Starting phenix.real_space_refine on Fri Aug 22 15:45:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p76_17519/08_2025/8p76_17519.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p76_17519/08_2025/8p76_17519.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8p76_17519/08_2025/8p76_17519.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p76_17519/08_2025/8p76_17519.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8p76_17519/08_2025/8p76_17519.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p76_17519/08_2025/8p76_17519.map" } resolution = 2.0 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= 0.001 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 3296 2.51 5 N 870 2.21 5 O 1064 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5261 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: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'X1W': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "I" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 66 Classifications: {'water': 66} Link IDs: {None: 65} Chain: "J" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 63 Classifications: {'water': 63} Link IDs: {None: 62} Time building chain proxies: 1.62, per 1000 atoms: 0.31 Number of scatterers: 5261 At special positions: 0 Unit cell: (84.7875, 93.3375, 68.4, 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 1064 8.00 N 870 7.00 C 3296 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: 0.50 Conformation dependent library (CDL) restraints added in 211.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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 3 sheets defined 62.1% alpha, 4.9% 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 262 through 275 removed outlier: 4.474A pdb=" N GLY H 267 " --> pdb=" O GLU H 264 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLY H 270 " --> pdb=" O GLY H 267 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N TYR H 271 " --> pdb=" O ARG H 268 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LEU H 272 " --> pdb=" O LEU H 269 " (cutoff:3.500A) 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 36 Processing helix chain 'I' and resid 49 through 70 Processing helix chain 'I' and resid 76 through 93 removed outlier: 3.899A pdb=" N ASN I 93 " --> pdb=" O ARG I 89 " (cutoff:3.500A) Processing helix chain 'I' and resid 100 through 117 Processing helix chain 'I' and resid 121 through 127 Processing helix chain 'I' and resid 132 through 154 removed outlier: 4.706A pdb=" N LEU I 148 " --> pdb=" O LEU I 144 " (cutoff:3.500A) removed outlier: 4.626A 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 187 Processing helix chain 'I' and resid 188 through 201 removed outlier: 3.640A 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: 3.502A pdb=" N LEU I 232 " --> pdb=" O MET I 228 " (cutoff:3.500A) Processing helix chain 'I' and resid 237 through 240 Processing helix chain 'I' and resid 241 through 261 Processing helix chain 'I' and resid 266 through 283 Processing helix chain 'J' and resid 56 through 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 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: 3.877A 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 20 removed outlier: 6.042A pdb=" N LYS J 14 " --> pdb=" O ARG J 30 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ARG J 30 " --> pdb=" O LYS J 14 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N VAL J 26 " --> pdb=" O LEU J 18 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N ASP J 92 " --> pdb=" O LEU J 77 " (cutoff:3.500A) removed outlier: 7.901A 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 134 279 hydrogen bonds defined for protein. 765 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: 0.81 Time building geometry restraints manager: 0.65 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: 1642 1.34 - 1.46: 1183 1.46 - 1.58: 2358 1.58 - 1.70: 3 1.70 - 1.82: 49 Bond restraints: 5235 Sorted by residual: bond pdb=" C08 X1W J 401 " pdb=" N09 X1W J 401 " ideal model delta sigma weight residual 1.337 1.490 -0.153 2.00e-02 2.50e+03 5.86e+01 bond pdb=" C26 X1W J 401 " pdb=" C27 X1W J 401 " ideal model delta sigma weight residual 1.502 1.610 -0.108 2.00e-02 2.50e+03 2.91e+01 bond pdb=" C02 X1W J 401 " pdb=" C04 X1W J 401 " ideal model delta sigma weight residual 1.498 1.600 -0.102 2.00e-02 2.50e+03 