Starting phenix.real_space_refine on Thu Jun 5 04:52:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p72_17515/06_2025/8p72_17515.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p72_17515/06_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_17515/06_2025/8p72_17515.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p72_17515/06_2025/8p72_17515.map" model { file = "/net/cci-nas-00/data/ceres_data/8p72_17515/06_2025/8p72_17515.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p72_17515/06_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-5710/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: 4.61, per 1000 atoms: 0.88 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: 1.35 Conformation dependent library (CDL) restraints added in 591.4 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: 0.53 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: 1.36 Time building geometry restraints manager: 1.56 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: 0.000 Extract box with map and model: 0.260 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 17.090 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:13.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.750 ------------------------------------------------------------------------------- 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 : 0.623 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 92 average time/residue: 1.7172 time to fit residues: 162.8640 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 : 0.571 ------------------------------------------------------------------------------- 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 = 0.184977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.163495 restraints weight = 4507.942| |-----------------------------------------------------------------------------| 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: 0.3739 rms_B_bonded: 2.54 restraints_weight: 0.2500 r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 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 : 0.583 Fit side-chains REVERT: I 279 ARG cc_start: 0.6444 (mtp180) cc_final: 0.6226 (mtm-85) REVERT: J 10 LYS cc_start: 0.4711 (OUTLIER) cc_final: 0.4423 (tptp) outliers start: 15 outliers final: 2 residues processed: 97 average time/residue: 1.6707 time to fit residues: 167.9291 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 : 0.618 ------------------------------------------------------------------------------- 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: 0.7980 chunk 49 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 chunk 28 optimal weight: 0.5980 chunk 54 optimal weight: 0.9990 chunk 36 optimal weight: 7.9990 chunk 47 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 42 optimal weight: 7.9990 chunk 50 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.4228 r_free = 0.4228 target = 0.188146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.167192 restraints weight = 4569.140| |-----------------------------------------------------------------------------| r_work (start): 0.3982 rms_B_bonded: 0.87 r_work: 0.3874 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.3782 rms_B_bonded: 2.55 restraints_weight: 0.2500 r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.0857 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 : 0.551 5.219 7074 Z= 0.289 Chirality : 0.041 0.131 776 Planarity : 0.005 0.037 903 Dihedral : 4.941 56.529 708 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.49 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: 1.61 (0.33), residues: 618 helix: 1.97 (0.27), residues: 339 sheet: 0.69 (1.44), residues: 15 loop : -0.05 (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 0.017 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 0.04894 ( 276) hydrogen bonds : angle 4.76731 ( 774) covalent geometry : bond 0.00275 ( 5227) covalent geometry : angle 0.55146 ( 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 103 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 94 time to evaluate : 0.578 Fit side-chains REVERT: I 49 GLU cc_start: 0.5948 (OUTLIER) cc_final: 0.5399 (mp0) REVERT: I 234 GLU cc_start: 0.5990 (OUTLIER) cc_final: 0.5436 (mm-30) outliers start: 9 outliers final: 2 residues processed: 99 average time/residue: 1.5991 time to fit residues: 163.8202 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 : 0.798 ------------------------------------------------------------------------------- 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 119 LEU 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: 3.9990 chunk 29 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 57 optimal weight: 0.3980 chunk 47 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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 = 0.4229 r_free = 0.4229 target = 0.188276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.167084 restraints weight = 4654.335| |-----------------------------------------------------------------------------| r_work (start): 0.3980 rms_B_bonded: 0.89 r_work: 0.3873 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.3781 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.0982 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= 0.133 Angle : 0.556 6.061 