Starting phenix.real_space_refine on Sat May 2 12:38:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qjn_53205/05_2026/9qjn_53205.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qjn_53205/05_2026/9qjn_53205.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9qjn_53205/05_2026/9qjn_53205.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qjn_53205/05_2026/9qjn_53205.map" model { file = "/net/cci-nas-00/data/ceres_data/9qjn_53205/05_2026/9qjn_53205.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qjn_53205/05_2026/9qjn_53205.cif" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 32 5.16 5 C 3292 2.51 5 N 866 2.21 5 O 1056 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5246 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'NK3': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "I" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 59 Classifications: {'water': 59} Link IDs: {None: 58} Chain: "J" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 64 Classifications: {'water': 64} Link IDs: {None: 63} Time building chain proxies: 1.51, per 1000 atoms: 0.29 Number of scatterers: 5246 At special positions: 0 Unit cell: (83.64, 95.88, 67.32, 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 32 16.00 O 1056 8.00 N 866 7.00 C 3292 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.47 Conformation dependent library (CDL) restraints added in 199.8 milliseconds 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1196 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 3 sheets defined 62.2% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'H' and resid 270 through 275 removed outlier: 3.506A pdb=" N VAL H 275 " --> pdb=" O LEU H 272 " (cutoff:3.500A) Processing helix chain 'H' and resid 279 through 286 Processing helix chain 'H' and resid 288 through 302 removed outlier: 3.952A 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 71 Processing helix chain 'I' and resid 76 through 93 removed outlier: 4.006A pdb=" N ASN I 93 " --> pdb=" O ARG I 89 " (cutoff:3.500A) Processing helix chain 'I' and resid 100 through 116 removed outlier: 3.814A pdb=" N LEU I 106 " --> pdb=" O ARG I 102 " (cutoff:3.500A) Processing helix chain 'I' and resid 121 through 127 Processing helix chain 'I' and resid 132 through 154 removed outlier: 4.747A pdb=" N LEU I 148 " --> pdb=" O LEU I 144 " (cutoff:3.500A) removed outlier: 4.631A 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: 3.563A 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 235 removed outlier: 3.919A 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 284 Processing helix chain 'J' and resid 56 through 67 Processing helix chain 'J' and resid 98 through 104 Processing helix chain 'J' and resid 110 through 131 Processing helix chain 'J' and resid 139 through 141 No H-bonds generated for 'chain 'J' and resid 139 through 141' Processing helix chain 'J' and resid 155 through 159 removed outlier: 4.527A pdb=" N LEU J 158 " --> pdb=" O ASP J 155 " (cutoff:3.500A) Processing helix chain 'J' and resid 175 through 179 Processing helix chain 'J' and resid 180 through 185 Processing helix chain 'J' and resid 192 through 209 removed outlier: 3.567A pdb=" N ALA J 198 " --> pdb=" O VAL J 194 " (cutoff:3.500A) Processing helix chain 'J' and resid 217 through 230 Processing helix chain 'J' and resid 239 through 243 Processing helix chain 'J' and resid 256 through 261 Processing helix chain 'J' and resid 265 through 276 Processing helix chain 'J' and resid 285 through 292 Processing helix chain 'J' and resid 292 through 297 removed outlier: 4.046A 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 16 through 20 removed outlier: 6.799A pdb=" N VAL J 26 " --> pdb=" O LEU J 18 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N ASP J 92 " --> pdb=" O LEU J 77 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N LEU J 77 " --> pdb=" O ASP J 92 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'J' and resid 96 through 97 Processing sheet with id=AA3, first strand: chain 'J' and resid 133 through 134 277 hydrogen bonds defined for protein. 777 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: 0.83 Time building geometry restraints manager: 0.