Starting phenix.real_space_refine on Sun Mar 10 20:04:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8efp_28087/03_2024/8efp_28087.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8efp_28087/03_2024/8efp_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_28087/03_2024/8efp_28087.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8efp_28087/03_2024/8efp_28087.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8efp_28087/03_2024/8efp_28087.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8efp_28087/03_2024/8efp_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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 2.99, per 1000 atoms: 0.64 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: 1.99 Conformation dependent library (CDL) restraints added in 878.8 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: 0.45 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: 1.12 Time building geometry restraints manager: 2.12 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: 0.920 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: 3.590 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 16.920 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.460 ------------------------------------------------------------------------------- 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 : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 207 TYR cc_start: 0.7911 (m-10) cc_final: 0.7477 (m-10) REVERT: C 275 LEU cc_start: 0.8243 (pp) cc_final: 0.7875 (pp) outliers start: 16 outliers final: 4 residues processed: 77 average time/residue: 0.1877 time to fit residues: 18.2975 Evaluate side-chains 50 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 46 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 108 ARG Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain C residue 86 ILE 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: 2.9990 chunk 17 optimal weight: 4.9990 chunk 28 optimal weight: 0.1980 chunk 34 optimal weight: 7.9990 chunk 53 optimal weight: 5.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- 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 ** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6490 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 4790 Z= 0.265 Angle : 0.865 11.372 6495 Z= 0.434 Chirality : 0.046 0.177 747 Planarity : 0.006 0.068 848 Dihedral : 7.562 59.912 647 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 29.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.80 % Favored : 87.20 % Rotamer: Outliers : 4.60 % Allowed : 29.50 % Favored : 65.90 % 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: -1.77 (0.32), residues: 206 sheet: -3.65 (0.50), residues: 66 loop : -2.87 (0.33), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.005 TRP C 179 HIS 0.004 0.001 HIS B 26 PHE 0.015 0.002 PHE C 34 TYR 0.021 0.001 TYR B 27 ARG 0.006 0.001 ARG C 291 *********************** 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 75 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 51 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 75 LEU cc_start: 0.8903 (pp) cc_final: 0.8322 (mt) REVERT: B 108 ARG cc_start: 0.6538 (OUTLIER) cc_final: 0.5508 (pmt-80) REVERT: C 62 LEU cc_start: 0.9265 (pp) cc_final: 0.9007 (mm) REVERT: C 275 LEU cc_start: 0.8244 (pp) cc_final: 0.7934 (pp) outliers start: 24 outliers final: 14 residues processed: 70 average time/residue: 0.1498 time to fit residues: 14.1058 Evaluate side-chains 59 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 44 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 108 ARG Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 198 ARG Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 156 TYR Chi-restraints excluded: chain C residue 285 ARG Chi-restraints excluded: chain C residue 332 PHE Chi-restraints excluded: chain C residue 394 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 29 optimal weight: 5.9990 chunk 16 optimal weight: 8.9990 chunk 44 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 14 optimal weight: 0.8980 chunk 53 optimal weight: 0.0020 chunk 57 optimal weight: 0.9990 chunk 47 optimal weight: 9.9990 chunk 18 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 40 optimal weight: 20.0000 overall best weight: 2.3794 ------------------------------------------------------------------------------- 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 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6623 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 4790 Z= 0.301 Angle : 0.804 11.162 6495 Z= 0.411 Chirality : 0.043 0.144 747 Planarity : 0.005 0.068 848 Dihedral : 7.118 56.395 647 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 31.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.63 % Favored : 87.37 % Rotamer: Outliers : 4.79 % Allowed : 29.89 % Favored : 65.