7074 Z= 0.290 Chirality : 0.040 0.131 776 Planarity : 0.005 0.037 903 Dihedral : 4.824 59.119 708 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.94 % Favored : 97.90 % 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: 1.66 (0.33), residues: 618 helix: 2.02 (0.27), residues: 339 sheet: 0.71 (1.42), 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 0.003 0.000 ARG J 136 Details of bonding type rmsd hydrogen bonds : bond 0.04804 ( 276) hydrogen bonds : angle 4.67995 ( 774) covalent geometry : bond 0.00288 ( 5227) covalent geometry : angle 0.55584 ( 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 96 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 87 time to evaluate : 0.574 Fit side-chains REVERT: I 49 GLU cc_start: 0.5961 (OUTLIER) cc_final: 0.5328 (mp0) REVERT: I 234 GLU cc_start: 0.5993 (OUTLIER) cc_final: 0.5399 (mm-30) REVERT: J 10 LYS cc_start: 0.4671 (OUTLIER) cc_final: 0.4405 (tptp) REVERT: J 97 ASP cc_start: 0.7645 (p0) cc_final: 0.7371 (p0) outliers start: 9 outliers final: 1 residues processed: 91 average time/residue: 1.4556 time to fit residues: 137.4150 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 : 0.514 ------------------------------------------------------------------------------- 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: 0.0970 chunk 11 optimal weight: 0.6980 chunk 47 optimal weight: 0.7980 chunk 52 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 35 optimal weight: 8.9990 chunk 34 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- 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 = 0.4237 r_free = 0.4237 target = 0.189148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.167979 restraints weight = 4626.963| |-----------------------------------------------------------------------------| r_work (start): 0.3989 rms_B_bonded: 0.88 r_work: 0.3883 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.3791 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.1017 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= 0.123 Angle : 0.540 6.146 7074 Z= 0.283 Chirality : 0.041 0.131 776 Planarity : 0.005 0.037 903 Dihedral : 4.706 59.471 706 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.94 % Favored : 97.90 % Rotamer: Outliers : 1.62 % Allowed : 14.44 % Favored : 83.94 % 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: 1.76 (0.33), residues: 618 helix: 2.09 (0.27), residues: 339 sheet: 0.64 (1.41), 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 I 161 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 0.04599 ( 276) hydrogen bonds : angle 4.63230 ( 774) covalent geometry : bond 0.00264 ( 5227) covalent geometry : angle 0.54010 ( 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 96 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 87 time to evaluate : 0.626 Fit side-chains REVERT: I 49 GLU cc_start: 0.5905 (OUTLIER) cc_final: 0.5202 (mp0) REVERT: I 234 GLU cc_start: 0.6071 (OUTLIER) cc_final: 0.5442 (mm-30) REVERT: J 10 LYS cc_start: 0.4664 (OUTLIER) cc_final: 0.4395 (tptp) REVERT: J 97 ASP cc_start: 0.7661 (p0) cc_final: 0.7390 (p0) REVERT: J 292 MET cc_start: 0.7389 (OUTLIER) cc_final: 0.7008 (mtt) outliers start: 9 outliers final: 1 residues processed: 91 average time/residue: 1.4382 time to fit residues: 135.6818 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 : 0.628 ------------------------------------------------------------------------------- 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: 0.9990 chunk 41 optimal weight: 4.9990 chunk 15 optimal weight: 0.8980 chunk 18 optimal weight: 5.9990 chunk 11 optimal weight: 0.6980 chunk 55 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 1 optimal weight: 0.0980 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 = 0.4221 r_free = 0.4221 target = 0.187657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.166392 restraints weight = 4630.273| |-----------------------------------------------------------------------------| r_work (start): 0.3970 rms_B_bonded: 0.88 r_work: 0.3863 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.3772 rms_B_bonded: 2.57 restraints_weight: 0.2500 r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.1030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5227 Z= 0.147 Angle : 0.577 5.587 7074 Z= 0.302 Chirality : 0.041 0.134 776 Planarity : 0.005 0.037 903 Dihedral : 4.781 58.786 706 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.94 % Favored : 97.90 % Rotamer: Outliers : 1.26 % Allowed : 15.34 % 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: 1.63 (0.33), residues: 618 helix: 1.97 (0.27), residues: 339 sheet: 0.73 (1.39), residues: 15 loop : -0.02 (0.38), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP I 11 HIS 0.004 0.001 HIS I 281 PHE 0.016 0.002 PHE I 30 TYR 0.018 0.002 TYR I 91 ARG 0.005 0.000 ARG I 256 Details of bonding type rmsd hydrogen bonds : bond 0.05000 ( 276) hydrogen bonds : angle 4.72716 ( 774) covalent geometry : bond 0.00321 ( 5227) covalent geometry : angle 0.57736 ( 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 95 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 88 time to evaluate : 0.564 Fit side-chains REVERT: I 49 GLU cc_start: 0.5980 (OUTLIER) cc_final: 0.5331 (mp0) REVERT: I 234 GLU cc_start: 0.6052 (OUTLIER) cc_final: 0.5419 (mm-30) REVERT: J 10 LYS cc_start: 0.4694 (OUTLIER) cc_final: 0.4408 (tptp) REVERT: J 292 MET cc_start: 0.7380 (OUTLIER) cc_final: 0.7015 (mtt) outliers start: 7 outliers final: 1 residues processed: 90 average time/residue: 1.4924 time to fit residues: 139.1993 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 : 0.639 ------------------------------------------------------------------------------- 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: 0.5980 chunk 31 optimal weight: 1.9990 chunk 23 optimal weight: 0.1980 chunk 35 optimal weight: 7.9990 chunk 50 optimal weight: 4.9990 chunk 9 optimal weight: 10.0000 chunk 28 optimal weight: 10.0000 chunk 61 optimal weight: 3.