Starting phenix.real_space_refine on Sat May 10 05:32:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p72_17515/05_2025/8p72_17515.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p72_17515/05_2025/8p72_17515.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/8p72_17515/05_2025/8p72_17515.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p72_17515/05_2025/8p72_17515.map" model { file = "/net/cci-nas-00/data/ceres_data/8p72_17515/05_2025/8p72_17515.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p72_17515/05_2025/8p72_17515.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 3290 2.51 5 N 870 2.21 5 O 1036 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 5227 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: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'X2Z': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "I" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 53 Classifications: {'water': 53} Link IDs: {None: 52} Chain: "J" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 54 Classifications: {'water': 54} Link IDs: {None: 53} Time building chain proxies: 4.83, per 1000 atoms: 0.92 Number of scatterers: 5227 At special positions: 0 Unit cell: (82.65, 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 1036 8.00 N 870 7.00 C 3290 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: 1.50 Conformation dependent library (CDL) restraints added in 713.3 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: 33 helices and 4 sheets defined 61.7% alpha, 5.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'H' and resid 263 through 267 removed outlier: 4.042A pdb=" N GLY H 267 " --> pdb=" O GLU H 264 " (cutoff:3.500A) Processing helix chain 'H' and resid 270 through 275 Processing helix chain 'H' and resid 279 through 286 Processing helix chain 'H' and resid 288 through 302 removed outlier: 3.872A pdb=" N ALA H 292 " --> pdb=" O THR H 288 " (cutoff:3.500A) Processing helix 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: 3.914A pdb=" N ASN I 93 " --> pdb=" O ARG I 89 " (cutoff:3.500A) Processing helix chain 'I' and resid 100 through 116 removed outlier: 3.931A pdb=" N LEU I 106 " --> pdb=" O ARG I 102 " (cutoff:3.500A) Processing helix chain 'I' and resid 121 through 129 removed outlier: 3.862A pdb=" N LEU I 129 " --> pdb=" O PHE I 125 " (cutoff:3.500A) Processing helix chain 'I' and resid 132 through 154 removed outlier: 4.707A pdb=" N LEU I 148 " --> pdb=" O LEU I 144 " (cutoff:3.500A) removed outlier: 4.555A 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: 3.682A 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 removed outlier: 3.795A pdb=" N LEU I 232 " --> pdb=" O MET I 228 " (cutoff:3.500A) Processing helix chain 'I' and resid 241 through 262 Processing helix chain 'I' and resid 266 through 283 removed outlier: 3.862A pdb=" N ALA I 283 " --> pdb=" O ARG I 279 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 68 removed outlier: 3.899A 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 175 through 179 Processing helix chain 'J' and resid 180 through 185 Processing helix chain 'J' and resid 192 through 209 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 292 Processing helix chain 'J' and resid 292 through 297 removed outlier: 3.959A 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 13 through 14 removed outlier: 3.562A pdb=" N GLU J 13 " --> pdb=" O ARG J 30 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'J' and resid 13 through 14 removed outlier: 3.562A pdb=" N GLU J 13 " --> pdb=" O ARG J 30 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ASP J 92 " --> pdb=" O LEU J 77 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N LEU J 77 " --> pdb=" O ASP J 92 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'J' and resid 96 through 97 Processing sheet with id=AA4, first strand: chain 'J' and resid 133 through 134 277 hydrogen bonds defined for protein. 774 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: 1.47 Time building geometry restraints manager: 1.