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 821 1.31 - 1.43: 1399 1.43 - 1.56: 2957 1.56 - 1.68: 0 1.68 - 1.81: 51 Bond restraints: 5228 Sorted by residual: bond pdb=" C09 NK3 J 401 " pdb=" C11 NK3 J 401 " ideal model delta sigma weight residual 1.434 1.506 -0.072 2.00e-02 2.50e+03 1.28e+01 bond pdb=" C09 NK3 J 401 " pdb=" O10 NK3 J 401 " ideal model delta sigma weight residual 1.238 1.183 0.055 2.00e-02 2.50e+03 7.62e+00 bond pdb=" C07 NK3 J 401 " pdb=" N08 NK3 J 401 " ideal model delta sigma weight residual 1.420 1.475 -0.055 2.00e-02 2.50e+03 7.45e+00 bond pdb=" C27 NK3 J 401 " pdb=" N25 NK3 J 401 " ideal model delta sigma weight residual 1.497 1.452 0.045 2.00e-02 2.50e+03 5.08e+00 bond pdb=" C05 NK3 J 401 " pdb=" C16 NK3 J 401 " ideal model delta sigma weight residual 1.476 1.433 0.043 2.00e-02 2.50e+03 4.72e+00 ... (remaining 5223 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.74: 6940 1.74 - 3.48: 111 3.48 - 5.22: 20 5.22 - 6.96: 6 6.96 - 8.71: 2 Bond angle restraints: 7079 Sorted by residual: angle pdb=" C09 NK3 J 401 " pdb=" C11 NK3 J 401 " pdb=" S15 NK3 J 401 " ideal model delta sigma weight residual 123.31 132.02 -8.71 3.00e+00 1.11e-01 8.42e+00 angle pdb=" CB MET I 237 " pdb=" CG MET I 237 " pdb=" SD MET I 237 " ideal model delta sigma weight residual 112.70 120.03 -7.33 3.00e+00 1.11e-01 5.97e+00 angle pdb=" CB GLU I 229 " pdb=" CG GLU I 229 " pdb=" CD GLU I 229 " ideal model delta sigma weight residual 112.60 116.49 -3.89 1.70e+00 3.46e-01 5.24e+00 angle pdb=" CA GLU J 147 " pdb=" CB GLU J 147 " pdb=" CG GLU J 147 " ideal model delta sigma weight residual 114.10 118.47 -4.37 2.00e+00 2.50e-01 4.78e+00 angle pdb=" N SER I 15 " pdb=" CA SER I 15 " pdb=" C SER I 15 " ideal model delta sigma weight residual 108.79 111.94 -3.15 1.53e+00 4.27e-01 4.25e+00 ... (remaining 7074 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.50: 2691 17.50 - 35.00: 331 35.00 - 52.51: 108 52.51 - 70.01: 24 70.01 - 87.51: 7 Dihedral angle restraints: 3161 sinusoidal: 1314 harmonic: 1847 Sorted by residual: 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 -161.20 -18.80 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" CG ARG I 31 " pdb=" CD ARG I 31 " pdb=" NE ARG I 31 " pdb=" CZ ARG I 31 " ideal model delta sinusoidal sigma weight residual -90.00 -134.88 44.88 2 1.50e+01 4.44e-03 1.06e+01 dihedral pdb=" CB GLU I 137 " pdb=" CG GLU I 137 " pdb=" CD GLU I 137 " pdb=" OE1 GLU I 137 " ideal model delta sinusoidal sigma weight residual 0.00 87.51 -87.51 1 3.00e+01 1.11e-03 1.02e+01 ... (remaining 3158 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 429 0.025 - 0.049: 190 0.049 - 0.074: 96 0.074 - 0.099: 35 0.099 - 0.123: 26 Chirality restraints: 776 Sorted by residual: 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 2.39 0.12 2.00e-01 2.50e+01 3.80e-01 chirality pdb=" CA PRO J 140 " pdb=" N PRO J 140 " pdb=" C PRO J 140 " pdb=" CB PRO J 140 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.77e-01 chirality pdb=" CA ILE I 226 " pdb=" N ILE I 226 " pdb=" C ILE I 226 " pdb=" CB ILE I 226 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.56e-01 ... (remaining 773 not shown) Planarity restraints: 905 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN I 162 " -0.027 5.00e-02 4.00e+02 4.08e-02 2.67e+00 pdb=" N PRO I 163 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO I 163 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO I 163 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU I 49 " 0.027 5.00e-02 4.00e+02 4.05e-02 2.63e+00 pdb=" N PRO I 50 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO I 50 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO I 50 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS J 71 " -0.026 5.00e-02 4.00e+02 3.87e-02 2.40e+00 pdb=" N PRO J 72 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO J 72 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO J 72 " -0.022 5.00e-02 4.00e+02 ... (remaining 902 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 279 2.73 - 3.27: 5182 3.27 - 3.81: 9253 3.81 - 4.36: 11290 4.36 - 4.90: 18911 Nonbonded interactions: 44915 Sorted by model distance: nonbonded pdb=" N GLU J 147 " pdb=" OE1 GLU J 147 " model vdw 2.186 3.120 nonbonded pdb=" OD2 ASP J 267 " pdb=" O HOH J 501 " model vdw 2.204 3.040 nonbonded pdb=" OH TYR J 294 " pdb=" O HOH J 502 " model vdw 2.231 3.040 nonbonded pdb=" OE2 GLU J 68 " pdb=" O HOH J 503 " model vdw 2.237 3.040 nonbonded pdb=" O PHE J 295 " pdb=" O HOH J 504 " model vdw 2.241 3.040 ... (remaining 44910 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: 0.500 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.370 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.000 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:7.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 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 0.072 5228 Z= 0.179 Angle : 0.593 8.705 7079 Z= 0.298 Chirality : 0.040 0.123 776 Planarity : 0.005 0.041 905 Dihedral : 17.680 87.509 1965 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.46 % Favored : 98.38 % Rotamer: Outliers : 1.08 % Allowed : 23.10 % Favored : 75.