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 = 0.4212 r_free = 0.4212 target = 0.186713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.165250 restraints weight = 4585.032| |-----------------------------------------------------------------------------| r_work (start): 0.3959 rms_B_bonded: 0.88 r_work: 0.3855 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.3762 rms_B_bonded: 2.54 restraints_weight: 0.2500 r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.0968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5227 Z= 0.175 Angle : 0.624 6.078 7074 Z= 0.327 Chirality : 0.043 0.137 776 Planarity : 0.005 0.038 903 Dihedral : 4.910 58.482 706 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 7.16 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: 1.45 (0.33), residues: 618 helix: 1.83 (0.27), residues: 337 sheet: 0.85 (1.40), residues: 15 loop : -0.12 (0.37), residues: 266 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 71 TYR 0.019 0.002 TYR I 91 ARG 0.004 0.001 ARG J 136 Details of bonding type rmsd hydrogen bonds : bond 0.05362 ( 276) hydrogen bonds : angle 4.84778 ( 774) covalent geometry : bond 0.00384 ( 5227) covalent geometry : angle 0.62450 ( 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 95 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 0.566 Fit side-chains REVERT: I 49 GLU cc_start: 0.6015 (OUTLIER) cc_final: 0.5405 (mp0) REVERT: I 234 GLU cc_start: 0.6058 (OUTLIER) cc_final: 0.5414 (mm-30) REVERT: J 10 LYS cc_start: 0.4671 (OUTLIER) cc_final: 0.4400 (tptp) outliers start: 9 outliers final: 1 residues processed: 89 average time/residue: 1.4825 time to fit residues: 136.8497 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 : 0.635 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 46 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 32 optimal weight: 0.0370 chunk 53 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 47 optimal weight: 0.0170 chunk 54 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 overall best weight: 0.5700 ------------------------------------------------------------------------------- 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 = 0.4241 r_free = 0.4241 target = 0.189566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.168498 restraints weight = 4607.000| |-----------------------------------------------------------------------------| r_work (start): 0.3996 rms_B_bonded: 0.88 r_work: 0.3890 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.3798 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.1057 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= 0.120 Angle : 0.549 4.881 7074 Z= 0.289 Chirality : 0.041 0.135 776 Planarity : 0.005 0.037 903 Dihedral : 4.715 58.828 706 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.94 % Favored : 97.90 % 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: 1.76 (0.33), residues: 618 helix: 2.08 (0.28), residues: 339 sheet: 0.32 (1.34), residues: 16 loop : 0.06 (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 0.04481 ( 276) hydrogen bonds : angle 4.59810 ( 774) covalent geometry : bond 0.00258 ( 5227) covalent geometry : angle 0.54861 ( 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 96 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 87 time to evaluate : 0.611 Fit side-chains REVERT: I 49 GLU cc_start: 0.5880 (OUTLIER) cc_final: 0.5223 (mp0) REVERT: I 234 GLU cc_start: 0.6013 (OUTLIER) cc_final: 0.5360 (mm-30) REVERT: J 10 LYS cc_start: 0.4677 (OUTLIER) cc_final: 0.4415 (tptp) REVERT: J 292 MET cc_start: 0.7378 (OUTLIER) cc_final: 0.7007 (mtt) outliers start: 9 outliers final: 1 residues processed: 91 average time/residue: 1.5516 time to fit residues: 146.1357 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 : 0.609 ------------------------------------------------------------------------------- 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: 4.9990 chunk 33 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 = 0.188039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.166773 restraints weight = 4590.468| |-----------------------------------------------------------------------------| r_work (start): 0.3979 rms_B_bonded: 0.87 r_work: 0.3871 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.3779 rms_B_bonded: 2.56 restraints_weight: 0.2500 r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.1029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5227 Z= 0.146 Angle : 0.593 8.416 7074 Z= 0.309 Chirality : 0.042 0.137 776 Planarity : 0.005 0.038 903 Dihedral : 4.791 59.257 706 