Starting phenix.real_space_refine on Fri Dec 27 14:04:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8plz_17754/12_2024/8plz_17754.cif Found real_map, /net/cci-nas-00/data/ceres_data/8plz_17754/12_2024/8plz_17754.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8plz_17754/12_2024/8plz_17754.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8plz_17754/12_2024/8plz_17754.map" model { file = "/net/cci-nas-00/data/ceres_data/8plz_17754/12_2024/8plz_17754.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8plz_17754/12_2024/8plz_17754.cif" } resolution = 1.9 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= 0.002 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 31 5.16 5 C 3292 2.51 5 N 870 2.21 5 O 1078 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 5271 Number of models: 1 Model: "" Number of chains: 7 Chain: "H" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 512 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 5, 'TRANS': 59} Chain: "I" Number of atoms: 2281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2281 Unusual residues: {'ACE': 1} Classifications: {'peptide': 279, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 264} Chain breaks: 1 Chain: "J" Number of atoms: 2283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2283 Classifications: {'peptide': 286} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 267} Chain breaks: 2 Chain: "J" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ZQ6': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "I" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 65 Classifications: {'water': 65} Link IDs: {None: 64} Chain: "J" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 81 Classifications: {'water': 81} Link IDs: {None: 80} Time building chain proxies: 5.01, per 1000 atoms: 0.95 Number of scatterers: 5271 At special positions: 0 Unit cell: (83.3625, 94.05, 67.6875, 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 31 16.00 O 1078 8.00 N 870 7.00 C 3292 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.46 Conformation dependent library (CDL) restraints added in 620.1 milliseconds 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1196 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 3 sheets defined 61.3% alpha, 4.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'H' and resid 270 through 275 removed outlier: 3.555A pdb=" N ASN H 273 " --> pdb=" O GLY H 270 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL H 275 " --> pdb=" O LEU H 272 " (cutoff:3.500A) Processing helix chain 'H' and resid 279 through 285 Processing helix chain 'H' and resid 288 through 302 removed outlier: 3.953A pdb=" N ALA H 292 " --> pdb=" O THR H 288 " (cutoff:3.500A) Processing helix chain 'I' and resid 1 through 4 removed outlier: 3.537A pdb=" N ASN I 4 " --> pdb=" O MET I 1 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 1 through 4' Processing helix chain 'I' and resid 5 through 11 Processing helix chain 'I' and resid 15 through 38 Processing helix chain 'I' and resid 49 through 70 Processing helix chain 'I' and resid 76 through 93 removed outlier: 4.079A pdb=" N ASN I 93 " --> pdb=" O ARG I 89 " (cutoff:3.500A) Processing helix chain 'I' and resid 100 through 116 removed outlier: 3.596A pdb=" N LEU I 106 " --> pdb=" O ARG I 102 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS I 114 " --> pdb=" O PHE I 110 " (cutoff:3.500A) Processing helix chain 'I' and resid 121 through 127 Processing helix chain 'I' and resid 132 through 154 removed outlier: 4.765A pdb=" N LEU I 148 " --> pdb=" O LEU I 144 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N LEU I 149 " --> pdb=" O GLU I 145 " (cutoff:3.500A) Processing helix chain 'I' and resid 163 through 178 Processing helix chain 'I' and resid 183 through 186 Processing helix chain 'I' and resid 187 through 201 removed outlier: 3.612A pdb=" N LEU I 200 " --> pdb=" O ASN I 196 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR I 201 " --> pdb=" O ARG I 197 " (cutoff:3.500A) Processing helix chain 'I' and resid 202 through 206 Processing helix chain 'I' and resid 208 through 224 Processing helix chain 'I' and resid 228 through 234 Processing helix chain 'I' and resid 237 