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.73 (0.33), residues: 618 helix: 2.38 (0.28), residues: 333 sheet: -0.65 (0.90), residues: 30 loop : -0.29 (0.35), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 295 TYR 0.013 0.002 TYR I 91 PHE 0.013 0.001 PHE J 17 TRP 0.008 0.001 TRP I 11 HIS 0.004 0.001 HIS J 258 Details of bonding type rmsd covalent geometry : bond 0.00385 ( 5228) covalent geometry : angle 0.59255 ( 7079) hydrogen bonds : bond 0.10333 ( 277) hydrogen bonds : angle 4.66431 ( 777) *********************** 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 109 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 103 time to evaluate : 0.221 Fit side-chains REVERT: I 77 ARG cc_start: 0.7532 (ttp-170) cc_final: 0.7310 (ttp-170) REVERT: I 229 GLU cc_start: 0.7707 (pm20) cc_final: 0.7273 (mm-30) outliers start: 6 outliers final: 5 residues processed: 108 average time/residue: 0.8044 time to fit residues: 89.5550 Evaluate side-chains 105 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 100 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 122 SER Chi-restraints excluded: chain I residue 219 SER Chi-restraints excluded: chain J residue 216 ASP Chi-restraints excluded: chain J residue 287 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 54 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 48 optimal weight: 9.9990 chunk 56 optimal weight: 0.2980 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 249 GLN H 273 ASN I 142 GLN I 162 ASN I 247 GLN J 273 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.127465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.104522 restraints weight = 6407.814| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 1.78 r_work: 0.3124 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.0646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 5228 Z= 0.111 Angle : 0.483 4.638 7079 Z= 0.252 Chirality : 0.039 0.124 776 Planarity : 0.004 0.037 905 Dihedral : 6.302 58.991 709 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.16 % Allowed : 0.97 % Favored : 98.87 % Rotamer: Outliers : 2.71 % Allowed : 20.04 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.75 (0.34), residues: 618 helix: 2.32 (0.28), residues: 345 sheet: -0.37 (0.91), residues: 25 loop : -0.34 (0.37), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 266 TYR 0.013 0.001 TYR I 91 PHE 0.012 0.001 PHE J 252 TRP 0.007 0.001 TRP I 11 HIS 0.003 0.001 HIS H 274 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 5228) covalent geometry : angle 0.48277 ( 7079) hydrogen bonds : bond 0.04286 ( 277) hydrogen bonds : angle 4.23077 ( 777) *********************** 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 119 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 104 time to evaluate : 0.223 Fit side-chains REVERT: H 262 GLU cc_start: 0.7366 (mm-30) cc_final: 0.7020 (mm-30) REVERT: I 77 ARG cc_start: 0.7576 (ttp-170) cc_final: 0.7334 (ttp-170) outliers start: 15 outliers final: 8 residues processed: 113 average time/residue: 0.7757 time to fit residues: 90.4478 Evaluate side-chains 106 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 98 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 245 LEU Chi-restraints excluded: chain I residue 70 VAL Chi-restraints excluded: chain I residue 78 SER Chi-restraints excluded: chain I residue 122 SER Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain I residue 132 SER Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 251 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 14 optimal weight: 5.9990 chunk 36 optimal weight: 7.9990 chunk 46 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 9 optimal weight: 7.9990 chunk 56 optimal weight: 0.7980 chunk 10 optimal weight: 4.9990 chunk 19 optimal weight: 7.9990 chunk 1 optimal weight: 4.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 247 GLN ** J 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 141 ASN J 236 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.122627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.099603 restraints weight = 6376.995| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 1.76 r_work: 0.3059 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.0936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 5228 Z= 0.232 Angle : 0.596 5.382 7079 Z= 0.306 Chirality : 0.045 0.138 776 Planarity : 0.005 0.040 905 Dihedral : 6.300 57.809 704 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.29 % Favored : 98.54 % Rotamer: Outliers : 3.25 % Allowed : 19.13 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.33), residues: 618 helix: 1.97 (0.28), residues: 346 sheet: -0.34 (0.89), residues: 25 loop : -0.56 (0.37), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 266 TYR 0.017 0.002 TYR I 2 PHE 0.016 0.002 PHE J 91 TRP 0.008 0.002 TRP I 11 HIS 0.006 0.002 HIS J 131 Details of bonding type rmsd covalent geometry : bond 0.00564 ( 5228) covalent geometry : angle 