Starting phenix.real_space_refine on Sun Apr 27 09:31:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p76_17519/04_2025/8p76_17519.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p76_17519/04_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8p76_17519/04_2025/8p76_17519.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p76_17519/04_2025/8p76_17519.map" model { file = "/net/cci-nas-00/data/ceres_data/8p76_17519/04_2025/8p76_17519.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p76_17519/04_2025/8p76_17519.cif" } resolution = 2.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: 3.95, per 1000 atoms: 0.75 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: 1.38 Conformation dependent library (CDL) restraints added in 927.8 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: 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: 0.50 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: 1.29 Time building geometry restraints manager: 1.47 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: 3.040 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 15.810 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.910 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (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 TRP 0.011 0.001 TRP J 132 HIS 0.003 0.001 HIS J 131 PHE 0.019 0.002 PHE I 30 TYR 0.016 0.001 TYR I 60 ARG 0.009 0.001 ARG I 279 Details of bonding type rmsd hydrogen bonds : bond 0.12963 ( 279) hydrogen bonds : angle 5.55643 ( 765) covalent geometry : bond 0.00497 ( 5235) covalent geometry : angle 0.61456 ( 7085) *********************** 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 : 0.647 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 103 average time/residue: 1.5995 time to fit residues: 170.2626 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 : 0.608 ------------------------------------------------------------------------------- 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 52 optimal weight: 3.9990 chunk 46 optimal weight: 6.9990 chunk 26 optimal weight: 0.6980 chunk 16 optimal weight: 7.9990 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 48 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 29 optimal weight: 10.0000 chunk 36 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 249 GLN I 136 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 = 0.4030 r_free = 0.4030 target = 0.169027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.151394 restraints weight = 4813.226| |-----------------------------------------------------------------------------| r_work (start): 0.3815 rms_B_bonded: 0.87 r_work: 0.3724 rms_B_bonded: 1.37 restraints_weight: 0.5000 r_work: 0.3635 rms_B_bonded: 2.30 restraints_weight: 0.2500 r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.0627 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= 0.151 Angle : 0.590 6.964 7085 Z= 0.302 Chirality : 0.042 0.139 777 Planarity : 0.005 0.034 904 Dihedral : 6.449 82.183 720 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.78 % Favored : 98.06 % Rotamer: Outliers : 1.62 % Allowed : 14.44 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.35), residues: 618 helix: 1.93 (0.29), residues: 341 sheet: 2.29 (1.35), residues: 15 loop : 0.31 (0.40), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP J 132 HIS 0.006 0.001 HIS J 131 PHE 0.020 0.002 PHE I 30 TYR 0.017 0.002 TYR I 2 ARG 0.006 0.001 ARG I 23 Details of bonding type rmsd hydrogen bonds : bond 0.05278 ( 279) hydrogen bonds : angle 4.86900 ( 765) covalent geometry : bond 0.00332 ( 5235) covalent geometry : angle 0.58994 ( 7085) *********************** 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 110 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 101 time to evaluate : 0.612 Fit side-chains outliers start: 9 outliers final: 3 residues processed: 104 average time/residue: 1.5088 time to fit residues: 162.4102 Evaluate side-chains 98 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 95 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 46 VAL 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 28 optimal weight: 9.9990 chunk 30 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 25 optimal weight: 0.6980 chunk 49 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.4036 r_free = 0.4036 target = 0.169609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.151894 restraints weight = 4862.253| |-----------------------------------------------------------------------------| r_work (start): 0.3820 rms_B_bonded: 0.88 r_work: 0.3729 rms_B_bonded: 1.38 restraints_weight: 0.5000 r_work: 0.3639 rms_B_bonded: 2.34 restraints_weight: 0.2500 r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.0703 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= 0.135 Angle : 0.561 6.564 7085 Z= 0.287 Chirality : 0.041 0.139 777 Planarity : 0.004 0.036 904 Dihedral : 5.273 55.920 714 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.62 % Favored : 98.22 % Rotamer: Outliers : 0.90 % Allowed : 15.52 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.35), residues: 618 helix: 1.95 (0.28), residues: 343 sheet: 2.27 (1.40), residues: 15 loop : 0.22 (0.40), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 132 HIS 0.006 0.001 HIS J 131 PHE 0.018 0.002 PHE I 30 TYR 0.016 0.002 TYR I 91 ARG 0.005 0.001 ARG I 279 Details of bonding type rmsd hydrogen bonds : bond 0.04871 ( 279) hydrogen bonds : angle 4.70311 ( 765) covalent geometry : bond 0.00296 ( 5235) covalent geometry : angle 0.56108 ( 7085) *********************** 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 105 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 100 time to evaluate : 0.539 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 102 average time/residue: 1.5226 time to fit residues: 160.6152 Evaluate side-chains 95 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 91 time to evaluate : 0.595 ------------------------------------------------------------------------------- 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 54 optimal weight: 0.6980 chunk 45 optimal weight: 4.9990 chunk 28 optimal weight: 8.9990 chunk 29 optimal weight: 3.9990 chunk 48 optimal weight: 7.9990 chunk 21 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 35 optimal weight: 10.0000 chunk 0 optimal weight: 7.9990 chunk 25 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 249 GLN H 307 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** J 297 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.165892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.147967 restraints weight = 4946.911| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 0.88 r_work: 0.3681 rms_B_bonded: 1.39 restraints_weight: 0.5000 r_work: 0.3591 rms_B_bonded: 2.33 restraints_weight: 0.2500 r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.1022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 5235 Z= 0.286 Angle : 0.760 7.624 7085 Z= 0.389 Chirality : 0.048 0.153 777 Planarity : 0.006 0.043 904 Dihedral : 5.641 58.249 714 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.10 % Favored : 97.73 % Rotamer: Outliers : 2.17 % Allowed : 14.80 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.33), residues: 618 helix: 1.21 (0.28), residues: 347 sheet: 2.00 (1.30), residues: 15 loop : -0.03 (0.39), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP J 132 HIS 0.009 0.002 HIS J 131 PHE 0.024 0.003 PHE I 30 TYR 0.028 0.003 TYR I 2 ARG 0.015 0.001 ARG I 23 Details of bonding type rmsd hydrogen bonds : bond 0.06455 ( 279) hydrogen bonds : angle 5.14892 ( 765) covalent geometry : bond 0.00641 ( 5235) covalent geometry : angle 0.76038 ( 7085) *********************** 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 103 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 1.660 Fit side-chains REVERT: I 33 LYS cc_start: 0.7264 (ttpp) cc_final: 0.6829 (mptt) REVERT: I 63 ARG cc_start: 0.7559 (OUTLIER) cc_final: 0.7258 (mmm160) REVERT: J 227 GLU cc_start: 0.7385 (OUTLIER) cc_final: 0.6964 (tt0) outliers start: 12 outliers final: 5 residues processed: 95 average time/residue: 1.5700 time to fit residues: 154.8881 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 : 0.587 ------------------------------------------------------------------------------- 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 145 GLU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 57 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 60 optimal weight: 0.7980 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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 = 0.4030 r_free = 0.4030 target = 0.168783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.151049 restraints weight = 4836.987| |-----------------------------------------------------------------------------| r_work (start): 0.3799 rms_B_bonded: 0.87 r_work: 0.3706 rms_B_bonded: 1.38 restraints_weight: 0.5000 r_work: 0.3616 rms_B_bonded: 2.32 restraints_weight: 0.2500 