through 240 removed outlier: 3.581A pdb=" N GLU I 240 " --> pdb=" O MET I 237 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 237 through 240' Processing helix chain 'I' and resid 241 through 261 Processing helix chain 'I' and resid 266 through 283 Processing helix chain 'J' and resid 56 through 68 removed outlier: 3.995A pdb=" N GLU J 68 " --> pdb=" O LYS J 64 " (cutoff:3.500A) Processing helix chain 'J' and resid 98 through 104 Processing helix chain 'J' and resid 110 through 131 Processing helix chain 'J' and resid 139 through 141 No H-bonds generated for 'chain 'J' and resid 139 through 141' Processing helix chain 'J' and resid 175 through 179 Processing helix chain 'J' and resid 180 through 185 Processing helix chain 'J' and resid 192 through 209 removed outlier: 3.807A pdb=" N ALA J 198 " --> pdb=" O VAL J 194 " (cutoff:3.500A) Processing helix chain 'J' and resid 217 through 230 Processing helix chain 'J' and resid 239 through 243 Processing helix chain 'J' and resid 256 through 261 Processing helix chain 'J' and resid 265 through 276 Processing helix chain 'J' and resid 285 through 291 Processing helix chain 'J' and resid 292 through 297 removed outlier: 3.618A pdb=" N SER J 296 " --> pdb=" O MET J 292 " (cutoff:3.500A) Processing helix chain 'J' and resid 303 through 307 Processing sheet with id=AA1, first strand: chain 'J' and resid 14 through 21 removed outlier: 5.786A pdb=" N PHE J 17 " --> pdb=" O LYS J 28 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N LYS J 28 " --> pdb=" O PHE J 17 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASP J 79 " --> pdb=" O VAL J 90 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ASP J 92 " --> pdb=" O LEU J 77 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N LEU J 77 " --> pdb=" O ASP J 92 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'J' and resid 96 through 97 Processing sheet with id=AA3, first strand: chain 'J' and resid 133 through 134 267 hydrogen bonds defined for protein. 756 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: 1.30 Time building geometry restraints manager: 1.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1641 1.34 - 1.46: 1145 1.46 - 1.58: 2395 1.58 - 1.70: 1 1.70 - 1.82: 49 Bond restraints: 5231 Sorted by residual: bond pdb=" C11 ZQ6 J 401 " pdb=" N10 ZQ6 J 401 " ideal model delta sigma weight residual 1.339 1.455 -0.116 2.00e-02 2.50e+03 3.37e+01 bond pdb=" C13 ZQ6 J 401 " pdb=" N14 ZQ6 J 401 " ideal model delta sigma weight residual 1.350 1.448 -0.098 2.00e-02 2.50e+03 2.40e+01 bond pdb=" C24 ZQ6 J 401 " pdb=" N28 ZQ6 J 401 " ideal model delta sigma weight residual 1.376 1.296 0.080 2.00e-02 2.50e+03 1.60e+01 bond pdb=" N27 ZQ6 J 401 " pdb=" N28 ZQ6 J 401 " ideal model delta sigma weight residual 1.344 1.400 -0.056 2.00e-02 2.50e+03 7.95e+00 bond pdb=" C15 ZQ6 J 401 " pdb=" C16 ZQ6 J 401 " ideal model delta sigma weight residual 1.530 1.584 -0.054 2.00e-02 2.50e+03 7.37e+00 ... (remaining 5226 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 6893 2.04 - 4.07: 155 4.07 - 6.11: 26 6.11 - 8.15: 5 8.15 - 10.18: 1 Bond angle restraints: 7080 Sorted by residual: angle pdb=" CB MET J 189 " pdb=" CG MET J 189 " pdb=" SD MET J 189 " ideal model delta sigma weight residual 112.70 122.88 -10.18 3.00e+00 1.11e-01 1.15e+01 angle pdb=" CB ARG I 102 " pdb=" CG ARG I 102 " pdb=" CD ARG I 102 " ideal model delta sigma weight residual 111.30 118.90 -7.60 2.30e+00 1.89e-01 1.09e+01 angle pdb=" CA GLU I 17 " pdb=" CB GLU I 17 " pdb=" CG GLU I 17 " ideal model delta sigma weight residual 114.10 120.40 -6.30 2.00e+00 2.50e-01 9.91e+00 angle pdb=" C LEU I 65 " pdb=" N GLU I 66 " pdb=" CA GLU I 66 " ideal model delta sigma weight residual 121.14 115.74 5.40 1.75e+00 3.27e-01 9.53e+00 angle pdb=" C PHE I 90 " pdb=" N TYR I 91 " pdb=" CA TYR I 91 " ideal model delta sigma weight residual 122.38 116.95 5.43 1.81e+00 3.05e-01 9.01e+00 ... (remaining 7075 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.18: 2949 24.18 - 48.37: 173 48.37 - 72.55: 32 72.55 - 96.73: 15 96.73 - 120.92: 1 Dihedral angle restraints: 3170 sinusoidal: 1323 harmonic: 1847 Sorted by residual: dihedral pdb=" C17 ZQ6 J 401 " pdb=" C18 ZQ6 J 401 " pdb=" N19 