0.59649 ( 7079) hydrogen bonds : bond 0.05779 ( 277) hydrogen bonds : angle 4.59143 ( 777) *********************** 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 118 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 100 time to evaluate : 0.193 Fit side-chains REVERT: H 262 GLU cc_start: 0.7501 (mm-30) cc_final: 0.7241 (mm-30) REVERT: H 276 ARG cc_start: 0.7105 (OUTLIER) cc_final: 0.6573 (ttp-110) REVERT: I 177 ARG cc_start: 0.8630 (OUTLIER) cc_final: 0.7623 (mtp85) REVERT: J 86 ASN cc_start: 0.7050 (m110) cc_final: 0.6553 (m110) outliers start: 18 outliers final: 11 residues processed: 112 average time/residue: 0.8053 time to fit residues: 92.9117 Evaluate side-chains 111 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 98 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 245 LEU Chi-restraints excluded: chain H residue 276 ARG Chi-restraints excluded: chain I residue 70 VAL Chi-restraints excluded: chain I residue 78 SER Chi-restraints excluded: chain I residue 122 SER Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain I residue 132 SER Chi-restraints excluded: chain I residue 155 ASN Chi-restraints excluded: chain I residue 177 ARG Chi-restraints excluded: chain I residue 241 ASN Chi-restraints excluded: chain J residue 106 SER Chi-restraints excluded: chain J residue 247 VAL Chi-restraints excluded: chain J residue 251 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 29 optimal weight: 0.9980 chunk 1 optimal weight: 0.0870 chunk 20 optimal weight: 0.7980 chunk 50 optimal weight: 6.9990 chunk 53 optimal weight: 0.0770 chunk 56 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 chunk 54 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 overall best weight: 0.5716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 130 GLN J 273 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.126619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.103987 restraints weight = 6374.811| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 1.77 r_work: 0.3119 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.1068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 5228 Z= 0.100 Angle : 0.466 4.730 7079 Z= 0.245 Chirality : 0.039 0.125 776 Planarity : 0.004 0.039 905 Dihedral : 5.881 58.057 704 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.29 % Favored : 98.54 % Rotamer: Outliers : 2.89 % Allowed : 19.31 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.72 (0.34), residues: 618 helix: 2.28 (0.28), residues: 345 sheet: -0.28 (0.89), residues: 25 loop : -0.34 (0.38), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 266 TYR 0.013 0.001 TYR I 60 PHE 0.012 0.001 PHE I 30 TRP 0.006 0.001 TRP I 11 HIS 0.007 0.001 HIS J 83 Details of bonding type rmsd covalent geometry : bond 0.00213 ( 5228) covalent geometry : angle 0.46576 ( 7079) hydrogen bonds : bond 0.04063 ( 277) hydrogen bonds : angle 4.20771 ( 777) *********************** 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 118 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 102 time to evaluate : 0.195 Fit side-chains REVERT: H 262 GLU cc_start: 0.7426 (mm-30) cc_final: 0.7166 (mm-30) REVERT: H 276 ARG cc_start: 0.7089 (OUTLIER) cc_final: 0.6258 (ttp-110) REVERT: I 229 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7893 (pm20) REVERT: J 86 ASN cc_start: 0.7169 (m110) cc_final: 0.6800 (m110) outliers start: 16 outliers final: 11 residues processed: 113 average time/residue: 0.7570 time to fit residues: 88.1727 Evaluate side-chains 109 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 97 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 245 LEU Chi-restraints excluded: chain H residue 268 ARG Chi-restraints excluded: chain H residue 276 ARG Chi-restraints excluded: chain I residue 78 SER Chi-restraints excluded: chain I residue 122 SER Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain I residue 132 SER Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 216 ASP Chi-restraints excluded: chain J residue 247 VAL Chi-restraints excluded: chain J residue 251 SER Chi-restraints excluded: chain J residue 259 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 35 optimal weight: 6.9990 chunk 1 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 21 optimal weight: 0.8980 chunk 55 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 chunk 50 optimal weight: 8.9990 chunk 20 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 247 GLN J 273 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.126049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.103518 restraints weight = 6464.452| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 1.76 r_work: 0.3113 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.1082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5228 