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1641 1.34 - 1.46: 1038 1.46 - 1.58: 2499 1.58 - 1.69: 0 1.69 - 1.81: 49 Bond restraints: 5227 Sorted by residual: bond pdb=" C08 X2Z J 401 " pdb=" N09 X2Z J 401 " ideal model delta sigma weight residual 1.346 1.456 -0.110 2.00e-02 2.50e+03 3.03e+01 bond pdb=" C18 X2Z J 401 " pdb=" N19 X2Z J 401 " ideal model delta sigma weight residual 1.363 1.449 -0.086 2.00e-02 2.50e+03 1.83e+01 bond pdb=" C27 X2Z J 401 " pdb=" N07 X2Z J 401 " ideal model delta sigma weight residual 1.386 1.302 0.084 2.00e-02 2.50e+03 1.78e+01 bond pdb=" C20 X2Z J 401 " pdb=" C21 X2Z J 401 " ideal model delta sigma weight residual 1.528 1.479 0.049 2.00e-02 2.50e+03 5.97e+00 bond pdb=" C21 X2Z J 401 " pdb=" C22 X2Z J 401 " ideal model delta sigma weight residual 1.530 1.482 0.048 2.00e-02 2.50e+03 5.68e+00 ... (remaining 5222 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 6816 1.40 - 2.79: 193 2.79 - 4.19: 47 4.19 - 5.58: 11 5.58 - 6.98: 7 Bond angle restraints: 7074 Sorted by residual: angle pdb=" CA LYS J 293 " pdb=" CB LYS J 293 " pdb=" CG LYS J 293 " ideal model delta sigma weight residual 114.10 119.95 -5.85 2.00e+00 2.50e-01 8.56e+00 angle pdb=" CA LYS I 189 " pdb=" CB LYS I 189 " pdb=" CG LYS I 189 " ideal model delta sigma weight residual 114.10 119.10 -5.00 2.00e+00 2.50e-01 6.26e+00 angle pdb=" CB LYS I 253 " pdb=" CG LYS I 253 " pdb=" CD LYS I 253 " ideal model delta sigma weight residual 111.30 117.01 -5.71 2.30e+00 1.89e-01 6.16e+00 angle pdb=" CA TYR I 91 " pdb=" CB TYR I 91 " pdb=" CG TYR I 91 " ideal model delta sigma weight residual 113.90 109.61 4.29 1.80e+00 3.09e-01 5.67e+00 angle pdb=" CB MET J 94 " pdb=" CG MET J 94 " pdb=" SD MET J 94 " ideal model delta sigma weight residual 112.70 119.68 -6.98 3.00e+00 1.11e-01 5.41e+00 ... (remaining 7069 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.44: 2748 17.44 - 34.88: 301 34.88 - 52.32: 86 52.32 - 69.76: 18 69.76 - 87.21: 11 Dihedral angle restraints: 3164 sinusoidal: 1317 harmonic: 1847 Sorted by residual: dihedral pdb=" CA TYR I 91 " pdb=" C TYR I 91 " pdb=" N LEU I 92 " pdb=" CA LEU I 92 " ideal model delta harmonic sigma weight residual 180.00 162.37 17.63 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CG ARG I 197 " pdb=" CD ARG I 197 " pdb=" NE ARG I 197 " pdb=" CZ ARG I 197 " ideal model delta sinusoidal sigma weight residual 180.00 -136.20 -43.80 2 1.50e+01 4.44e-03 1.02e+01 dihedral pdb=" CA THR I 176 " pdb=" C THR I 176 " pdb=" N ARG I 177 " pdb=" CA ARG I 177 " ideal model delta harmonic sigma weight residual -180.00 -164.26 -15.74 0 5.00e+00 4.00e-02 9.91e+00 ... (remaining 3161 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 459 0.028 - 0.055: 191 0.055 - 0.083: 76 0.083 - 0.110: 36 0.110 - 0.138: 14 Chirality restraints: 776 Sorted by residual: chirality pdb=" CG LEU I 236 " pdb=" CB LEU I 236 " pdb=" CD1 LEU I 236 " pdb=" CD2 LEU I 236 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 4.76e-01 chirality pdb=" CA TYR I 91 " pdb=" N TYR I 91 " pdb=" C TYR I 91 " pdb=" CB TYR I 91 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.74e-01 chirality pdb=" CA VAL J 210 " pdb=" N VAL J 210 " pdb=" C VAL J 210 " pdb=" CB VAL J 210 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.06e-01 ... (remaining 773 not shown) Planarity restraints: 903 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU I 49 " 0.025 5.00e-02 4.00e+02 3.78e-02 2.29e+00 pdb=" N PRO I 50 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO I 50 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO I 50 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU I 141 " 0.007 2.00e-02 2.50e+03 1.49e-02 2.22e+00 pdb=" CD GLU I 141 " -0.026 2.00e-02 2.50e+03 pdb=" OE1 GLU I 141 " 0.009 2.00e-02 2.50e+03 pdb=" OE2 GLU I 141 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN I 162 " -0.025 5.00e-02 4.00e+02 3.72e-02 2.22e+00 pdb=" N PRO I 163 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO I 163 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO I 163 " -0.021 5.00e-02 4.00e+02 ... (remaining 900 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 732 2.75 - 3.29: 5361 3.29 - 3.83: 9925 3.83 - 4.36: 11676 4.36 - 4.90: 19254 Nonbonded interactions: 46948 Sorted by model distance: nonbonded pdb=" O HOH J 501 " pdb=" O HOH J 537 " model vdw 2.215 3.040 nonbonded pdb=" OG SER I 78 " pdb=" OD2 ASP I 116 " model vdw 2.220 3.040 nonbonded pdb=" O GLY H 285 " pdb=" O HOH H 401 " model vdw 2.225 3.040 nonbonded pdb=" O PRO J 280 " pdb=" O HOH J 501 " model vdw 2.256 3.040 nonbonded pdb=" O HOH J 544 " pdb=" O HOH J 550 " model vdw 2.273 3.040 ... (remaining 46943 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: 3.