ZQ6 J 401 " pdb=" C20 ZQ6 J 401 " ideal model delta sinusoidal sigma weight residual -70.42 50.50 -120.92 1 3.00e+01 1.11e-03 1.61e+01 dihedral pdb=" CA ILE I 180 " pdb=" C ILE I 180 " pdb=" N LEU I 181 " pdb=" CA LEU I 181 " ideal model delta harmonic sigma weight residual 180.00 161.82 18.18 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" CA GLU J 20 " pdb=" C GLU J 20 " pdb=" N GLY J 21 " pdb=" CA GLY J 21 " ideal model delta harmonic sigma weight residual 180.00 163.40 16.60 0 5.00e+00 4.00e-02 1.10e+01 ... (remaining 3167 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 400 0.029 - 0.058: 227 0.058 - 0.087: 95 0.087 - 0.116: 39 0.116 - 0.145: 16 Chirality restraints: 777 Sorted by residual: chirality pdb=" CA PRO J 238 " pdb=" N PRO J 238 " pdb=" C PRO J 238 " pdb=" CB PRO J 238 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.14 2.00e-01 2.50e+01 5.24e-01 chirality pdb=" CA GLU I 66 " pdb=" N GLU I 66 " pdb=" C GLU I 66 " pdb=" CB GLU I 66 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.20e-01 chirality pdb=" CA VAL I 120 " pdb=" N VAL I 120 " pdb=" C VAL I 120 " pdb=" CB VAL I 120 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.08e-01 ... (remaining 774 not shown) Planarity restraints: 903 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C11 ZQ6 J 401 " -0.002 2.00e-02 2.50e+03 1.27e-02 3.22e+00 pdb=" C24 ZQ6 J 401 " -0.004 2.00e-02 2.50e+03 pdb=" C25 ZQ6 J 401 " 0.032 2.00e-02 2.50e+03 pdb=" C26 ZQ6 J 401 " -0.006 2.00e-02 2.50e+03 pdb=" C29 ZQ6 J 401 " -0.015 2.00e-02 2.50e+03 pdb=" N23 ZQ6 J 401 " -0.001 2.00e-02 2.50e+03 pdb=" N27 ZQ6 J 401 " -0.003 2.00e-02 2.50e+03 pdb=" N28 ZQ6 J 401 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN I 162 " -0.027 5.00e-02 4.00e+02 4.05e-02 2.62e+00 pdb=" N PRO I 163 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO I 163 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO I 163 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA CYS J 201 " 0.008 2.00e-02 2.50e+03 1.52e-02 2.30e+00 pdb=" C CYS J 201 " -0.026 2.00e-02 2.50e+03 pdb=" O CYS J 201 " 0.010 2.00e-02 2.50e+03 pdb=" N ILE J 202 " 0.009 2.00e-02 2.50e+03 ... (remaining 900 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 686 2.75 - 3.29: 5435 3.29 - 3.82: 9882 3.82 - 4.36: 11948 4.36 - 4.90: 19207 Nonbonded interactions: 47158 Sorted by model distance: nonbonded pdb=" O HOH J 567 " pdb=" O HOH J 573 " model vdw 2.212 3.040 nonbonded pdb=" O HOH J 577 " pdb=" O HOH J 581 " model vdw 2.218 3.040 nonbonded pdb=" O HOH H 413 " pdb=" O HOH H 417 " model vdw 2.250 3.040 nonbonded pdb=" OD1 ASN J 279 " pdb=" O HOH J 501 " model vdw 2.256 3.040 nonbonded pdb=" O ARG J 283 " pdb=" O HOH J 502 " model vdw 2.267 3.040 ... (remaining 47153 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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 individual isotropic 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: 6.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 17.750 Find NCS groups from input model: 0.070 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:14.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.116 5231 Z= 0.342 Angle : 0.766 10.185 7080 Z= 0.398 Chirality : 0.046 0.145 777 Planarity : 0.006 0.043 903 Dihedral : 16.791 120.919 1974 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.62 % Favored : 98.22 % Rotamer: Outliers : 0.90 % Allowed : 13.36 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.32), residues: 618 helix: 1.23 (0.28), residues: 337 sheet: 0.74 (0.96), residues: 15 loop : -0.17 (0.36), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP J 132 HIS 0.006 0.001 HIS J 131 PHE 0.017 0.002 PHE I 30 TYR 0.020 0.002 TYR I 91 ARG 0.006 0.001 ARG I 102 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 83 time to evaluate : 0.750 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 86 average time/residue: 1.8631 time to fit residues: 166.1509 Evaluate side-chains 85 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 81 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 290 SER Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain J residue 120 MET Chi-restraints excluded: chain J residue 170 