal weight: 5.9990 chunk 49 optimal weight: 6.9990 chunk 52 optimal weight: 0.1980 chunk 31 optimal weight: 0.7980 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6637 moved from start: 0.5274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4790 Z= 0.215 Angle : 0.811 15.291 6495 Z= 0.382 Chirality : 0.042 0.133 747 Planarity : 0.004 0.042 848 Dihedral : 5.746 22.395 637 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 24.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.58 % Favored : 89.42 % Rotamer: Outliers : 0.19 % Allowed : 32.57 % Favored : 67.24 % 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: -2.75 (0.34), residues: 586 helix: -0.66 (0.34), residues: 211 sheet: -3.62 (0.52), residues: 66 loop : -2.26 (0.36), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 179 HIS 0.003 0.001 HIS B 78 PHE 0.007 0.001 PHE C 47 TYR 0.011 0.002 TYR C 382 ARG 0.002 0.000 ARG B 108 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 42 time to evaluate : 0.631 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 43 average time/residue: 0.1323 time to fit residues: 8.4256 Evaluate side-chains 43 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 42 time to evaluate : 0.594 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0767 time to fit residues: 0.9427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 23 optimal weight: 0.0370 chunk 41 optimal weight: 6.9990 chunk 16 optimal weight: 0.4980 chunk 47 optimal weight: 5.9990 chunk 50 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 56 optimal weight: 0.0670 chunk 26 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 overall best weight: 0.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 302 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6555 moved from start: 0.5459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4790 Z= 0.203 Angle : 0.833 15.261 6495 Z= 0.392 Chirality : 0.044 0.195 747 Planarity : 0.004 0.036 848 Dihedral : 5.609 24.259 637 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 22.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.22 % Favored : 90.78 % Rotamer: Outliers : 0.19 % Allowed : 33.52 % Favored : 66.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.57 (0.34), residues: 586 helix: -0.45 (0.35), residues: 211 sheet: -3.39 (0.51), residues: 76 loop : -2.17 (0.36), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 179 HIS 0.006 0.001 HIS B 209 PHE 0.008 0.001 PHE C 315 TYR 0.009 0.001 TYR B 227 ARG 0.003 0.000 ARG B 44 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 51 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 51 average time/residue: 0.1564 time to fit residues: 10.8443 Evaluate side-chains 45 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 44 time to evaluate : 0.588 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0538 time to fit residues: 0.8238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 54 optimal weight: 5.9990 chunk 46 optimal weight: 0.9980 chunk 4 optimal weight: 0.0570 chunk 36 optimal weight: 0.6980 chunk 28 optimal weight: 9.9990 chunk 37 optimal weight: 9.9990 chunk 49 optimal weight: 8.9990 chunk 14 optimal weight: 5.9990 chunk 43 optimal weight: 7.9990 chunk 6 optimal weight: 0.7980 chunk 13 optimal weight: 0.3980 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 273 ASN C 302 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6548 moved from start: 0.5660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4790 Z= 0.203 Angle : 0.819 14.403 6495 Z= 0.386 Chirality : 0.043 0.180 747 Planarity : 0.004 0.039 848 Dihedral : 5.649 34.413 637 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 22.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.07 % Favored : 89.93 % Rotamer: Outliers : 0.57 % Allowed : 33.52 % Favored : 65.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -2.52 (0.34), residues: 586 helix: -0.44 (0.34), residues: 211 sheet: -3.45 (0.55), residues: 65 loop : -2.18 (0.36), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 179 HIS 0.004 0.001 HIS B 209 PHE 0.008 0.001 PHE C 47 TYR 0.011 0.001 TYR B 165 ARG 0.003 0.000 ARG B 44 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 45 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 46 average time/residue: 0.1273 time to fit residues: 8.4287 Evaluate side-chains 46 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 45 time to evaluate : 0.506 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0433 time to fit residues: 0.8005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 46 optimal weight: 8.9990 chunk 19 optimal weight: 7.9990 chunk 48 optimal weight: 0.9990 chunk 5 optimal weight: 8.9990 chunk 8 optimal weight: 0.9990 chunk 41 optimal weight: 0.0010 chunk 2 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 40 optimal weight: 0.4980 overall best weight: 1.0992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 302 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.078987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.061417 restraints weight = 29630.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.062701 restraints weight = 20597.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.063588 restraints weight = 15941.592| |-----------------------------------------------------------------------------| r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.5849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4790 Z= 0.207 Angle : 0.786 13.188 6495 Z= 0.377 Chirality : 0.042 0.159 747 Planarity : 0.004 0.039 848 Dihedral : 5.574 32.709 637 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 23.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.39 % Favored : 90.61 % Rotamer: Outliers : 0.38 % Allowed : 33.91 % Favored : 65.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -2.53 (0.34), residues: 586 helix: -0.41 (0.34), residues: 211 sheet: -3.49 (0.54), residues: 66 loop : -2.20 (0.36), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 179 HIS 0.004 0.001 HIS B 26 PHE 0.016 0.001 PHE B 48 TYR 0.016 0.001 TYR C 393 ARG 0.002 0.000 ARG B 44 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1286.29 seconds wall clock time: 24 minutes 2.25 seconds (1442.25 seconds total)