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 17.850 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 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:14.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.110 5227 Z= 0.191 Angle : 0.615 6.981 7074 Z= 0.308 Chirality : 0.041 0.138 776 Planarity : 0.005 0.038 903 Dihedral : 16.505 87.206 1968 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.78 % Favored : 98.06 % Rotamer: Outliers : 0.54 % Allowed : 18.23 % Favored : 81.23 % 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: 1.91 (0.28), residues: 339 sheet: -0.00 (1.28), residues: 16 loop : -0.09 (0.37), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 11 HIS 0.004 0.001 HIS I 161 PHE 0.019 0.002 PHE I 30 TYR 0.016 0.002 TYR I 91 ARG 0.003 0.000 ARG I 256 Details of bonding type rmsd hydrogen bonds : bond 0.14784 ( 276) hydrogen bonds : angle 5.83157 ( 774) covalent geometry : bond 0.00402 ( 5227) covalent geometry : angle 0.61502 ( 7074) *********************** 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 93 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 90 time to evaluate : 0.575 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 92 average time/residue: 1.6479 time to fit residues: 156.5101 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 : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 254 SER Chi-restraints excluded: chain J residue 119 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 7.9990 chunk 46 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 25 optimal weight: 0.6980 chunk 48 optimal weight: 10.0000 chunk 18 optimal weight: 8.9990 chunk 29 optimal weight: 6.9990 chunk 36 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 281 GLN I 119 ASN I 142 GLN ** I 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 258 HIS ** J 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.184974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.163484 restraints weight = 4507.975| |-----------------------------------------------------------------------------| r_work (start): 0.3941 rms_B_bonded: 0.88 r_work: 0.3833 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.3740 rms_B_bonded: 2.52 restraints_weight: 0.2500 r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.0845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 5227 Z= 0.241 Angle : 0.707 6.546 7074 Z= 0.369 Chirality : 0.046 0.142 776 Planarity : 0.006 0.040 903 Dihedral : 5.375 56.320 709 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.78 % Favored : 98.06 % Rotamer: Outliers : 2.71 % Allowed : 14.80 % Favored : 82.49 % 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: 1.08 (0.32), residues: 618 helix: 1.50 (0.27), residues: 337 sheet: 0.76 (1.40), residues: 15 loop : -0.24 (0.37), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP I 11 HIS 0.007 0.002 HIS I 281 PHE 0.023 0.003 PHE I 71 TYR 0.020 0.003 TYR I 91 ARG 0.006 0.001 ARG J 188 Details of bonding type rmsd hydrogen bonds : bond 0.06434 ( 276) hydrogen bonds : angle 5.21835 ( 774) covalent geometry : bond 0.00528 ( 5227) covalent geometry : angle 0.70666 ( 7074) *********************** 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 106 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 91 time to evaluate : 0.640 Fit side-chains REVERT: I 279 ARG cc_start: 0.6442 (mtp180) cc_final: 0.6222 (mtm-85) REVERT: J 10 LYS cc_start: 0.4708 (OUTLIER) cc_final: 0.4419 (tptp) outliers start: 15 outliers final: 2 residues processed: 97 average time/residue: 1.4563 time to fit residues: 146.4712 Evaluate side-chains 89 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 86 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 186 ILE Chi-restraints excluded: chain J residue 10 LYS Chi-restraints excluded: chain J residue 119 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 38 optimal weight: 3.9990 chunk 49 optimal weight: 0.5980 chunk 27 optimal weight: 0.9980 chunk 28 optimal weight: 0.0470 chunk 54 optimal weight: 0.9990 chunk 36 optimal weight: 7.9990 chunk 47 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 42 optimal weight: 7.9990 chunk 50 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 281 GLN I 18 GLN I 119 ASN I 183 