2.61e+01 bond pdb=" C18 X1W J 401 " pdb=" N19 X1W J 401 " ideal model delta sigma weight residual 1.356 1.454 -0.098 2.00e-02 2.50e+03 2.42e+01 bond pdb=" C20 X1W J 401 " pdb=" C24 X1W J 401 " ideal model delta sigma weight residual 1.528 1.621 -0.093 2.00e-02 2.50e+03 2.17e+01 ... (remaining 5230 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 6917 1.63 - 3.25: 128 3.25 - 4.88: 27 4.88 - 6.51: 8 6.51 - 8.14: 5 Bond angle restraints: 7085 Sorted by residual: angle pdb=" CG ARG I 279 " pdb=" CD ARG I 279 " pdb=" NE ARG I 279 " ideal model delta sigma weight residual 112.00 118.65 -6.65 2.20e+00 2.07e-01 9.15e+00 angle pdb=" CA MET I 237 " pdb=" CB MET I 237 " pdb=" CG MET I 237 " ideal model delta sigma weight residual 114.10 119.90 -5.80 2.00e+00 2.50e-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 112.70 120.84 -8.14 3.00e+00 1.11e-01 7.35e+00 angle pdb=" CB MET J 94 " pdb=" CG MET J 94 " pdb=" SD MET J 94 " ideal model delta sigma weight residual 112.70 120.06 -7.36 3.00e+00 1.11e-01 6.01e+00 angle pdb=" CA GLU I 137 " pdb=" CB GLU I 137 " pdb=" CG GLU I 137 " ideal model delta sigma weight residual 114.10 118.98 -4.88 2.00e+00 2.50e-01 5.96e+00 ... (remaining 7080 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 2751 17.71 - 35.43: 317 35.43 - 53.14: 72 53.14 - 70.86: 23 70.86 - 88.57: 8 Dihedral angle restraints: 3171 sinusoidal: 1324 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 180.00 161.45 18.55 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CG ARG I 279 " pdb=" CD ARG I 279 " pdb=" NE ARG I 279 " pdb=" CZ ARG I 279 " ideal model delta sinusoidal sigma weight residual 90.00 39.27 50.73 2 1.50e+01 4.44e-03 1.28e+01 dihedral pdb=" CB GLU I 141 " pdb=" CG GLU I 141 " pdb=" CD GLU I 141 " pdb=" OE1 GLU I 141 " ideal model delta sinusoidal sigma weight residual 0.00 -88.57 88.57 1 3.00e+01 1.11e-03 1.04e+01 ... (remaining 3168 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 612 0.045 - 0.090: 129 0.090 - 0.136: 33 0.136 - 0.181: 1 0.181 - 0.226: 2 Chirality restraints: 777 Sorted by residual: chirality pdb=" C20 X1W J 401 " pdb=" C21 X1W J 401 " pdb=" C24 X1W J 401 " pdb=" N19 X1W J 401 " both_signs ideal model delta sigma weight residual False -2.45 -2.68 0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" C24 X1W J 401 " pdb=" C20 X1W J 401 " pdb=" C23 X1W J 401 " pdb=" O25 X1W J 401 " both_signs ideal model delta sigma weight residual False -2.71 -2.90 0.19 2.00e-01 2.50e+01 9.16e-01 chirality pdb=" CA MET I 237 " pdb=" N MET I 237 " pdb=" C MET I 237 " pdb=" CB MET I 237 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.75e-01 ... (remaining 774 not shown) Planarity restraints: 904 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP I 116 " -0.008 2.00e-02 2.50e+03 1.66e-02 2.75e+00 pdb=" CG ASP I 116 " 0.029 2.00e-02 2.50e+03 pdb=" OD1 ASP I 116 " -0.010 2.00e-02 2.50e+03 pdb=" OD2 ASP I 116 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG I 165 " 0.024 5.00e-02 4.00e+02 3.60e-02 2.07e+00 pdb=" N PRO I 166 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO I 166 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO I 166 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS J 139 " 0.022 5.00e-02 4.00e+02 3.36e-02 1.80e+00 pdb=" N PRO J 140 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO J 140 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO J 140 " 0.019 5.00e-02 4.00e+02 ... (remaining 901 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1258 2.79 - 3.32: 5206 3.32 - 3.84: 9884 3.84 - 4.37: 11771 4.37 - 4.90: 18853 Nonbonded interactions: 46972 Sorted by model distance: nonbonded pdb=" O TRP J 177 " pdb=" O HOH J 501 " model vdw 2.258 3.040 nonbonded pdb=" O GLY H 286 " pdb=" O HOH H 401 " model vdw 2.261 3.040 nonbonded pdb=" O ARG I 89 " pdb=" O HOH I 401 " model vdw 2.287 3.040 nonbonded pdb=" O HOH J 504 " pdb=" O HOH J 549 " model vdw 2.304 3.040 nonbonded pdb=" O HOH J 554 " pdb=" O HOH J 557 " model vdw 2.306 3.040 ... (remaining 46967 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: 4.500 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.300 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.153 5235 Z= 0.243 Angle : 0.615 8.136 7085 Z= 0.298 Chirality : 0.041 0.226 777 Planarity : 0.004 0.036 904 Dihedral : 16.638 88.570 1975 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.29 % Favored : 98.54 % Rotamer: Outliers : 0.90 % Allowed : 16.43 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.97 (0.34), residues: 618 helix: 2.09 (0.29), residues: 335 sheet: 2.90 (1.24), residues: 14 loop : 0.29 (0.39), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I 279 TYR 0.016 0.001 TYR I 60 PHE 0.019 0.002 PHE I 30 TRP 0.011 0.001 TRP J 132 HIS 0.003 0.001 HIS J 131 Details of bonding type rmsd covalent geometry : bond 0.00497 ( 5235) covalent geometry : angle 0.61456 ( 7085) hydrogen bonds : bond 0.12963 ( 279) hydrogen bonds : angle 5.55643 ( 765) *********************** 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 103 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 98 time to evaluate : 0.224 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 103 average time/residue: 0.8106 time to fit residues: 86.0729 Evaluate side-chains 96 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 92 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 145 GLU Chi-restraints excluded: chain J residue 158 LEU Chi-restraints excluded: chain J residue 228 THR Chi-restraints excluded: chain J residue 302 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 54 optimal weight: 7.9990 chunk 24 optimal weight: 2.9990 chunk 48 optimal weight: 6.9990 chunk 56 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 7.9990 chunk 61 optimal weight: 0.2980 chunk 32 optimal weight: 8.9990 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 249 GLN I 136 GLN I 142 GLN I 275 GLN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 171 HIS ** 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 = 0.4041 r_free = 0.4041 target = 0.170028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.152374 restraints weight = 4902.992| |-----------------------------------------------------------------------------| r_work (start): 0.3826 rms_B_bonded: 0.88 r_work: 0.3735 rms_B_bonded: 1.38 restraints_weight: 0.5000 r_work: 0.3646 rms_B_bonded: 2.33 restraints_weight: 0.2500 r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.0592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5235 Z= 0.132 Angle : 0.559 6.841 7085 Z= 0.287 Chirality : 0.041 0.138 777 Planarity : 0.004 0.036 904 Dihedral : 6.387 81.974 720 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.62 % Favored : 98.22 % Rotamer: Outliers : 1.44 % Allowed : 15.16 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.91 (0.35), residues: 618 helix: 2.00 (0.29), residues: 343 sheet: 2.33 (1.37), residues: 15 loop : 0.29 (0.41), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG I 279 TYR 0.016 0.002 TYR I 91 PHE 0.019 0.002 PHE I 30 TRP 0.011 0.001 TRP J 132 HIS 0.005 0.001 HIS J 131 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 5235) covalent geometry : angle 0.55941 ( 7085) hydrogen bonds : bond 0.04930 ( 279) hydrogen bonds : angle 4.78507 ( 765) *********************** 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 111 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 103 time to evaluate : 0.195 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 106 average time/residue: 0.8081 time to fit residues: 88.3962 Evaluate side-chains 100 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 96 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 105 MET Chi-restraints excluded: chain J residue 292 MET Chi-restraints excluded: chain J residue 302 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 33 optimal weight: 3.9990 chunk 39 optimal weight: 8.9990 chunk 50 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 chunk 34 optimal weight: 0.0050 chunk 26 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 48 optimal weight: 8.9990 chunk 23 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 overall best weight: 3.