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 16 optimal weight: 8.9990 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 18 optimal weight: 7.9990 chunk 29 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 56 optimal weight: 0.5980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 307 GLN I 247 GLN J 236 GLN J 297 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.0831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5231 Z= 0.179 Angle : 0.593 6.944 7080 Z= 0.305 Chirality : 0.042 0.134 777 Planarity : 0.005 0.036 903 Dihedral : 8.548 111.141 719 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.29 % Favored : 98.54 % Rotamer: Outliers : 1.26 % Allowed : 12.27 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.33), residues: 618 helix: 1.83 (0.28), residues: 339 sheet: 0.58 (1.03), residues: 15 loop : -0.22 (0.37), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 132 HIS 0.006 0.001 HIS J 131 PHE 0.017 0.002 PHE I 30 TYR 0.018 0.002 TYR I 91 ARG 0.004 0.000 ARG I 63 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 88 time to evaluate : 0.705 Fit side-chains revert: symmetry clash REVERT: I 192 ASP cc_start: 0.7261 (t70) cc_final: 0.6945 (t70) outliers start: 7 outliers final: 2 residues processed: 92 average time/residue: 1.5715 time to fit residues: 149.9111 Evaluate side-chains 86 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 84 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 290 SER Chi-restraints excluded: chain I residue 129 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 31 optimal weight: 7.9990 chunk 17 optimal weight: 9.9990 chunk 46 optimal weight: 10.0000 chunk 38 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 60 optimal weight: 0.0770 chunk 50 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 19 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 overall best weight: 1.3544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 307 GLN I 247 GLN J 113 HIS J 236 GLN J 297 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.0954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5231 Z= 0.191 Angle : 0.594 6.731 7080 Z= 0.305 Chirality : 0.042 0.136 777 Planarity : 0.005 0.037 903 Dihedral : 8.246 111.534 715 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.62 % Favored : 98.22 % Rotamer: Outliers : 1.26 % Allowed : 13.72 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.33), residues: 618 helix: 1.95 (0.28), residues: 338 sheet: 0.45 (1.08), residues: 15 loop : -0.16 (0.37), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 132 HIS 0.006 0.001 HIS J 131 PHE 0.016 0.002 PHE I 30 TYR 0.019 0.002 TYR I 91 ARG 0.003 0.000 ARG J 30 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 87 time to evaluate : 1.024 Fit side-chains REVERT: I 138 LYS cc_start: 0.7434 (ttpt) cc_final: 0.6906 (tptt) REVERT: I 192 ASP cc_start: 0.7210 (t70) cc_final: 0.6879 (t70) REVERT: I 255 MET cc_start: 0.8003 (mtp) cc_final: 0.7717 (ttm) outliers start: 7 outliers final: 2 residues processed: 90 average time/residue: 1.5328 time to fit residues: 143.4680 Evaluate side-chains 85 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 83 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 290 SER Chi-restraints excluded: chain I residue 129 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 55 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 29 optimal weight: 0.1980 chunk 6 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 37 optimal weight: 7.9990 chunk 56 optimal weight: 1.9990 chunk 59 optimal weight: 0.2980 chunk 53 optimal weight: 1.9990 chunk 16 optimal weight: 8.9990 chunk 49 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 307 GLN I 247 GLN J 113 HIS J 236 GLN J 297 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.1024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5231 Z= 0.183 Angle : 0.575 6.676 7080 Z= 0.295 Chirality : 0.042 0.138 777 Planarity : 0.004 0.036 903 Dihedral : 8.105 111.459 715 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.46 % Favored : 98.38 % Rotamer: Outliers : 1.62 % Allowed : 13.36 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.33), residues: 618 helix: 2.02 (0.28), residues: 338 sheet: 0.41 (1.09), residues: 