ASN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 258 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.188484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.167574 restraints weight = 4574.287| |-----------------------------------------------------------------------------| r_work (start): 0.3986 rms_B_bonded: 0.87 r_work: 0.3879 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.3789 rms_B_bonded: 2.53 restraints_weight: 0.2500 r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.0873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 5227 Z= 0.125 Angle : 0.545 5.122 7074 Z= 0.286 Chirality : 0.040 0.130 776 Planarity : 0.005 0.037 903 Dihedral : 4.908 56.499 708 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.94 % Favored : 97.90 % Rotamer: Outliers : 1.81 % Allowed : 14.98 % 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: 1.65 (0.33), residues: 618 helix: 2.00 (0.27), residues: 339 sheet: 0.69 (1.44), residues: 15 loop : -0.04 (0.37), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 11 HIS 0.004 0.001 HIS J 131 PHE 0.016 0.002 PHE I 30 TYR 0.017 0.002 TYR I 91 ARG 0.002 0.000 ARG J 136 Details of bonding type rmsd hydrogen bonds : bond 0.04816 ( 276) hydrogen bonds : angle 4.73992 ( 774) covalent geometry : bond 0.00267 ( 5227) covalent geometry : angle 0.54478 ( 7074) *********************** 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 104 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 94 time to evaluate : 0.574 Fit side-chains REVERT: I 49 GLU cc_start: 0.5938 (OUTLIER) cc_final: 0.5377 (mp0) REVERT: I 234 GLU cc_start: 0.5989 (OUTLIER) cc_final: 0.5432 (mm-30) REVERT: J 292 MET cc_start: 0.7348 (OUTLIER) cc_final: 0.7022 (mtp) outliers start: 10 outliers final: 1 residues processed: 99 average time/residue: 1.4636 time to fit residues: 150.0121 Evaluate side-chains 86 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 82 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 49 GLU Chi-restraints excluded: chain I residue 186 ILE Chi-restraints excluded: chain I residue 234 GLU Chi-restraints excluded: chain J residue 292 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 27 optimal weight: 3.9990 chunk 48 optimal weight: 9.9990 chunk 12 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 21 optimal weight: 0.0970 chunk 30 optimal weight: 3.9990 chunk 57 optimal weight: 6.9990 chunk 47 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 281 GLN H 294 HIS I 18 GLN I 119 ASN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 148 ASN J 258 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.188521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.167306 restraints weight = 4661.404| |-----------------------------------------------------------------------------| r_work (start): 0.3983 rms_B_bonded: 0.89 r_work: 0.3876 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.3784 rms_B_bonded: 2.57 restraints_weight: 0.2500 r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.0999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5227 Z= 0.129 Angle : 0.550 6.092 7074 Z= 0.287 Chirality : 0.040 0.130 776 Planarity : 0.005 0.036 903 Dihedral : 4.741 59.305 706 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.78 % Favored : 98.06 % Rotamer: Outliers : 1.99 % Allowed : 13.72 % 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: 1.69 (0.33), residues: 618 helix: 2.05 (0.27), residues: 339 sheet: 0.71 (1.42), residues: 15 loop : -0.03 (0.37), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 11 HIS 0.003 0.001 HIS I 161 PHE 0.016 0.002 PHE I 30 TYR 0.017 0.002 TYR I 91 ARG 0.003 0.000 ARG J 136 Details of bonding type rmsd hydrogen bonds : bond 0.04746 ( 276) hydrogen bonds : angle 4.65570 ( 774) covalent geometry : bond 0.00278 ( 5227) covalent geometry : angle 0.55034 ( 7074) *********************** 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 98 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 87 time to evaluate : 0.639 Fit side-chains REVERT: I 49 GLU cc_start: 0.5963 (OUTLIER) cc_final: 0.5271 (mp0) REVERT: I 234 GLU cc_start: 0.5993 (OUTLIER) cc_final: 0.5398 (mm-30) REVERT: J 10 LYS cc_start: 0.4737 (OUTLIER) cc_final: 0.4481 (tptp) REVERT: J 97 ASP cc_start: 0.7682 (p0) cc_final: 0.7411 (p0) outliers start: 11 outliers final: 1 residues processed: 