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.47 (0.32), residues: 586 helix: -1.35 (0.32), residues: 216 sheet: -3.12 (0.55), residues: 66 loop : -2.88 (0.34), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 34 HIS 0.007 0.002 HIS C 186 PHE 0.018 0.002 PHE C 5 TYR 0.014 0.002 TYR B 27 ARG 0.004 0.001 ARG B 50 *********************** 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 74 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 49 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 108 ARG cc_start: 0.6604 (OUTLIER) cc_final: 0.5528 (pmt-80) REVERT: B 230 ASN cc_start: 0.8662 (t0) cc_final: 0.8379 (t0) outliers start: 25 outliers final: 15 residues processed: 70 average time/residue: 0.1545 time to fit residues: 14.3427 Evaluate side-chains 58 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 42 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 103 ASN Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 108 ARG Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 145 GLU Chi-restraints excluded: chain B residue 198 ARG Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 156 TYR Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 285 ARG Chi-restraints excluded: chain C residue 332 PHE Chi-restraints excluded: chain C residue 379 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 27 optimal weight: 9.9990 chunk 5 optimal weight: 20.0000 chunk 25 optimal weight: 0.1980 chunk 36 optimal weight: 10.0000 chunk 53 optimal weight: 1.9990 chunk 57 optimal weight: 8.9990 chunk 28 optimal weight: 9.9990 chunk 51 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 47 optimal weight: 6.9990 chunk 32 optimal weight: 0.0470 overall best weight: 1.0482 ------------------------------------------------------------------------------- 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 286 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6568 moved from start: 0.3602 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= 0.212 Angle : 0.777 12.871 6495 Z= 0.382 Chirality : 0.043 0.135 747 Planarity : 0.005 0.061 848 Dihedral : 6.394 30.741 645 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 24.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.58 % Favored : 89.42 % Rotamer: Outliers : 4.02 % Allowed : 30.27 % Favored : 65.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.26 (0.32), residues: 586 helix: -1.10 (0.32), residues: 224 sheet: -3.11 (0.58), residues: 56 loop : -2.87 (0.33), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP B 34 HIS 0.005 0.001 HIS C 186 PHE 0.011 0.002 PHE B 192 TYR 0.012 0.001 TYR B 27 ARG 0.003 0.000 ARG C 285 *********************** 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 71 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 50 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 75 LEU cc_start: 0.8977 (pp) cc_final: 0.8570 (mt) REVERT: B 108 ARG cc_start: 0.6666 (OUTLIER) cc_final: 0.5536 (pmt-80) REVERT: B 230 ASN cc_start: 0.8574 (t0) cc_final: 0.8229 (t0) REVERT: C 275 LEU cc_start: 0.7991 (pp) cc_final: 0.7711 (pp) outliers start: 21 outliers final: 14 residues processed: 66 average time/residue: 0.1635 time to fit residues: 14.1789 Evaluate side-chains 61 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 46 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 78 HIS Chi-restraints excluded: chain B residue 85 GLU Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 108 ARG Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 198 ARG Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 285 ARG Chi-restraints excluded: chain C residue 332 PHE Chi-restraints excluded: chain C residue 379 ASP 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: 9.9990 chunk 23 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 39 optimal weight: 10.0000 chunk 29 optimal weight: 3.9990 chunk 51 optimal weight: 6.9990 chunk 14 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6718 moved from start: 0.4239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 4790 Z= 0.322 Angle : 0.812 10.900 6495 Z= 0.403 Chirality : 0.044 0.175 747 Planarity : 0.005 0.057 848 Dihedral : 6.433 31.034 645 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 30.