Z= 0.110 Angle : 0.483 6.614 7079 Z= 0.250 Chirality : 0.039 0.124 776 Planarity : 0.004 0.038 905 Dihedral : 5.648 58.085 704 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.46 % Favored : 98.38 % Rotamer: Outliers : 3.97 % Allowed : 18.77 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.82 (0.34), residues: 618 helix: 2.34 (0.28), residues: 345 sheet: -0.03 (0.93), residues: 25 loop : -0.28 (0.38), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 266 TYR 0.013 0.001 TYR I 91 PHE 0.012 0.001 PHE I 30 TRP 0.007 0.001 TRP I 11 HIS 0.004 0.001 HIS J 83 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 5228) covalent geometry : angle 0.48250 ( 7079) hydrogen bonds : bond 0.04168 ( 277) hydrogen bonds : angle 4.19200 ( 777) *********************** 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 119 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 97 time to evaluate : 0.204 Fit side-chains REVERT: H 262 GLU cc_start: 0.7448 (mm-30) cc_final: 0.7187 (mm-30) REVERT: H 276 ARG cc_start: 0.7104 (OUTLIER) cc_final: 0.6332 (ttp-110) REVERT: I 177 ARG cc_start: 0.8524 (OUTLIER) cc_final: 0.7571 (mtp85) REVERT: I 229 GLU cc_start: 0.8170 (mt-10) cc_final: 0.7893 (pm20) REVERT: J 86 ASN cc_start: 0.7217 (m110) cc_final: 0.6870 (m110) REVERT: J 306 GLN cc_start: 0.8405 (OUTLIER) cc_final: 0.7976 (mm110) outliers start: 22 outliers final: 14 residues processed: 112 average time/residue: 0.7322 time to fit residues: 84.6348 Evaluate side-chains 111 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 94 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 245 LEU Chi-restraints excluded: chain H residue 276 ARG Chi-restraints excluded: chain I residue 70 VAL Chi-restraints excluded: chain I residue 78 SER Chi-restraints excluded: chain I residue 122 SER Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain I residue 132 SER Chi-restraints excluded: chain I residue 155 ASN Chi-restraints excluded: chain I residue 177 ARG Chi-restraints excluded: chain I residue 241 ASN Chi-restraints excluded: chain J residue 30 ARG Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 145 LEU Chi-restraints excluded: chain J residue 216 ASP Chi-restraints excluded: chain J residue 251 SER Chi-restraints excluded: chain J residue 259 HIS Chi-restraints excluded: chain J residue 306 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 56 optimal weight: 0.2980 chunk 55 optimal weight: 0.4980 chunk 54 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 chunk 28 optimal weight: 6.9990 chunk 15 optimal weight: 6.9990 chunk 17 optimal weight: 3.9990 chunk 31 optimal weight: 6.9990 chunk 4 optimal weight: 3.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 281 GLN I 247 GLN J 141 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.122998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.100263 restraints weight = 6502.977| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 1.79 r_work: 0.3069 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.1218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 5228 Z= 0.177 Angle : 0.551 6.984 7079 Z= 0.284 Chirality : 0.042 0.130 776 Planarity : 0.005 0.037 905 Dihedral : 5.631 57.057 704 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.29 % Favored : 98.54 % Rotamer: Outliers : 3.97 % Allowed : 18.59 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.34), residues: 618 helix: 2.12 (0.28), residues: 347 sheet: 0.10 (0.96), residues: 25 loop : -0.42 (0.38), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 266 TYR 0.017 0.002 TYR I 91 PHE 0.013 0.002 PHE J 91 TRP 0.007 0.001 TRP I 11 HIS 0.005 0.001 HIS J 131 Details of bonding type rmsd covalent geometry : bond 0.00425 ( 5228) covalent geometry : angle 0.55139 ( 7079) hydrogen bonds : bond 0.05183 ( 277) hydrogen bonds : angle 4.43907 ( 777) *********************** 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 118 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 96 time to evaluate : 0.220 Fit side-chains REVERT: H 262 GLU cc_start: 0.7495 (mm-30) cc_final: 0.7198 (mm-30) REVERT: H 276 ARG cc_start: 0.7069 (OUTLIER) cc_final: 0.6532 (ttp-110) REVERT: I 141 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7795 (mm-30) REVERT: I 177 ARG cc_start: 0.8590 (OUTLIER) cc_final: 0.7536 (mtp85) REVERT: I 229 GLU cc_start: 0.8221 (mt-10) cc_final: 0.7873 (pm20) REVERT: J 86 ASN cc_start: 0.7140 (m110) cc_final: 0.6765 (m110) REVERT: J 306 GLN cc_start: 0.8311 (OUTLIER) cc_final: 0.7892 (mm110) outliers start: 22 outliers final: 14 residues processed: 109 average time/residue: 0.7599 time to fit residues: 85.4295 Evaluate side-chains 113 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 95 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 