15 loop : -0.13 (0.37), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 132 HIS 0.006 0.001 HIS J 131 PHE 0.016 0.002 PHE J 81 TYR 0.019 0.002 TYR I 91 ARG 0.003 0.000 ARG J 30 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 91 time to evaluate : 0.742 Fit side-chains REVERT: I 138 LYS cc_start: 0.7429 (ttpt) cc_final: 0.6898 (tptt) REVERT: I 192 ASP cc_start: 0.7184 (t70) cc_final: 0.6858 (t70) outliers start: 9 outliers final: 2 residues processed: 95 average time/residue: 1.7069 time to fit residues: 167.8537 Evaluate side-chains 89 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 87 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain J residue 120 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 34 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 44 optimal weight: 1.9990 chunk 24 optimal weight: 9.9990 chunk 51 optimal weight: 8.9990 chunk 41 optimal weight: 8.9990 chunk 30 optimal weight: 7.9990 chunk 53 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 307 GLN I 247 GLN J 236 GLN J 297 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.1094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5231 Z= 0.206 Angle : 0.609 6.862 7080 Z= 0.311 Chirality : 0.043 0.139 777 Planarity : 0.005 0.037 903 Dihedral : 8.061 110.442 714 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.29 % Favored : 98.54 % Rotamer: Outliers : 1.62 % Allowed : 14.08 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.33), residues: 618 helix: 1.99 (0.28), residues: 338 sheet: 0.43 (1.13), residues: 15 loop : -0.15 (0.37), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 132 HIS 0.007 0.001 HIS J 131 PHE 0.016 0.002 PHE I 30 TYR 0.020 0.002 TYR I 91 ARG 0.005 0.001 ARG I 21 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 89 time to evaluate : 0.571 Fit side-chains REVERT: I 102 ARG cc_start: 0.7315 (OUTLIER) cc_final: 0.7096 (ttt180) REVERT: I 138 LYS cc_start: 0.7411 (ttpt) cc_final: 0.6899 (tptt) REVERT: I 192 ASP cc_start: 0.7189 (t70) cc_final: 0.6865 (t70) REVERT: J 30 ARG cc_start: 0.5395 (tpt170) cc_final: 0.5171 (tpt170) outliers start: 9 outliers final: 3 residues processed: 93 average time/residue: 1.7761 time to fit residues: 170.8915 Evaluate side-chains 89 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 85 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 54 MET Chi-restraints excluded: chain I residue 102 ARG Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain J residue 120 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 35 optimal weight: 4.9990 chunk 14 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 chunk 49 optimal weight: 7.9990 chunk 27 optimal weight: 6.9990 chunk 4 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 chunk 31 optimal weight: 0.7980 chunk 57 optimal weight: 6.9990 chunk 6 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 307 GLN I 247 GLN J 236 GLN J 297 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.1067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5231 Z= 0.233 Angle : 0.638 6.980 7080 Z= 0.327 Chirality : 0.044 0.141 777 Planarity : 0.005 0.038 903 Dihedral : 8.086 108.887 714 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.29 % Favored : 98.54 % Rotamer: Outliers : 1.44 % Allowed : 14.44 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.33), residues: 618 helix: 1.90 (0.28), residues: 337 sheet: 0.43 (1.13), residues: 15 loop : -0.18 (0.37), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP J 132 HIS 0.008 0.001 HIS J 131 PHE 0.019 0.002 PHE J 81 TYR 0.021 0.002 TYR I 91 ARG 0.004 0.001 ARG I 21 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 88 time to evaluate : 0.710 Fit side-chains REVERT: I 102 ARG cc_start: 0.7322 (OUTLIER) cc_final: 0.7092 (ttt180) REVERT: I 192 ASP cc_start: 0.7192 (t70) cc_final: 0.6865 (t70) outliers start: 8 outliers final: 4 residues processed: 91 average time/residue: 1.5950 time to fit residues: 150.2391 Evaluate side-chains 89 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 84 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 102 ARG Chi-restraints excluded: chain I residue 105 MET Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain J residue 120 MET Chi-restraints excluded: chain J residue 170 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 43 optimal weight: 9.9990 chunk 33 optimal weight: 10.0000 chunk 50 optimal weight: 8.9990 chunk 59 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 27 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 chunk 35 optimal weight: 0.6980 chunk 18 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 overall best weight: 2.