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.14 % Favored : 86.86 % Rotamer: Outliers : 4.79 % Allowed : 28.35 % Favored : 66.86 % 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: -3.16 (0.32), residues: 586 helix: -0.99 (0.32), residues: 223 sheet: -3.16 (0.59), residues: 56 loop : -2.81 (0.34), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 34 HIS 0.008 0.002 HIS C 302 PHE 0.014 0.002 PHE B 48 TYR 0.013 0.002 TYR C 393 ARG 0.010 0.001 ARG B 44 *********************** 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 67 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 42 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 108 ARG cc_start: 0.6652 (OUTLIER) cc_final: 0.5737 (pmt-80) REVERT: B 230 ASN cc_start: 0.8646 (t0) cc_final: 0.8421 (t0) REVERT: C 275 LEU cc_start: 0.7963 (pp) cc_final: 0.7753 (pp) outliers start: 25 outliers final: 19 residues processed: 63 average time/residue: 0.1569 time to fit residues: 13.3241 Evaluate side-chains 60 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 40 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 103 ASN Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 108 ARG Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 145 GLU Chi-restraints excluded: chain B residue 198 ARG Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 146 PHE Chi-restraints excluded: chain C residue 156 TYR Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 285 ARG Chi-restraints excluded: chain C residue 332 PHE Chi-restraints excluded: chain C residue 379 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 14 optimal weight: 8.9990 chunk 57 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 chunk 4 optimal weight: 10.0000 chunk 18 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 41 optimal weight: 10.0000 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 127 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 135 ASN ** 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: 0.6699 moved from start: 0.4658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 4790 Z= 0.256 Angle : 0.805 16.591 6495 Z= 0.386 Chirality : 0.043 0.141 747 Planarity : 0.005 0.060 848 Dihedral : 6.342 31.034 645 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 28.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.95 % Favored : 88.05 % Rotamer: Outliers : 4.21 % Allowed : 28.74 % 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: -2.84 (0.33), residues: 586 helix: -0.67 (0.34), residues: 211 sheet: -3.18 (0.57), residues: 56 loop : -2.57 (0.34), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 34 HIS 0.004 0.001 HIS C 186 PHE 0.009 0.002 PHE B 48 TYR 0.010 0.001 TYR B 227 ARG 0.010 0.001 ARG B 44 *********************** 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 65 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 43 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 75 LEU cc_start: 0.8996 (pp) cc_final: 0.8733 (mm) REVERT: B 108 ARG cc_start: 0.6648 (OUTLIER) cc_final: 0.5618 (pmt-80) REVERT: B 230 ASN cc_start: 0.8552 (t0) cc_final: 0.8352 (t0) outliers start: 22 outliers final: 18 residues processed: 62 average time/residue: 0.1701 time to fit residues: 13.6739 Evaluate side-chains 59 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 40 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 108 ARG Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 165 TYR Chi-restraints excluded: chain B residue 198 ARG Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 146 PHE Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 285 ARG Chi-restraints excluded: chain C residue 379 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 32 optimal weight: 0.6980 chunk 48 optimal weight: 40.0000 chunk 31 optimal weight: 6.9990 chunk 56 optimal weight: 0.0670 chunk 35 optimal weight: 0.3980 chunk 34 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 33 optimal weight: 7.9990 chunk 17 optimal weight: 0.0030 chunk 11 optimal weight: 0.9990 overall best weight: 0.4328 ------------------------------------------------------------------------------- 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 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6567 moved from start: 0.4889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4790 Z= 0.191 Angle : 0.776 11.563 6495 Z= 0.369 Chirality : 0.042 0.124 747 Planarity : 0.004 0.049 848 Dihedral : 5.907 30.967 645 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 21.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.26 % Favored : 88.74 % Rotamer: Outliers : 3.07 % Allowed : 30.84 % 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: -2.51 (0.34), residues: 586 helix: -0.36 (0.35), residues: 211 sheet: -3.13 (0.58), residues: 56 loop : -2.36 (0.35), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 34 HIS 0.004 0.001 HIS B 209 PHE 0.008 0.001 PHE C 47 TYR 0.009 0.001 TYR B 27 ARG 0.007 0.000 ARG B 44 *********************** 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 64 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 48 time to evaluate : 0.