245 LEU Chi-restraints excluded: chain H residue 276 ARG Chi-restraints excluded: chain I residue 70 VAL Chi-restraints excluded: chain I residue 78 SER Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain I residue 132 SER Chi-restraints excluded: chain I residue 141 GLU Chi-restraints excluded: chain I residue 155 ASN Chi-restraints excluded: chain I residue 177 ARG Chi-restraints excluded: chain I residue 241 ASN Chi-restraints excluded: chain J residue 30 ARG Chi-restraints excluded: chain J residue 106 SER Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 145 LEU Chi-restraints excluded: chain J residue 216 ASP Chi-restraints excluded: chain J residue 247 VAL Chi-restraints excluded: chain J residue 251 SER Chi-restraints excluded: chain J residue 306 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 59 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 9 optimal weight: 6.9990 chunk 1 optimal weight: 0.0020 chunk 39 optimal weight: 7.9990 chunk 41 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 overall best weight: 0.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 247 GLN J 273 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.126514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.103687 restraints weight = 6450.143| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 1.78 r_work: 0.3118 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.1177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 5228 Z= 0.106 Angle : 0.482 5.920 7079 Z= 0.252 Chirality : 0.039 0.125 776 Planarity : 0.004 0.038 905 Dihedral : 5.162 57.964 703 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.29 % Favored : 98.54 % Rotamer: Outliers : 2.89 % Allowed : 19.49 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.81 (0.34), residues: 618 helix: 2.33 (0.28), residues: 345 sheet: 0.18 (0.96), residues: 25 loop : -0.31 (0.38), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 266 TYR 0.013 0.001 TYR I 60 PHE 0.012 0.001 PHE I 30 TRP 0.007 0.001 TRP I 11 HIS 0.003 0.001 HIS J 131 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 5228) covalent geometry : angle 0.48192 ( 7079) hydrogen bonds : bond 0.04087 ( 277) hydrogen bonds : angle 4.19607 ( 777) *********************** 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 111 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 95 time to evaluate : 0.225 Fit side-chains REVERT: H 262 GLU cc_start: 0.7439 (mm-30) cc_final: 0.7166 (mm-30) REVERT: H 276 ARG cc_start: 0.7114 (OUTLIER) cc_final: 0.6351 (ttp-110) REVERT: I 177 ARG cc_start: 0.8543 (OUTLIER) cc_final: 0.7574 (mtp85) REVERT: I 229 GLU cc_start: 0.8164 (mt-10) cc_final: 0.7893 (pm20) REVERT: J 86 ASN cc_start: 0.7197 (m110) cc_final: 0.6850 (m110) outliers start: 16 outliers final: 10 residues processed: 106 average time/residue: 0.7598 time to fit residues: 83.1036 Evaluate side-chains 106 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 94 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 245 LEU Chi-restraints excluded: chain H residue 276 ARG Chi-restraints excluded: chain I residue 78 SER Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain I residue 132 SER Chi-restraints excluded: chain I residue 155 ASN Chi-restraints excluded: chain I residue 177 ARG Chi-restraints excluded: chain J residue 30 ARG Chi-restraints excluded: chain J residue 106 SER Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 216 ASP Chi-restraints excluded: chain J residue 251 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 57 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 60 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 34 optimal weight: 10.0000 chunk 44 optimal weight: 2.9990 chunk 50 optimal weight: 0.0470 overall best weight: 1.5082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 247 GLN J 141 ASN J 273 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.124452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.101648 restraints weight = 6422.605| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 1.77 r_work: 0.3085 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5228 Z= 0.150 Angle : 0.535 6.807 7079 Z= 0.276 Chirality : 0.041 0.128 776 Planarity : 0.005 0.037 905 Dihedral : 5.158 57.695 703 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.29 % Favored : 98.54 % Rotamer: Outliers : 3.61 % Allowed : 19.68 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.64 (0.34), residues: 618 helix: 2.18 (0.28), residues: 347 sheet: 0.23 (0.97), residues: 25 loop : -0.39 (0.38), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 266 TYR 0.015 0.002 TYR I 91 PHE 0.013 0.002 PHE J 91 TRP 0.008 0.001 TRP I 11 HIS 0.004 0.001 HIS H 274 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 5228) covalent