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 247 GLN J 148 ASN J 297 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.1006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5231 Z= 0.277 Angle : 0.686 7.160 7080 Z= 0.349 Chirality : 0.045 0.144 777 Planarity : 0.005 0.039 903 Dihedral : 8.105 106.224 714 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.78 % Favored : 98.06 % Rotamer: Outliers : 1.62 % Allowed : 14.98 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.33), residues: 618 helix: 1.75 (0.28), residues: 337 sheet: 0.72 (1.20), residues: 15 loop : -0.22 (0.37), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP J 132 HIS 0.009 0.002 HIS J 131 PHE 0.016 0.002 PHE I 30 TYR 0.021 0.002 TYR I 91 ARG 0.005 0.001 ARG I 63 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 87 time to evaluate : 0.620 Fit side-chains REVERT: I 102 ARG cc_start: 0.7317 (OUTLIER) cc_final: 0.7091 (ttt180) REVERT: I 192 ASP cc_start: 0.7265 (t70) cc_final: 0.6916 (t70) outliers start: 9 outliers final: 4 residues processed: 91 average time/residue: 1.5821 time to fit residues: 149.1618 Evaluate side-chains 90 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 85 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 102 ARG Chi-restraints excluded: chain I residue 105 MET Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain J residue 120 MET Chi-restraints excluded: chain J residue 170 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 11 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 5 optimal weight: 7.9990 chunk 46 optimal weight: 2.9990 chunk 54 optimal weight: 9.9990 chunk 57 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 33 optimal weight: 10.0000 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 307 GLN I 247 GLN J 148 ASN J 236 GLN J 297 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.1098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5231 Z= 0.227 Angle : 0.648 8.347 7080 Z= 0.330 Chirality : 0.044 0.142 777 Planarity : 0.005 0.039 903 Dihedral : 8.132 109.712 714 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.46 % Favored : 98.38 % Rotamer: Outliers : 1.99 % Allowed : 14.44 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.33), residues: 618 helix: 1.83 (0.28), residues: 338 sheet: 0.81 (1.27), residues: 15 loop : -0.23 (0.37), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP J 132 HIS 0.007 0.001 HIS J 131 PHE 0.016 0.002 PHE I 30 TYR 0.021 0.002 TYR I 91 ARG 0.005 0.001 ARG I 63 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 89 time to evaluate : 0.593 Fit side-chains REVERT: I 102 ARG cc_start: 0.7324 (OUTLIER) cc_final: 0.7120 (ttt180) REVERT: I 192 ASP cc_start: 0.7272 (t70) cc_final: 0.6930 (t70) outliers start: 11 outliers final: 3 residues processed: 95 average time/residue: 1.5907 time to fit residues: 156.6108 Evaluate side-chains 94 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 90 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 102 ARG Chi-restraints excluded: chain I residue 105 MET Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain J residue 170 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 24 optimal weight: 9.9990 chunk 43 optimal weight: 10.0000 chunk 17 optimal weight: 4.9990 chunk 50 optimal weight: 9.9990 chunk 52 optimal weight: 4.9990 chunk 55 optimal weight: 0.4980 chunk 36 optimal weight: 0.9980 chunk 58 optimal weight: 0.5980 chunk 35 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 307 GLN I 247 GLN J 148 ASN J 297 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.1233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5231 Z= 0.191 Angle : 0.619 9.678 7080 Z= 0.313 Chirality : 0.043 0.139 777 Planarity : 0.005 0.038 903 Dihedral : 8.065 111.609 714 