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 249 GLN I 142 GLN I 275 GLN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 297 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.166348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.148609 restraints weight = 4812.651| |-----------------------------------------------------------------------------| r_work (start): 0.3780 rms_B_bonded: 0.87 r_work: 0.3688 rms_B_bonded: 1.36 restraints_weight: 0.5000 r_work: 0.3598 rms_B_bonded: 2.29 restraints_weight: 0.2500 r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.0897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 5235 Z= 0.253 Angle : 0.728 7.177 7085 Z= 0.371 Chirality : 0.046 0.149 777 Planarity : 0.006 0.040 904 Dihedral : 5.581 57.685 714 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.27 % Favored : 97.57 % Rotamer: Outliers : 1.26 % Allowed : 14.98 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.17 (0.34), residues: 618 helix: 1.35 (0.28), residues: 347 sheet: 2.09 (1.31), residues: 15 loop : 0.01 (0.39), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG I 23 TYR 0.026 0.003 TYR I 2 PHE 0.023 0.003 PHE I 30 TRP 0.018 0.003 TRP J 132 HIS 0.009 0.002 HIS J 131 Details of bonding type rmsd covalent geometry : bond 0.00566 ( 5235) covalent geometry : angle 0.72767 ( 7085) hydrogen bonds : bond 0.06261 ( 279) hydrogen bonds : angle 5.11414 ( 765) *********************** 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 99 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 92 time to evaluate : 0.228 Fit side-chains REVERT: J 227 GLU cc_start: 0.7329 (OUTLIER) cc_final: 0.6922 (tt0) outliers start: 7 outliers final: 4 residues processed: 95 average time/residue: 0.8234 time to fit residues: 80.7077 Evaluate side-chains 97 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 92 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 105 MET Chi-restraints excluded: chain I residue 239 LYS Chi-restraints excluded: chain J residue 227 GLU Chi-restraints excluded: chain J residue 292 MET Chi-restraints excluded: chain J residue 302 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 49 optimal weight: 1.9990 chunk 34 optimal weight: 0.1980 chunk 30 optimal weight: 3.9990 chunk 18 optimal weight: 0.3980 chunk 46 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 36 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 249 GLN I 18 GLN I 142 GLN I 155 ASN I 275 GLN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.170310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.152631 restraints weight = 4849.115| |-----------------------------------------------------------------------------| r_work (start): 0.3829 rms_B_bonded: 0.87 r_work: 0.3740 rms_B_bonded: 1.38 restraints_weight: 0.5000 r_work: 0.3651 rms_B_bonded: 2.32 restraints_weight: 0.2500 r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.0762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5235 Z= 0.118 Angle : 0.545 6.287 7085 Z= 0.279 Chirality : 0.040 0.138 777 Planarity : 0.004 0.036 904 Dihedral : 5.252 55.166 714 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.46 % Favored : 98.38 % Rotamer: Outliers : 1.26 % Allowed : 15.52 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.80 (0.34), residues: 618 helix: 1.96 (0.28), residues: 342 sheet: 2.24 (1.41), residues: 15 loop : 0.17 (0.40), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 279 TYR 0.017 0.001 TYR I 60 PHE 0.019 0.002 PHE I 30 TRP 0.010 0.001 TRP J 132 HIS 0.005 0.001 HIS J 131 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 5235) covalent geometry : angle 0.54464 ( 7085) hydrogen bonds : bond 0.04543 ( 279) hydrogen bonds : angle 4.61511 ( 765) *********************** 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 107 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 100 time to evaluate : 0.227 Fit side-chains REVERT: I 85 MET cc_start: 0.8181 (tpp) cc_final: 0.7972 (tpp) outliers start: 7 outliers final: 3 residues processed: 103 average time/residue: 0.8164 time to fit residues: 86.8284 Evaluate side-chains 96 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 93 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 251 SER Chi-restraints excluded: chain J residue 292 MET Chi-restraints excluded: chain J residue 302 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 14 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 37 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 30 optimal weight: 10.0000 chunk 20 optimal weight: 0.7980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 249 GLN I 18 GLN I 142 GLN I 275 GLN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 171 HIS ** 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 = 0.4029 r_free = 0.4029 target = 0.168824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.151028 restraints weight = 4903.769| |-----------------------------------------------------------------------------| r_work (start): 0.3812 rms_B_bonded: 0.88 r_work: 0.3721 rms_B_bonded: 1.38 restraints_weight: 0.5000 r_work: 0.3630 rms_B_bonded: 2.34 restraints_weight: 0.2500 r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.0853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5235 Z= 0.147 Angle : 0.583 7.537 7085 Z= 0.298 Chirality : 0.041 0.137 777 Planarity : 0.005 0.034 904 Dihedral : 5.295 55.922 714 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.10 % Favored : 97.73 % Rotamer: Outliers : 1.44 % Allowed : 15.70 % Favored : 82.85 % 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 aren not related in a simple way. whole: 1.72 (0.34), residues: 618 helix: 1.89 (0.28), residues: 343 sheet: 2.30 (1.40), residues: 15 loop : 0.14 (0.40), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 23 TYR 0.017 0.002 TYR I 2 PHE 0.022 0.002 PHE I 125 TRP 0.012 0.002 TRP J 132 HIS 0.007 0.001 HIS J 131 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 5235) covalent geometry : angle 0.58285 ( 7085) hydrogen bonds : bond 0.05006 ( 279) hydrogen bonds : angle 4.68493 ( 765) *********************** 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 101 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 93 time to evaluate : 0.225 Fit side-chains REVERT: I 33 LYS cc_start: 0.7178 (ttpp) cc_final: 0.6805 (mptt) REVERT: J 227 GLU cc_start: 0.7335 (OUTLIER) cc_final: 0.6925 (tt0) outliers start: 8 outliers final: 5 residues processed: 96 average time/residue: 0.8207 time to fit residues: 81.4449 Evaluate side-chains 97 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 91 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 105 MET Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 145 GLU Chi-restraints excluded: chain J residue 227 GLU Chi-restraints excluded: chain J residue 292 MET Chi-restraints excluded: chain J residue 302 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 44 optimal weight: 4.9990 chunk 53 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 21 optimal weight: 0.2980 chunk 43 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 3 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 overall best weight: 2.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 249 GLN I 142 GLN I 155 ASN I 275 GLN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 171 HIS ** 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 = 0.4009 r_free = 0.4009 target = 0.167108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.149193 restraints weight = 4924.999| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 0.88 r_work: 0.3697 rms_B_bonded: 1.39 restraints_weight: 0.5000 r_work: 0.3605 rms_B_bonded: 2.35 restraints_weight: 0.2500 r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.0995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 5235 Z= 0.207 Angle : 0.668 7.869 7085 Z= 0.341 Chirality : 0.044 0.146 777 Planarity : 0.005 0.037 904 Dihedral : 5.457 56.914 714 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.10 % Favored : 97.73 % Rotamer: Outliers : 2.35 % Allowed : 14.26 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.40 (0.34), residues: 618 helix: 1.64 (0.28), residues: 342 sheet: 2.24 (1.36), residues: 15 loop : -0.02 (0.39), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG I 23 TYR 0.023 0.002 TYR I 2 PHE 0.021 0.003 PHE I 30 TRP 0.015 0.002 TRP J 132 HIS 0.009 0.002 HIS J 131 Details of bonding type rmsd covalent geometry : bond 0.00463 ( 5235) covalent geometry : angle 0.66772 ( 7085) hydrogen bonds : bond 0.05748 ( 279) hydrogen bonds : angle 4.90388 ( 765) *********************** 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 104 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 91 time to evaluate : 0.256 Fit side-chains REVERT: H 268 ARG cc_start: 0.7121 (ptp90) cc_final: 0.6893 (ptp90) REVERT: I 33 LYS cc_start: 0.7206 (ttpp) cc_final: 0.6837 (mptt) REVERT: I 63 ARG cc_start: 0.7579 (OUTLIER) cc_final: 0.7240 (mmm160) REVERT: I 77 ARG cc_start: 0.7101 (OUTLIER) cc_final: 0.6892 (mmp80) REVERT: I 239 LYS cc_start: 0.6034 (OUTLIER) cc_final: 0.5808 (ptpp) REVERT: J 227 GLU cc_start: 0.7380 (OUTLIER) cc_final: 0.6977 (tt0) outliers start: 13 outliers final: 8 residues processed: 98 average time/residue: 0.7905 time to fit residues: 80.0529 Evaluate side-chains 99 