geometry : angle 0.53537 ( 7079) hydrogen bonds : bond 0.04773 ( 277) hydrogen bonds : angle 4.34661 ( 777) *********************** 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 116 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 96 time to evaluate : 0.209 Fit side-chains REVERT: H 262 GLU cc_start: 0.7524 (mm-30) cc_final: 0.7231 (mm-30) REVERT: H 276 ARG cc_start: 0.7097 (OUTLIER) cc_final: 0.6322 (ttp-110) REVERT: I 131 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7251 (mm-30) REVERT: I 141 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7856 (mm-30) REVERT: I 177 ARG cc_start: 0.8580 (OUTLIER) cc_final: 0.7546 (mtp85) REVERT: J 86 ASN cc_start: 0.7171 (m110) cc_final: 0.6809 (m110) REVERT: J 306 GLN cc_start: 0.8323 (OUTLIER) cc_final: 0.7917 (mm110) outliers start: 20 outliers final: 14 residues processed: 109 average time/residue: 0.7988 time to fit residues: 89.7335 Evaluate side-chains 115 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 245 LEU Chi-restraints excluded: chain H residue 276 ARG Chi-restraints excluded: chain I residue 70 VAL Chi-restraints excluded: chain I residue 78 SER Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain I residue 131 GLU Chi-restraints excluded: chain I residue 132 SER Chi-restraints excluded: chain I residue 141 GLU Chi-restraints excluded: chain I residue 155 ASN Chi-restraints excluded: chain I residue 177 ARG Chi-restraints excluded: chain I residue 241 ASN Chi-restraints excluded: chain J residue 30 ARG Chi-restraints excluded: chain J residue 106 SER Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 145 LEU Chi-restraints excluded: chain J residue 216 ASP Chi-restraints excluded: chain J residue 247 VAL Chi-restraints excluded: chain J residue 251 SER Chi-restraints excluded: chain J residue 306 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 49 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 chunk 53 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 35 optimal weight: 8.9990 chunk 26 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 61 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 247 GLN J 273 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.126690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.103998 restraints weight = 6410.488| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 1.77 r_work: 0.3120 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.1228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 5228 Z= 0.107 Angle : 0.493 6.692 7079 Z= 0.257 Chirality : 0.039 0.125 776 Planarity : 0.004 0.038 905 Dihedral : 4.907 58.287 703 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.13 % Favored : 98.71 % Rotamer: Outliers : 3.25 % Allowed : 19.68 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.83 (0.34), residues: 618 helix: 2.34 (0.28), residues: 345 sheet: 0.34 (0.98), residues: 25 loop : -0.30 (0.37), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 266 TYR 0.015 0.001 TYR J 27 PHE 0.012 0.001 PHE I 30 TRP 0.008 0.001 TRP I 11 HIS 0.003 0.001 HIS J 131 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 5228) covalent geometry : angle 0.49285 ( 7079) hydrogen bonds : bond 0.04058 ( 277) hydrogen bonds : angle 4.17818 ( 777) *********************** 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 114 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 96 time to evaluate : 0.206 Fit side-chains REVERT: H 262 GLU cc_start: 0.7459 (mm-30) cc_final: 0.7183 (mm-30) REVERT: H 276 ARG cc_start: 0.7113 (OUTLIER) cc_final: 0.6349 (ttp-110) REVERT: I 131 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7210 (mm-30) REVERT: I 141 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7847 (mm-30) REVERT: I 177 ARG cc_start: 0.8549 (OUTLIER) cc_final: 0.7576 (mtp85) REVERT: I 229 GLU cc_start: 0.8171 (mt-10) cc_final: 0.7865 (pm20) REVERT: J 86 ASN cc_start: 0.7112 (m110) cc_final: 0.6769 (m110) outliers start: 18 outliers final: 13 residues processed: 108 average time/residue: 0.8310 time to fit residues: 92.4657 Evaluate side-chains 110 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 93 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 245 LEU Chi-restraints excluded: chain H residue 276 ARG Chi-restraints excluded: chain I residue 70 VAL Chi-restraints excluded: chain I residue 78 SER Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain I residue 131 GLU Chi-restraints excluded: chain I residue 132 SER Chi-restraints excluded: chain I residue 141 GLU Chi-restraints excluded: chain I residue 155 ASN Chi-restraints excluded: chain I residue 177 ARG Chi-restraints excluded: chain J residue 30 ARG Chi-restraints excluded: chain J residue 106 SER Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 145 LEU Chi-restraints