92 average time/residue: 1.4872 time to fit residues: 141.7085 Evaluate side-chains 86 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 82 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 49 GLU Chi-restraints excluded: chain I residue 186 ILE Chi-restraints excluded: chain I residue 234 GLU Chi-restraints excluded: chain J residue 10 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 3 optimal weight: 0.2980 chunk 11 optimal weight: 0.6980 chunk 47 optimal weight: 4.9990 chunk 52 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 35 optimal weight: 7.9990 chunk 34 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 281 GLN I 119 ASN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 148 ASN J 258 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.189082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.167904 restraints weight = 4627.015| |-----------------------------------------------------------------------------| r_work (start): 0.3989 rms_B_bonded: 0.88 r_work: 0.3882 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.3790 rms_B_bonded: 2.57 restraints_weight: 0.2500 r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.1004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5227 Z= 0.124 Angle : 0.541 6.134 7074 Z= 0.283 Chirality : 0.041 0.143 776 Planarity : 0.005 0.037 903 Dihedral : 4.700 59.441 706 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.78 % Favored : 98.06 % Rotamer: Outliers : 1.62 % Allowed : 14.62 % Favored : 83.75 % 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: 1.75 (0.33), residues: 618 helix: 2.09 (0.27), residues: 339 sheet: 0.63 (1.40), residues: 15 loop : 0.02 (0.38), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 11 HIS 0.003 0.001 HIS J 131 PHE 0.017 0.002 PHE I 30 TYR 0.017 0.002 TYR I 91 ARG 0.002 0.000 ARG J 136 Details of bonding type rmsd hydrogen bonds : bond 0.04613 ( 276) hydrogen bonds : angle 4.63183 ( 774) covalent geometry : bond 0.00267 ( 5227) covalent geometry : angle 0.54087 ( 7074) *********************** 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 100 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 91 time to evaluate : 0.648 Fit side-chains REVERT: I 49 GLU cc_start: 0.5905 (OUTLIER) cc_final: 0.5195 (mp0) REVERT: I 234 GLU cc_start: 0.6064 (OUTLIER) cc_final: 0.5437 (mm-30) REVERT: J 10 LYS cc_start: 0.4663 (OUTLIER) cc_final: 0.4415 (tptp) REVERT: J 97 ASP cc_start: 0.7662 (p0) cc_final: 0.7392 (p0) REVERT: J 292 MET cc_start: 0.7353 (OUTLIER) cc_final: 0.6984 (mtt) outliers start: 9 outliers final: 1 residues processed: 96 average time/residue: 1.4137 time to fit residues: 140.7776 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 : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 49 GLU Chi-restraints excluded: chain I residue 186 ILE Chi-restraints excluded: chain I residue 234 GLU Chi-restraints excluded: chain J residue 10 LYS Chi-restraints excluded: chain J residue 292 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 21 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 15 optimal weight: 0.4980 chunk 18 optimal weight: 6.9990 chunk 11 optimal weight: 0.7980 chunk 55 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 7 optimal weight: 0.4980 chunk 1 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 281 GLN I 119 ASN I 142 GLN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 148 ASN J 258 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.188293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.167083 restraints weight = 4630.578| |-----------------------------------------------------------------------------| r_work (start): 0.3976 rms_B_bonded: 0.88 r_work: 0.3869 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.3778 rms_B_bonded: 2.57 restraints_weight: 0.2500 r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.1034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5227 Z= 0.136 Angle : 0.562 5.367 7074 Z= 0.295 Chirality : 0.041 0.132 776 Planarity : 0.005 0.037 903 Dihedral : 4.728 58.791 706 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.94 % Favored : 97.90 % 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: 1.70 (0.33), residues: 618 helix: 2.03 (0.27), residues: 339 sheet: 0.68 (1.36), residues: 15 loop : 0.02 (0.38), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 