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 87 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 63 ARG Chi-restraints excluded: chain I residue 77 ARG Chi-restraints excluded: chain I residue 102 ARG Chi-restraints excluded: chain I residue 105 MET Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 145 GLU Chi-restraints excluded: chain I residue 239 LYS Chi-restraints excluded: chain J residue 158 LEU Chi-restraints excluded: chain J residue 227 GLU Chi-restraints excluded: chain J residue 251 SER Chi-restraints excluded: chain J residue 292 MET Chi-restraints excluded: chain J residue 302 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 35 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 47 optimal weight: 0.7980 chunk 11 optimal weight: 4.9990 chunk 39 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 30 optimal weight: 4.9990 chunk 40 optimal weight: 0.0040 chunk 50 optimal weight: 7.9990 chunk 17 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 18 GLN I 142 GLN I 275 GLN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 171 HIS ** 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 = 0.4049 r_free = 0.4049 target = 0.170690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.152990 restraints weight = 4919.818| |-----------------------------------------------------------------------------| r_work (start): 0.3834 rms_B_bonded: 0.88 r_work: 0.3743 rms_B_bonded: 1.40 restraints_weight: 0.5000 r_work: 0.3652 rms_B_bonded: 2.37 restraints_weight: 0.2500 r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.0904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5235 Z= 0.119 Angle : 0.555 8.071 7085 Z= 0.285 Chirality : 0.040 0.141 777 Planarity : 0.004 0.037 904 Dihedral : 5.231 54.963 714 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.62 % Favored : 98.22 % Rotamer: Outliers : 1.44 % Allowed : 15.70 % Favored : 82.85 % 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 aren not related in a simple way. whole: 1.83 (0.35), residues: 618 helix: 2.03 (0.28), residues: 343 sheet: 2.03 (1.37), residues: 15 loop : 0.12 (0.40), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 279 TYR 0.016 0.002 TYR J 169 PHE 0.018 0.002 PHE I 125 TRP 0.010 0.001 TRP J 132 HIS 0.004 0.001 HIS J 131 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 5235) covalent geometry : angle 0.55503 ( 7085) hydrogen bonds : bond 0.04441 ( 279) hydrogen bonds : angle 4.53528 ( 765) *********************** 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 106 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 98 time to evaluate : 0.220 Fit side-chains REVERT: H 268 ARG cc_start: 0.7093 (ptp90) cc_final: 0.6867 (ptp90) REVERT: I 33 LYS cc_start: 0.7161 (ttpp) cc_final: 0.6787 (mptt) REVERT: I 63 ARG cc_start: 0.7546 (OUTLIER) cc_final: 0.7222 (mmm160) REVERT: J 227 GLU cc_start: 0.7353 (OUTLIER) cc_final: 0.6963 (tt0) outliers start: 8 outliers final: 5 residues processed: 102 average time/residue: 0.7741 time to fit residues: 81.6304 Evaluate side-chains 94 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 87 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 63 ARG Chi-restraints excluded: chain I residue 105 MET Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain J residue 227 GLU Chi-restraints excluded: chain J residue 251 SER Chi-restraints excluded: chain J residue 292 MET Chi-restraints excluded: chain J residue 302 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 49 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 5 optimal weight: 7.9990 chunk 27 optimal weight: 3.9990 chunk 25 optimal weight: 0.4980 chunk 22 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 249 GLN I 142 GLN I 155 ASN I 275 GLN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 171 HIS ** 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 = 0.4027 r_free = 0.4027 target = 0.168748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.150972 restraints weight = 4868.644| |-----------------------------------------------------------------------------| r_work (start): 0.3810 rms_B_bonded: 0.87 r_work: 0.3717 rms_B_bonded: 1.39 restraints_weight: 0.5000 r_work: 0.3627 rms_B_bonded: 2.33 restraints_weight: 0.2500 r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.0934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5235 Z= 0.160 Angle : 0.628 8.286 7085 Z= 0.319 