excluded: chain J residue 216 ASP Chi-restraints excluded: chain J residue 247 VAL Chi-restraints excluded: chain J residue 251 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 9 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 34 optimal weight: 9.9990 chunk 36 optimal weight: 7.9990 chunk 10 optimal weight: 6.9990 chunk 3 optimal weight: 0.7980 chunk 41 optimal weight: 6.9990 chunk 2 optimal weight: 4.9990 chunk 46 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 273 ASN J 141 ASN J 273 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.123417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.100648 restraints weight = 6417.221| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 1.78 r_work: 0.3073 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5228 Z= 0.181 Angle : 0.575 7.497 7079 Z= 0.294 Chirality : 0.042 0.130 776 Planarity : 0.005 0.037 905 Dihedral : 4.976 57.345 703 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.29 % Favored : 98.54 % Rotamer: Outliers : 3.25 % Allowed : 19.68 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.34), residues: 618 helix: 2.10 (0.28), residues: 347 sheet: 0.28 (1.00), residues: 25 loop : -0.43 (0.37), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 266 TYR 0.018 0.002 TYR J 27 PHE 0.014 0.002 PHE I 71 TRP 0.008 0.002 TRP I 11 HIS 0.004 0.001 HIS J 131 Details of bonding type rmsd covalent geometry : bond 0.00437 ( 5228) covalent geometry : angle 0.57543 ( 7079) hydrogen bonds : bond 0.05159 ( 277) hydrogen bonds : angle 4.43908 ( 777) ********************** 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 113 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 95 time to evaluate : 0.217 Fit side-chains REVERT: H 262 GLU cc_start: 0.7467 (mm-30) cc_final: 0.7205 (mm-30) REVERT: H 276 ARG cc_start: 0.7075 (OUTLIER) cc_final: 0.6514 (ttp-110) REVERT: I 131 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7249 (mm-30) REVERT: I 141 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7822 (mm-30) REVERT: I 177 ARG cc_start: 0.8586 (OUTLIER) cc_final: 0.7578 (mtp85) REVERT: J 86 ASN cc_start: 0.7154 (m110) cc_final: 0.6784 (m110) outliers start: 18 outliers final: 13 residues processed: 107 average time/residue: 0.8078 time to fit residues: 89.1486 Evaluate side-chains 111 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 94 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 245 LEU Chi-restraints excluded: chain H residue 276 ARG Chi-restraints excluded: chain I residue 70 VAL Chi-restraints excluded: chain I residue 78 SER Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain I residue 131 GLU Chi-restraints excluded: chain I residue 132 SER Chi-restraints excluded: chain I residue 141 GLU Chi-restraints excluded: chain I residue 155 ASN Chi-restraints excluded: chain I residue 177 ARG Chi-restraints excluded: chain J residue 30 ARG Chi-restraints excluded: chain J residue 106 SER Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 145 LEU Chi-restraints excluded: chain J residue 216 ASP Chi-restraints excluded: chain J residue 247 VAL Chi-restraints excluded: chain J residue 251 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 50 optimal weight: 0.0070 chunk 12 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 chunk 39 optimal weight: 10.0000 chunk 15 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 55 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 chunk 34 optimal weight: 8.9990 overall best weight: 1.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 273 ASN H 281 GLN J 130 GLN J 273 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.125175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.102338 restraints weight = 6456.646| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 1.77 r_work: 0.3095 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5228 Z= 0.133 Angle : 0.532 7.235 7079 Z= 0.274 Chirality : 0.040 0.127 776 Planarity : 0.005 0.037 905 Dihedral : 4.819 57.490 703 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.16 % Allowed : 0.81 % Favored : 99.03 % Rotamer: Outliers : 3.61 % Allowed : 19.13 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.64 (0.34), residues: 618 helix: 2.18 (0.28), residues: 347 sheet: 0.24 (1.00), residues: 25 loop : -0.39 (0.37), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 266 TYR 0.016 0.002 TYR J 27 PHE 0.013 0.001 PHE I 30 TRP 0.008 0.001 TRP I 11 HIS 0.003 0.001 HIS H 274 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 5228) covalent geometry : angle 0.53195 ( 7079) hydrogen bonds : bond 0.04563 ( 277) hydrogen bonds : angle 4.32394 ( 777) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2539.75 seconds wall clock time: 43 minutes 51.89 seconds (2631.89 seconds total)