11 HIS 0.004 0.001 HIS J 131 PHE 0.017 0.002 PHE I 30 TYR 0.017 0.002 TYR I 91 ARG 0.003 0.000 ARG J 136 Details of bonding type rmsd hydrogen bonds : bond 0.04815 ( 276) hydrogen bonds : angle 4.66272 ( 774) covalent geometry : bond 0.00294 ( 5227) covalent geometry : angle 0.56236 ( 7074) *********************** 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: 9 poor density : 87 time to evaluate : 0.562 Fit side-chains REVERT: I 49 GLU cc_start: 0.5910 (OUTLIER) cc_final: 0.5197 (mp0) REVERT: I 234 GLU cc_start: 0.6062 (OUTLIER) cc_final: 0.5424 (mm-30) REVERT: J 10 LYS cc_start: 0.4680 (OUTLIER) cc_final: 0.4400 (tptp) REVERT: J 292 MET cc_start: 0.7354 (OUTLIER) cc_final: 0.6985 (mtt) outliers start: 9 outliers final: 1 residues processed: 90 average time/residue: 1.3588 time to fit residues: 126.8667 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 : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 49 GLU Chi-restraints excluded: chain I residue 186 ILE Chi-restraints excluded: chain I residue 234 GLU Chi-restraints excluded: chain J residue 10 LYS Chi-restraints excluded: chain J residue 292 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 13 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 35 optimal weight: 7.9990 chunk 50 optimal weight: 4.9990 chunk 9 optimal weight: 6.9990 chunk 28 optimal weight: 7.9990 chunk 61 optimal weight: 0.6980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 281 GLN H 294 HIS H 298 GLN I 119 ASN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 148 ASN J 258 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.186923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.165455 restraints weight = 4589.878| |-----------------------------------------------------------------------------| r_work (start): 0.3961 rms_B_bonded: 0.88 r_work: 0.3854 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.3762 rms_B_bonded: 2.57 restraints_weight: 0.2500 r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.0970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5227 Z= 0.169 Angle : 0.618 5.931 7074 Z= 0.324 Chirality : 0.043 0.155 776 Planarity : 0.005 0.037 903 Dihedral : 4.870 58.456 706 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.10 % Favored : 97.73 % Rotamer: Outliers : 1.81 % Allowed : 14.98 % 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: 1.52 (0.33), residues: 618 helix: 1.85 (0.27), residues: 338 sheet: 0.82 (1.40), residues: 15 loop : -0.03 (0.38), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP I 11 HIS 0.005 0.001 HIS I 281 PHE 0.016 0.002 PHE I 30 TYR 0.019 0.002 TYR I 91 ARG 0.004 0.001 ARG J 136 Details of bonding type rmsd hydrogen bonds : bond 0.05285 ( 276) hydrogen bonds : angle 4.81097 ( 774) covalent geometry : bond 0.00373 ( 5227) covalent geometry : angle 0.61774 ( 7074) *********************** 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: 10 poor density : 86 time to evaluate : 0.575 Fit side-chains REVERT: I 49 GLU cc_start: 0.6012 (OUTLIER) cc_final: 0.5386 (mp0) REVERT: I 234 GLU cc_start: 0.6097 (OUTLIER) cc_final: 0.5464 (mm-30) REVERT: J 10 LYS cc_start: 0.4688 (OUTLIER) cc_final: 0.4419 (tptp) outliers start: 10 outliers final: 2 residues processed: 91 average time/residue: 1.4779 time to fit residues: 139.3678 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 : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 49 GLU Chi-restraints excluded: chain I residue 186 ILE Chi-restraints excluded: chain I residue 234 GLU Chi-restraints excluded: chain J residue 10 LYS Chi-restraints excluded: chain J residue 119 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 46 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 32 optimal weight: 0.0980 chunk 53 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 52 optimal weight: 0.6980 chunk 57 optimal weight: 10.0000 chunk 12 optimal weight: 0.7980 chunk 47 optimal weight: 0.6980 chunk 54 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 281 GLN I 119 ASN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 148 ASN J 258 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.189455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.168464 restraints weight = 4602.427| |-----------------------------------------------------------------------------| r_work (start): 0.3995 rms_B_bonded: 0.87 r_work: 0.3888 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.3796 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.1056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5227 Z= 0.122 Angle : 0.550 5.279 7074 Z= 0.289 Chirality : 0.041 0.132 776 Planarity : 0.005 0.037 903 Dihedral : 4.702 58.611 706 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.10 % Favored : 97.73 % Rotamer: Outliers : 1.62 % Allowed : 15.16 % 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: 1.77 (0.33), residues: 618 helix: 2.09 (0.27), residues: 339 sheet: 0.33 (1.33), residues: 16 loop : 0.08 (0.38), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 11 HIS 0.003 0.001 HIS I 161 PHE 0.018 0.002 PHE I 30 TYR 0.017 0.002 TYR I 91 ARG 0.003 0.000 ARG I 279 Details of bonding type rmsd hydrogen bonds : bond 0.04510 ( 276) hydrogen bonds : angle 4.58523 ( 774) covalent geometry : bond 0.00264 ( 5227) covalent geometry : angle 0.54965 ( 7074) *********************** 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 98 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 89 time to evaluate : 0.647 Fit side-chains REVERT: I 49 GLU cc_start: 0.5882 (OUTLIER) cc_final: 0.5221 (mp0) REVERT: I 234 GLU cc_start: 0.6051 (OUTLIER) cc_final: 0.5403 (mm-30) REVERT: J 10 LYS cc_start: 0.4684 (OUTLIER) cc_final: 0.4423 (tptp) REVERT: J 292 MET cc_start: 0.7373 (OUTLIER) cc_final: 0.6996 (mtt) outliers start: 9 outliers final: 1 residues processed: 94 average time/residue: 1.4419 time to fit residues: 140.5119 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 : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 49 GLU Chi-restraints excluded: chain I residue 186 ILE Chi-restraints excluded: chain I residue 234 GLU Chi-restraints excluded: chain J residue 10 LYS Chi-restraints excluded: chain J residue 292 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 41 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 44 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 281 GLN I 119 ASN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 258 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.187465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.166266 restraints weight = 4583.170| |-----------------------------------------------------------------------------| r_work (start): 0.3972 rms_B_bonded: 0.87 r_work: 0.3863 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.3769 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.1028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5227 Z= 0.161 Angle : 0.618 8.488 7074 Z= 0.320 Chirality : 0.043 0.146 776 Planarity : 0.005 0.037 903 Dihedral : 4.825 58.881 706 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.10 % Favored : 97.73 % Rotamer: Outliers : 1.08 % Allowed : 15.34 % 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: 1.63 (0.33), residues: 618 helix: 1.92 (0.27), residues: 338 sheet: 0.78 (1.40), residues: 15 loop : 0.06 (0.38), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP I 11 HIS 0.004 0.001 HIS I 100 PHE 0.016 0.002 PHE I 30 TYR 0.020 0.002 TYR I 164 ARG 0.004 0.000 ARG J 136 Details of bonding type rmsd hydrogen bonds : bond 0.05099 ( 276) hydrogen bonds : angle 4.75932 ( 774) covalent geometry : bond 0.00356 ( 5227) covalent geometry : angle 0.61787 ( 7074) *********************** 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 92 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 86 time to evaluate : 0.622 Fit side-chains REVERT: I 49 GLU cc_start: 0.5998 (OUTLIER) cc_final: 0.5380 (mp0) REVERT: I 234 GLU cc_start: 0.6097 (OUTLIER) cc_final: 0.5456 (mm-30) REVERT: J 10 LYS cc_start: 0.4698 (OUTLIER) cc_final: 0.4417 (tptp) REVERT: J 292 MET cc_start: 0.7410 (OUTLIER) cc_final: 0.7020 (mtt) outliers start: 6 outliers final: 1 residues processed: 89 average time/residue: 1.5508 time to fit residues: 142.7692 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 : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 49 GLU Chi-restraints excluded: chain I residue 186 ILE Chi-restraints excluded: chain I residue 234 GLU Chi-restraints excluded: chain J residue 10 LYS Chi-restraints excluded: chain J residue 292 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 0.1980 chunk 10 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 