Chirality : 0.042 0.142 777 Planarity : 0.005 0.035 904 Dihedral : 5.324 56.182 714 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.27 % Favored : 97.57 % Rotamer: Outliers : 1.62 % Allowed : 15.70 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.67 (0.34), residues: 618 helix: 1.89 (0.28), residues: 343 sheet: 2.21 (1.38), residues: 15 loop : 0.05 (0.40), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 23 TYR 0.022 0.002 TYR H 287 PHE 0.019 0.002 PHE I 30 TRP 0.012 0.002 TRP J 132 HIS 0.007 0.001 HIS J 131 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 5235) covalent geometry : angle 0.62753 ( 7085) hydrogen bonds : bond 0.05139 ( 279) hydrogen bonds : angle 4.71579 ( 765) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 89 time to evaluate : 0.223 Fit side-chains REVERT: H 268 ARG cc_start: 0.7116 (ptp90) cc_final: 0.6872 (ptp90) REVERT: I 33 LYS cc_start: 0.7167 (ttpp) cc_final: 0.6801 (mptt) REVERT: I 63 ARG cc_start: 0.7569 (OUTLIER) cc_final: 0.7355 (mmm160) REVERT: J 227 GLU cc_start: 0.7366 (OUTLIER) cc_final: 0.6961 (tt0) outliers start: 9 outliers final: 4 residues processed: 93 average time/residue: 0.8434 time to fit residues: 80.8929 Evaluate side-chains 94 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 88 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 63 ARG Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain J residue 227 GLU Chi-restraints excluded: chain J residue 251 SER Chi-restraints excluded: chain J residue 292 MET Chi-restraints excluded: chain J residue 302 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 53 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 12 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 18 GLN I 142 GLN I 275 GLN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 171 HIS ** 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 = 0.4046 r_free = 0.4046 target = 0.170423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.152497 restraints weight = 4933.440| |-----------------------------------------------------------------------------| r_work (start): 0.3829 rms_B_bonded: 0.89 r_work: 0.3737 rms_B_bonded: 1.41 restraints_weight: 0.5000 r_work: 0.3647 rms_B_bonded: 2.37 restraints_weight: 0.2500 r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.0911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5235 Z= 0.132 Angle : 0.599 8.537 7085 Z= 0.304 Chirality : 0.041 0.143 777 Planarity : 0.004 0.036 904 Dihedral : 5.259 55.480 714 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.78 % Favored : 98.06 % Rotamer: Outliers : 1.44 % Allowed : 16.25 % Favored : 82.31 % 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 aren not related in a simple way. whole: 1.74 (0.35), residues: 618 helix: 2.02 (0.28), residues: 343 sheet: 0.50 (1.06), residues: 26 loop : 0.08 (0.41), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 279 TYR 0.024 0.002 TYR H 287 PHE 0.017 0.002 PHE I 30 TRP 0.011 0.001 TRP J 132 HIS 0.005 0.001 HIS J 131 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 5235) covalent geometry : angle 0.59874 ( 7085) hydrogen bonds : bond 0.04645 ( 279) hydrogen bonds : angle 4.57854 ( 765) *********************** 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 96 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 88 time to evaluate : 0.210 Fit side-chains REVERT: H 268 ARG cc_start: 0.7156 (ptp90) cc_final: 0.6900 (ptp90) REVERT: I 33 LYS cc_start: 0.7140 (ttpp) cc_final: 0.6764 (mptt) REVERT: I 63 ARG cc_start: 0.7553 (OUTLIER) cc_final: 0.7223 (mmm160) REVERT: J 227 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.6965 (tt0) outliers start: 8 outliers final: 4 residues processed: 92 average time/residue: 0.8168 time to fit residues: 77.4893 Evaluate side-chains 93 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 87 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 63 ARG Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain J residue 227 GLU Chi-restraints excluded: chain J residue 251 SER Chi-restraints excluded: chain J residue 292 MET Chi-restraints excluded: chain J residue 302 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 15 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 29 optimal weight: 9.9990 chunk 53 optimal weight: 5.9990 chunk 1 optimal weight: 0.2980 chunk 36 optimal weight: 8.9990 chunk 42 