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 75 LEU cc_start: 0.9018 (pp) cc_final: 0.8766 (mt) REVERT: B 108 ARG cc_start: 0.6654 (OUTLIER) cc_final: 0.5436 (pmt-80) REVERT: B 230 ASN cc_start: 0.8444 (t0) cc_final: 0.8188 (t0) REVERT: C 85 GLN cc_start: 0.7600 (mm110) cc_final: 0.7374 (tp-100) REVERT: C 308 LYS cc_start: 0.9084 (OUTLIER) cc_final: 0.8873 (mmmm) outliers start: 16 outliers final: 14 residues processed: 61 average time/residue: 0.1878 time to fit residues: 14.8091 Evaluate side-chains 61 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 45 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 108 ARG Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 165 TYR Chi-restraints excluded: chain B residue 198 ARG Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 285 ARG Chi-restraints excluded: chain C residue 308 LYS Chi-restraints excluded: chain C residue 332 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 11 optimal weight: 0.9980 chunk 36 optimal weight: 20.0000 chunk 38 optimal weight: 20.0000 chunk 28 optimal weight: 9.9990 chunk 5 optimal weight: 0.9980 chunk 44 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 49 optimal weight: 8.9990 chunk 52 optimal weight: 5.9990 chunk 31 optimal weight: 0.0970 overall best weight: 2.0182 ------------------------------------------------------------------------------- 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 286 GLN ** C 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6656 moved from start: 0.5202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 4790 Z= 0.242 Angle : 0.798 12.018 6495 Z= 0.383 Chirality : 0.042 0.134 747 Planarity : 0.004 0.052 848 Dihedral : 5.986 30.688 645 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 25.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.75 % Favored : 89.25 % Rotamer: Outliers : 3.45 % Allowed : 31.99 % Favored : 64.56 % 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: -2.53 (0.34), residues: 586 helix: -0.36 (0.34), residues: 211 sheet: -3.48 (0.54), residues: 54 loop : -2.33 (0.35), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 179 HIS 0.004 0.001 HIS C 186 PHE 0.008 0.002 PHE C 47 TYR 0.010 0.001 TYR C 382 ARG 0.008 0.001 ARG B 44 *********************** 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 65 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 47 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 75 LEU cc_start: 0.9053 (pp) cc_final: 0.8759 (mm) REVERT: B 108 ARG cc_start: 0.6608 (OUTLIER) cc_final: 0.5552 (pmt-80) REVERT: C 85 GLN cc_start: 0.7627 (mm110) cc_final: 0.7386 (tp-100) REVERT: C 308 LYS cc_start: 0.9074 (OUTLIER) cc_final: 0.8845 (mmmm) REVERT: C 366 MET cc_start: 0.2903 (mmm) cc_final: 0.2210 (mtp) outliers start: 18 outliers final: 15 residues processed: 61 average time/residue: 0.1572 time to fit residues: 12.7970 Evaluate side-chains 60 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 43 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 108 ARG Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 165 TYR Chi-restraints excluded: chain B residue 198 ARG Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 216 ASN Chi-restraints excluded: chain C residue 285 ARG Chi-restraints excluded: chain C residue 308 LYS Chi-restraints excluded: chain C residue 332 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 23 optimal weight: 0.9980 chunk 41 optimal weight: 7.9990 chunk 16 optimal weight: 8.9990 chunk 47 optimal weight: 10.0000 chunk 50 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 34 optimal weight: 4.9990 chunk 56 optimal weight: 0.0000 chunk 26 optimal weight: 8.9990 chunk 38 optimal weight: 20.0000 chunk 58 optimal weight: 4.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- 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 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6643 moved from start: 0.5392 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= 0.218 Angle : 0.807 12.961 6495 Z= 0.381 Chirality : 0.042 0.129 747 Planarity : 0.004 0.049 848 Dihedral : 5.965 30.669 645 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 24.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.92 % Favored : 89.08 % Rotamer: Outliers : 3.45 % Allowed : 31.42 % 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: -2.47 (0.34), residues: 586 helix: -0.32 (0.34), residues: 211 sheet: -3.13 (0.57), residues: 57 loop : -2.34 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 34 HIS 0.004 0.001 HIS B 209 PHE 0.008 0.001 PHE C 47 TYR 0.010 0.001 TYR C 393 ARG 0.008 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 64 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 46 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 108 ARG cc_start: 0.6690 (OUTLIER) cc_final: 0.5572 (pmt-80) REVERT: B 258 ILE cc_start: 0.9351 (pt) cc_final: 0.8958 (mt) REVERT: C 85 GLN cc_start: 0.7669 (mm110) cc_final: 0.7421 (tp-100) REVERT: C 308 LYS cc_start: 0.9053 (OUTLIER) cc_final: 0.8821 (mmmm) outliers start: 18 outliers