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.46 % Favored : 98.38 % Rotamer: Outliers : 0.90 % Allowed : 15.70 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.34), residues: 618 helix: 1.99 (0.28), residues: 338 sheet: 0.72 (1.26), residues: 15 loop : -0.15 (0.38), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 132 HIS 0.006 0.001 HIS J 131 PHE 0.020 0.002 PHE J 81 TYR 0.019 0.001 TYR I 91 ARG 0.007 0.001 ARG I 21 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 93 time to evaluate : 0.633 Fit side-chains REVERT: I 102 ARG cc_start: 0.7331 (OUTLIER) cc_final: 0.7109 (ttt180) REVERT: I 192 ASP cc_start: 0.7244 (t70) cc_final: 0.6909 (t70) outliers start: 5 outliers final: 2 residues processed: 96 average time/residue: 1.5992 time to fit residues: 158.9315 Evaluate side-chains 90 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 87 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 102 ARG Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain J residue 170 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 61 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 5 optimal weight: 9.9990 chunk 37 optimal weight: 10.0000 chunk 30 optimal weight: 5.9990 chunk 39 optimal weight: 7.9990 chunk 52 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 7 optimal weight: 3.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 247 GLN J 148 ASN J 297 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.1048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 5231 Z= 0.308 Angle : 0.732 10.738 7080 Z= 0.371 Chirality : 0.047 0.175 777 Planarity : 0.006 0.046 903 Dihedral : 8.050 103.427 714 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.94 % Favored : 97.90 % Rotamer: Outliers : 0.54 % Allowed : 16.06 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.33), residues: 618 helix: 1.65 (0.27), residues: 337 sheet: 0.95 (1.29), residues: 15 loop : -0.22 (0.37), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP J 132 HIS 0.009 0.002 HIS J 131 PHE 0.015 0.002 PHE I 30 TYR 0.022 0.002 TYR I 91 ARG 0.006 0.001 ARG I 21 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 87 time to evaluate : 0.604 Fit side-chains REVERT: I 102 ARG cc_start: 0.7315 (OUTLIER) cc_final: 0.7113 (ttt180) REVERT: I 192 ASP cc_start: 0.7303 (t70) cc_final: 0.6961 (t70) outliers start: 3 outliers final: 2 residues processed: 89 average time/residue: 1.5613 time to fit residues: 143.8497 Evaluate side-chains 88 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 85 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 102 ARG Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain J residue 170 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 13 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 20 optimal weight: 7.9990 chunk 50 optimal weight: 7.9990 chunk 6 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 33 optimal weight: 10.0000 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 247 GLN J 148 ASN J 236 GLN J 297 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.177615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.155991 restraints weight = 4723.636| |-----------------------------------------------------------------------------| r_work (start): 0.3820 rms_B_bonded: 0.94 r_work: 0.3713 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.3617 rms_B_bonded: 2.52 restraints_weight: 0.2500 r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.1083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 5231 Z= 0.295 Angle : 0.730 12.438 7080 Z= 0.370 Chirality : 0.047 0.191 777 Planarity : 0.006 0.041 903 Dihedral : 8.136 105.446 714 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.10 % Favored : 97.73 % Rotamer: Outliers : 1.08 % Allowed : 15.70 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.33), residues: 618 helix: 1.59 (0.27), residues: 337 sheet: 1.06 (1.26), residues: 15 loop : -0.27 (0.37), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP J 132 HIS 0.010 0.002 HIS J 131 PHE 0.024 0.003 PHE J 81 TYR 0.022 0.002 TYR I 91 ARG 0.006 0.001 ARG I 21 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2879.99 seconds wall clock time: 53 minutes 36.00 seconds (3216.00 seconds total)