38 optimal weight: 0.4980 chunk 39 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 9 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 281 GLN I 119 ASN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 258 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.188188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.166998 restraints weight = 4598.872| |-----------------------------------------------------------------------------| r_work (start): 0.3981 rms_B_bonded: 0.88 r_work: 0.3873 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.3780 rms_B_bonded: 2.57 restraints_weight: 0.2500 r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.1046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5227 Z= 0.150 Angle : 0.613 8.476 7074 Z= 0.318 Chirality : 0.043 0.139 776 Planarity : 0.005 0.037 903 Dihedral : 4.805 58.961 706 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.10 % Favored : 97.73 % Rotamer: Outliers : 1.08 % Allowed : 16.43 % Favored : 82.49 % 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: 1.60 (0.33), residues: 618 helix: 1.93 (0.27), residues: 339 sheet: 0.35 (1.34), residues: 16 loop : 0.02 (0.38), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 11 HIS 0.004 0.001 HIS I 281 PHE 0.018 0.002 PHE I 30 TYR 0.019 0.002 TYR I 164 ARG 0.003 0.000 ARG J 136 Details of bonding type rmsd hydrogen bonds : bond 0.04944 ( 276) hydrogen bonds : angle 4.73282 ( 774) covalent geometry : bond 0.00332 ( 5227) covalent geometry : angle 0.61330 ( 7074) ********************** 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 89 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 83 time to evaluate : 0.631 Fit side-chains REVERT: I 49 GLU cc_start: 0.5973 (OUTLIER) cc_final: 0.5344 (mp0) REVERT: I 234 GLU cc_start: 0.6104 (OUTLIER) cc_final: 0.5460 (mm-30) REVERT: J 10 LYS cc_start: 0.4697 (OUTLIER) cc_final: 0.4431 (tptp) REVERT: J 292 MET cc_start: 0.7410 (OUTLIER) cc_final: 0.7026 (mtt) outliers start: 6 outliers final: 1 residues processed: 85 average time/residue: 1.5039 time to fit residues: 132.5025 Evaluate side-chains 87 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 82 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 49 GLU Chi-restraints excluded: chain I residue 186 ILE Chi-restraints excluded: chain I residue 234 GLU Chi-restraints excluded: chain J residue 10 LYS Chi-restraints excluded: chain J residue 292 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 59 optimal weight: 0.6980 chunk 40 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 54 optimal weight: 4.9990 chunk 55 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 48 optimal weight: 10.0000 chunk 3 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 14 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 281 GLN I 119 ASN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 148 ASN J 258 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.187527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.165999 restraints weight = 4636.443| |-----------------------------------------------------------------------------| r_work (start): 0.3967 rms_B_bonded: 0.89 r_work: 0.3860 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.3766 rms_B_bonded: 2.60 restraints_weight: 0.2500 r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.1079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5227 Z= 0.165 Angle : 0.649 8.364 7074 Z= 0.336 Chirality : 0.043 0.149 776 Planarity : 0.005 0.037 903 Dihedral : 4.848 58.739 706 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.27 % Favored : 97.57 % Rotamer: Outliers : 1.44 % Allowed : 16.06 % Favored : 82.49 % 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: 1.56 (0.33), residues: 618 helix: 1.87 (0.27), residues: 338 sheet: 0.76 (1.39), residues: 15 loop : 0.02 (0.38), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP I 11 HIS 0.005 0.001 HIS I 281 PHE 0.017 0.002 PHE J 185 TYR 0.020 0.002 TYR I 164 ARG 0.005 0.001 ARG I 279 Details of bonding type rmsd hydrogen bonds : bond 0.05138 ( 276) hydrogen bonds : angle 4.79774 ( 774) covalent geometry : bond 0.00368 ( 5227) covalent geometry : angle 0.64856 ( 7074) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5788.04 seconds wall clock time: 100 minutes 9.18 seconds (6009.18 seconds total)