final: 16 residues processed: 62 average time/residue: 0.1669 time to fit residues: 13.5844 Evaluate side-chains 64 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 46 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 108 ARG Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 165 TYR Chi-restraints excluded: chain B residue 198 ARG Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 146 PHE Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 285 ARG Chi-restraints excluded: chain C residue 308 LYS Chi-restraints excluded: chain C residue 332 PHE 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: 2.9990 chunk 4 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 28 optimal weight: 8.9990 chunk 37 optimal weight: 4.9990 chunk 49 optimal weight: 7.9990 chunk 14 optimal weight: 2.9990 chunk 43 optimal weight: 6.9990 chunk 6 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- 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 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6668 moved from start: 0.5673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 4790 Z= 0.230 Angle : 0.847 18.245 6495 Z= 0.389 Chirality : 0.042 0.128 747 Planarity : 0.004 0.049 848 Dihedral : 5.955 30.623 645 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 23.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.09 % Favored : 88.91 % Rotamer: Outliers : 3.83 % Allowed : 31.03 % 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: -2.46 (0.34), residues: 586 helix: -0.27 (0.35), residues: 211 sheet: -3.34 (0.57), residues: 54 loop : -2.34 (0.35), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 34 HIS 0.004 0.001 HIS C 186 PHE 0.009 0.002 PHE C 47 TYR 0.013 0.001 TYR C 393 ARG 0.007 0.001 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 66 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 46 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 108 ARG cc_start: 0.6624 (OUTLIER) cc_final: 0.5470 (pmt-80) REVERT: B 258 ILE cc_start: 0.9451 (pt) cc_final: 0.9120 (mt) REVERT: C 85 GLN cc_start: 0.7612 (mm110) cc_final: 0.7312 (tp-100) REVERT: C 308 LYS cc_start: 0.9034 (OUTLIER) cc_final: 0.8801 (mmmm) REVERT: C 380 MET cc_start: 0.8646 (ppp) cc_final: 0.8268 (ppp) outliers start: 20 outliers final: 18 residues processed: 63 average time/residue: 0.1728 time to fit residues: 14.4056 Evaluate side-chains 63 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 43 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 103 ASN Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 108 ARG Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 165 TYR Chi-restraints excluded: chain B residue 198 ARG Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 146 PHE Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 285 ARG Chi-restraints excluded: chain C residue 308 LYS Chi-restraints excluded: chain C residue 332 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 46 optimal weight: 10.0000 chunk 19 optimal weight: 0.0270 chunk 48 optimal weight: 0.0470 chunk 5 optimal weight: 0.9990 chunk 8 optimal weight: 7.9990 chunk 41 optimal weight: 7.9990 chunk 2 optimal weight: 1.9990 chunk 33 optimal weight: 8.9990 chunk 53 optimal weight: 5.9990 chunk 31 optimal weight: 20.0000 chunk 40 optimal weight: 20.0000 overall best weight: 1.8142 ------------------------------------------------------------------------------- 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 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 273 ASN ** C 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.077495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.060030 restraints weight = 29940.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.061245 restraints weight = 21041.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.062141 restraints weight = 16348.893| |-----------------------------------------------------------------------------| r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.5848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 4790 Z= 0.230 Angle : 0.814 14.672 6495 Z= 0.388 Chirality : 0.043 0.189 747 Planarity : 0.004 0.049 848 Dihedral : 5.986 30.748 645 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 25.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.77 % Favored : 88.23 % Rotamer: Outliers : 4.21 % Allowed : 30.65 % 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: -2.49 (0.34), residues: 586 helix: -0.32 (0.34), residues: 213 sheet: -3.51 (0.59), residues: 53 loop : -2.32 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 179 HIS 0.004 0.001 HIS B 26 PHE 0.010 0.002 PHE C 146 TYR 0.009 0.001 TYR C 393 ARG 0.008 0.001 ARG B 44 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1327.07 seconds wall clock time: 24 minutes 48.42 seconds (1488.42 seconds total)