r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.0888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 5235 Z= 0.174 Angle : 0.630 6.656 7085 Z= 0.322 Chirality : 0.043 0.141 777 Planarity : 0.005 0.039 904 Dihedral : 5.444 56.334 714 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.78 % Favored : 98.06 % Rotamer: Outliers : 1.81 % Allowed : 14.62 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.34), residues: 618 helix: 1.48 (0.28), residues: 347 sheet: 2.17 (1.37), residues: 15 loop : -0.18 (0.39), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP J 132 HIS 0.007 0.001 HIS J 131 PHE 0.021 0.002 PHE I 30 TYR 0.019 0.002 TYR I 2 ARG 0.008 0.001 ARG I 23 Details of bonding type rmsd hydrogen bonds : bond 0.05448 ( 279) hydrogen bonds : angle 4.86233 ( 765) covalent geometry : bond 0.00386 ( 5235) covalent geometry : angle 0.62951 ( 7085) *********************** 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 102 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 92 time to evaluate : 0.623 Fit side-chains REVERT: I 33 LYS cc_start: 0.7277 (ttpp) cc_final: 0.6811 (mptt) REVERT: I 63 ARG cc_start: 0.7506 (OUTLIER) cc_final: 0.7169 (mmm160) REVERT: J 227 GLU cc_start: 0.7360 (OUTLIER) cc_final: 0.6955 (tt0) outliers start: 10 outliers final: 6 residues processed: 97 average time/residue: 1.5263 time to fit residues: 153.1656 Evaluate side-chains 99 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 91 time to evaluate : 0.551 ------------------------------------------------------------------------------- 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 I residue 145 GLU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 14 optimal weight: 5.9990 chunk 24 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 35 optimal weight: 9.9990 chunk 42 optimal weight: 3.9990 chunk 44 optimal weight: 8.9990 chunk 18 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 39 optimal weight: 7.9990 chunk 38 optimal weight: 0.5980 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 = 0.4028 r_free = 0.4028 target = 0.168847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.150958 restraints weight = 4888.184| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 0.88 r_work: 0.3718 rms_B_bonded: 1.39 restraints_weight: 0.5000 r_work: 0.3628 rms_B_bonded: 2.35 restraints_weight: 0.2500 r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 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 0.029 5235 Z= 0.148 Angle : 0.600 7.766 7085 Z= 0.307 Chirality : 0.042 0.141 777 Planarity : 0.005 0.038 904 Dihedral : 5.345 55.838 714 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.10 % Favored : 97.73 % Rotamer: Outliers : 1.62 % Allowed : 15.16 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.34), residues: 618 helix: 1.80 (0.28), residues: 342 sheet: 2.24 (1.41), residues: 15 loop : 0.05 (0.39), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP J 132 HIS 0.006 0.001 HIS J 131 PHE 0.019 0.002 PHE I 30 TYR 0.017 0.002 TYR I 2 ARG 0.006 0.001 ARG I 279 Details of bonding type rmsd hydrogen bonds : bond 0.05043 ( 279) hydrogen bonds : angle 4.72508 ( 765) covalent geometry : bond 0.00329 ( 5235) covalent geometry : angle 0.60013 ( 7085) *********************** 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: 9 poor density : 95 time to evaluate : 0.587 Fit side-chains REVERT: I 33 LYS cc_start: 0.7266 (ttpp) cc_final: 0.6805 (mptt) REVERT: J 227 GLU cc_start: 0.7363 (OUTLIER) cc_final: 0.6962 (tt0) outliers start: 9 outliers final: 4 residues processed: 101 average time/residue: 1.5561 time to fit residues: 162.6017 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 : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 7 optimal weight: 0.6980 chunk 35 optimal weight: 10.0000 chunk 29 optimal weight: 0.9980 chunk 54 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 56 optimal weight: 0.5980 chunk 60 optimal weight: 4.9990 chunk 44 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- 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 = 0.168922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.151204 restraints weight = 4808.690| |-----------------------------------------------------------------------------| r_work (start): 0.3812 rms_B_bonded: 0.87 r_work: 0.3720 rms_B_bonded: 1.37 restraints_weight: 0.5000 r_work: 0.3630 rms_B_bonded: 2.32 restraints_weight: 0.2500 r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.0824 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= 0.149 Angle : 0.606 8.067 