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.94 % Favored : 97.90 % Rotamer: Outliers : 1.44 % Allowed : 14.98 % 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: 1.66 (0.33), residues: 618 helix: 1.99 (0.27), residues: 339 sheet: 0.38 (1.34), residues: 16 loop : 0.03 (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 100 PHE 0.017 0.002 PHE I 30 TYR 0.020 0.002 TYR I 164 ARG 0.003 0.000 ARG J 136 Details of bonding type rmsd hydrogen bonds : bond 0.04896 ( 276) hydrogen bonds : angle 4.70632 ( 774) covalent geometry : bond 0.00320 ( 5227) covalent geometry : angle 0.59349 ( 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 91 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 83 time to evaluate : 0.568 Fit side-chains REVERT: I 49 GLU cc_start: 0.5909 (OUTLIER) cc_final: 0.5262 (mp0) REVERT: I 234 GLU cc_start: 0.6075 (OUTLIER) cc_final: 0.5430 (mm-30) REVERT: J 10 LYS cc_start: 0.4683 (OUTLIER) cc_final: 0.4420 (tptp) REVERT: J 292 MET cc_start: 0.7375 (OUTLIER) cc_final: 0.6995 (mtt) outliers start: 8 outliers final: 1 residues processed: 86 average time/residue: 1.6763 time to fit residues: 149.0496 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 : 0.606 ------------------------------------------------------------------------------- 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: 0.9990 chunk 10 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 9 optimal weight: 6.9990 chunk 5 optimal weight: 6.9990 chunk 19 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 ** J 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.187363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.166047 restraints weight = 4606.267| |-----------------------------------------------------------------------------| r_work (start): 0.3969 rms_B_bonded: 0.88 r_work: 0.3861 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.3768 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.1014 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 : 0.629 7.169 7074 Z= 0.327 Chirality : 0.043 0.144 776 Planarity : 0.005 0.037 903 Dihedral : 4.864 58.737 706 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.10 % Favored : 97.73 % Rotamer: Outliers : 0.90 % Allowed : 16.06 % Favored : 83.03 % 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: 1.88 (0.27), residues: 338 sheet: 0.44 (1.36), residues: 16 loop : 0.01 (0.38), residues: 264 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 0.004 0.000 ARG J 136 Details of bonding type rmsd hydrogen bonds : bond 0.05168 ( 276) hydrogen bonds : angle 4.79376 ( 774) covalent geometry : bond 0.00366 ( 5227) covalent geometry : angle 0.62907 ( 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 88 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 83 time to evaluate : 0.590 Fit side-chains REVERT: I 49 GLU cc_start: 0.5987 (OUTLIER) cc_final: 0.5370 (mp0) REVERT: I 234 GLU cc_start: 0.6133 (OUTLIER) cc_final: 0.5500 (mm-30) REVERT: J 10 LYS cc_start: 0.4690 (OUTLIER) cc_final: 0.4427 (tptp) REVERT: J 292 MET cc_start: 0.7358 (OUTLIER) cc_final: 0.6973 (mtt) outliers start: 5 outliers final: 1 residues processed: 85 average time/residue: 1.6017 time to fit residues: 140.8421 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 : 0.572 ------------------------------------------------------------------------------- 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: 0.0970 chunk 40 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 54 optimal weight: 7.9990 chunk 55 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 48 optimal weight: 10.0000 chunk 3 optimal weight: 0.0170 chunk 52 optimal weight: 0.7980 chunk 14 optimal weight: 4.9990 overall best weight: 1.1820 ------------------------------------------------------------------------------- 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 ** 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 = 0.4224 r_free = 0.4224 target = 0.187699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.166389 restraints weight = 4642.954| |-----------------------------------------------------------------------------| r_work (start): 0.3973 rms_B_bonded: 0.88 r_work: 0.3866 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.3773 rms_B_bonded: 2.59 restraints_weight: 0.2500 r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 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 0.036 5227 Z= 0.156 Angle : 0.623 7.867 7074 Z= 0.324 Chirality : 0.043 0.142 776 Planarity : 0.005 0.038 903 Dihedral : 4.845 58.982 706 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.27 % Favored : 97.57 % Rotamer: Outliers : 1.44 % Allowed : 15.88 % Favored : 82.67 % 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 (0.33), residues: 618 helix: 1.90 (0.27), residues: 338 sheet: 0.37 (1.36), residues: 16 loop : 0.03 (0.38), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP I 11 HIS 0.004 0.001 HIS I 281 PHE 0.017 0.002 PHE I 30 TYR 0.020 0.002 TYR I 164 ARG 0.003 0.000 ARG J 136 Details of bonding type rmsd hydrogen bonds : bond 0.05047 ( 276) hydrogen bonds : angle 4.79118 ( 774) covalent geometry : bond 0.00347 ( 5227) covalent geometry : angle 0.62311 ( 7074) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6363.58 seconds wall clock time: 109 minutes 46.90 seconds (6586.90 seconds total)