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 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 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 142 GLN I 275 GLN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.169926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.152118 restraints weight = 4892.720| |-----------------------------------------------------------------------------| r_work (start): 0.3824 rms_B_bonded: 0.88 r_work: 0.3731 rms_B_bonded: 1.39 restraints_weight: 0.5000 r_work: 0.3641 rms_B_bonded: 2.36 restraints_weight: 0.2500 r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 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 : 0.003 0.032 5235 Z= 0.144 Angle : 0.632 9.242 7085 Z= 0.320 Chirality : 0.042 0.149 777 Planarity : 0.005 0.035 904 Dihedral : 5.294 55.786 714 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.27 % Favored : 97.57 % Rotamer: Outliers : 1.44 % Allowed : 16.97 % Favored : 81.59 % 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 aren not related in a simple way. whole: 1.73 (0.35), residues: 618 helix: 2.06 (0.28), residues: 337 sheet: 0.47 (1.06), residues: 26 loop : 0.04 (0.41), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I 279 TYR 0.025 0.002 TYR H 287 PHE 0.018 0.002 PHE I 30 TRP 0.011 0.001 TRP J 132 HIS 0.006 0.001 HIS J 131 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 5235) covalent geometry : angle 0.63238 ( 7085) hydrogen bonds : bond 0.04819 ( 279) hydrogen bonds : angle 4.62695 ( 765) ********************** 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 98 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 90 time to evaluate : 0.260 Fit side-chains REVERT: H 268 ARG cc_start: 0.7133 (ptp90) cc_final: 0.6871 (ptp90) REVERT: I 33 LYS cc_start: 0.7137 (ttpp) cc_final: 0.6751 (mptt) REVERT: I 63 ARG cc_start: 0.7560 (OUTLIER) cc_final: 0.7224 (mmm160) REVERT: J 227 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.6962 (tt0) outliers start: 8 outliers final: 5 residues processed: 94 average time/residue: 0.8172 time to fit residues: 79.3484 Evaluate side-chains 93 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 86 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 63 ARG Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain J residue 227 GLU Chi-restraints excluded: chain J residue 251 SER Chi-restraints excluded: chain J residue 266 ASP Chi-restraints excluded: chain J residue 292 MET Chi-restraints excluded: chain J residue 302 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 59 optimal weight: 0.0470 chunk 48 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 43 optimal weight: 6.9990 chunk 12 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 45 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 18 GLN I 142 GLN I 275 GLN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 171 HIS ** 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 = 0.4064 r_free = 0.4064 target = 0.171988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.154155 restraints weight = 4965.669| |-----------------------------------------------------------------------------| r_work (start): 0.3847 rms_B_bonded: 0.89 r_work: 0.3756 rms_B_bonded: 1.41 restraints_weight: 0.5000 r_work: 0.3667 rms_B_bonded: 2.39 restraints_weight: 0.2500 r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.0998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5235 Z= 0.122 Angle : 0.593 8.605 7085 Z= 0.302 Chirality : 0.040 0.141 777 Planarity : 0.004 0.038 904 Dihedral : 5.213 54.852 714 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.62 % Favored : 98.22 % Rotamer: Outliers : 1.08 % Allowed : 17.51 % Favored : 81.41 % 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 aren not related in a simple way. whole: 1.94 (0.35), residues: 618 helix: 2.21 (0.29), residues: 337 sheet: 0.68 (1.07), residues: 25 loop : 0.17 (0.41), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I 279 TYR 0.025 0.002 TYR H 287 PHE 0.016 0.002 PHE I 30 TRP 0.009 0.001 TRP J 132 HIS 0.004 0.001 HIS J 131 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 5235) covalent geometry : angle 0.59278 ( 7085) hydrogen bonds : bond 0.04313 ( 279) hydrogen bonds : angle 4.47038 ( 765) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3096.24 seconds wall clock time: 53 minutes 35.44 seconds (3215.44 seconds total)