7085 Z= 0.309 Chirality : 0.042 0.141 777 Planarity : 0.005 0.037 904 Dihedral : 5.323 55.956 714 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.10 % Favored : 97.73 % Rotamer: Outliers : 1.26 % Allowed : 15.88 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.34), residues: 618 helix: 1.83 (0.28), residues: 343 sheet: 2.27 (1.41), residues: 15 loop : 0.04 (0.40), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP J 132 HIS 0.006 0.001 HIS J 131 PHE 0.018 0.002 PHE I 30 TYR 0.017 0.002 TYR I 2 ARG 0.006 0.001 ARG I 279 Details of bonding type rmsd hydrogen bonds : bond 0.05009 ( 279) hydrogen bonds : angle 4.70003 ( 765) covalent geometry : bond 0.00331 ( 5235) covalent geometry : angle 0.60572 ( 7085) *********************** 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 102 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 95 time to evaluate : 0.564 Fit side-chains REVERT: I 33 LYS cc_start: 0.7251 (ttpp) cc_final: 0.6792 (mptt) REVERT: J 227 GLU cc_start: 0.7363 (OUTLIER) cc_final: 0.6955 (tt0) outliers start: 7 outliers final: 5 residues processed: 99 average time/residue: 1.5461 time to fit residues: 158.3417 Evaluate side-chains 100 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 94 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 26 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 30 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 41 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 35 optimal weight: 6.9990 chunk 25 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.170450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.152771 restraints weight = 4825.299| |-----------------------------------------------------------------------------| r_work (start): 0.3830 rms_B_bonded: 0.87 r_work: 0.3739 rms_B_bonded: 1.38 restraints_weight: 0.5000 r_work: 0.3649 rms_B_bonded: 2.33 restraints_weight: 0.2500 r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.0849 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= 0.125 Angle : 0.571 8.299 7085 Z= 0.291 Chirality : 0.041 0.141 777 Planarity : 0.004 0.035 904 Dihedral : 5.248 55.208 714 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.94 % Favored : 97.90 % Rotamer: Outliers : 1.62 % Allowed : 15.34 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.35), residues: 618 helix: 2.03 (0.28), residues: 343 sheet: 1.79 (1.42), residues: 16 loop : 0.08 (0.40), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 132 HIS 0.005 0.001 HIS J 131 PHE 0.016 0.002 PHE I 30 TYR 0.016 0.002 TYR J 169 ARG 0.007 0.001 ARG I 279 Details of bonding type rmsd hydrogen bonds : bond 0.04551 ( 279) hydrogen bonds : angle 4.56085 ( 765) covalent geometry : bond 0.00274 ( 5235) covalent geometry : angle 0.57100 ( 7085) *********************** 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 103 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 94 time to evaluate : 0.628 Fit side-chains REVERT: I 33 LYS cc_start: 0.7236 (ttpp) cc_final: 0.6775 (mptt) REVERT: J 227 GLU cc_start: 0.7335 (OUTLIER) cc_final: 0.6933 (tt0) outliers start: 9 outliers final: 4 residues processed: 98 average time/residue: 1.7036 time to fit residues: 173.3158 Evaluate side-chains 94 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 89 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 0 optimal weight: 7.9990 chunk 31 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 53 optimal weight: 5.9990 chunk 10 optimal weight: 0.8980 chunk 35 optimal weight: 8.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.169500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.151724 restraints weight = 4824.340| |-----------------------------------------------------------------------------| r_work (start): 0.3818 rms_B_bonded: 0.87 r_work: 0.3727 rms_B_bonded: 1.38 restraints_weight: 0.5000 r_work: 0.3637 rms_B_bonded: 2.33 restraints_weight: 0.2500 r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.0882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5235 Z= 0.148 Angle : 0.620 8.532 7085 Z= 0.314 Chirality : 0.042 0.142 777 Planarity : 0.005 0.034 904 Dihedral : 5.304 56.006 714 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.27 % Favored : 97.57 % Rotamer: Outliers : 1.44 % Allowed : 16.61 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.35), residues: 618 helix: 1.92 (0.28), residues: 343 sheet: 0.60 (1.08), residues: 26 loop : 0.07 (0.41), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 132 HIS 0.006 0.001 HIS J 131 PHE 0.027 0.002 PHE I 125 TYR 0.017 0.002 TYR I 2 ARG 0.007 0.001 ARG I 279 Details of bonding type rmsd hydrogen bonds : bond 0.04908 ( 279) hydrogen bonds : angle 4.65782 ( 765) covalent geometry : bond 0.00331 ( 5235) covalent geometry : angle 0.61977 ( 7085) *********************** 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 101 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 93 time to evaluate : 0.560 Fit side-chains REVERT: I 33 LYS cc_start: 0.7261 (ttpp) cc_final: 0.6793 (mptt) REVERT: J 227 GLU cc_start: 0.7352 (OUTLIER) cc_final: 0.6949 (tt0) outliers start: 8 outliers final: 5 residues processed: 98 average time/residue: 1.6380 time to fit residues: 166.0663 Evaluate side-chains 95 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 89 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 41 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 56 optimal weight: 4.9990 chunk 36 optimal weight: 8.9990 chunk 59 optimal weight: 0.1980 chunk 28 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- 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 = 0.4021 r_free = 0.4021 target = 0.168176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.150309 restraints weight = 4886.542| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 0.88 r_work: 0.3710 rms_B_bonded: 1.38 restraints_weight: 0.5000 r_work: 0.3620 rms_B_bonded: 2.33 restraints_weight: 0.2500 r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.0951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5235 Z= 0.187 Angle : 0.685 10.453 7085 Z= 0.346 Chirality : 0.044 0.156 777 Planarity : 0.005 0.034 904 Dihedral : 5.433 56.773 714 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.27 % Favored : 97.57 % Rotamer: Outliers : 1.08 % Allowed : 16.61 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.34), residues: 618 helix: 1.73 (0.28), residues: 342 sheet: 0.43 (1.05), residues: 26 loop : -0.02 (0.41), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP J 132 HIS 0.008 0.002 HIS J 131 PHE 0.027 0.002 PHE I 125 TYR 0.024 0.002 TYR H 287 ARG 0.009 0.001 ARG I 23 Details of bonding type rmsd hydrogen bonds : bond 0.05413 ( 279) hydrogen bonds : angle 4.82786 ( 765) covalent geometry : bond 0.00422 ( 5235) covalent geometry : angle 0.68478 ( 7085) ********************** 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: 6 poor density : 92 time to evaluate : 0.633 Fit side-chains REVERT: I 33 LYS cc_start: 0.7250 (ttpp) cc_final: 0.6781 (mptt) REVERT: J 227 GLU cc_start: 0.7364 (OUTLIER) cc_final: 0.6959 (tt0) outliers start: 6 outliers final: 5 residues processed: 95 average time/residue: 1.5878 time to fit residues: 155.9882 Evaluate side-chains 96 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 90 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 15 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 61 optimal weight: 0.0970 chunk 3 optimal weight: 3.9990 chunk 44 optimal weight: 8.9990 chunk 51 optimal weight: 7.9990 chunk 35 optimal weight: 9.9990 chunk 54 optimal weight: 4.9990 chunk 22 optimal weight: 0.5980 chunk 47 optimal weight: 0.5980 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.169701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.151757 restraints weight = 4886.749| |-----------------------------------------------------------------------------| r_work (start): 0.3819 rms_B_bonded: 0.88 r_work: 0.3729 rms_B_bonded: 1.39 restraints_weight: 0.5000 r_work: 0.3639 rms_B_bonded: 2.35 restraints_weight: 0.2500 r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.0910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5235 Z= 0.146 Angle : 0.640 10.034 7085 Z= 0.325 Chirality : 0.042 0.162 777 Planarity : 0.005 0.036 904 Dihedral : 5.353 55.740 714 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.94 % Favored : 97.90 % Rotamer: Outliers : 1.08 % Allowed : 16.61 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.34), residues: 618 helix: 1.96 (0.28), residues: 337 sheet: 0.67 (1.08), residues: 25 loop : 0.12 (0.41), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 132 HIS 0.006 0.001 HIS J 131 PHE 0.025 0.002 PHE I 125 TYR 0.024 0.002 TYR H 287 ARG 0.009 0.001 ARG I 279 Details of bonding type rmsd hydrogen bonds : bond 0.04844 ( 279) hydrogen bonds : angle 4.67859 ( 765) covalent geometry : bond 0.00328 ( 5235) covalent geometry : angle 0.63987 ( 7085) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5751.19 seconds wall clock time: 98 minutes 38.89 seconds (5918.89 seconds total)