Starting phenix.real_space_refine on Sun Dec 29 11:42:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8s0t_19628/12_2024/8s0t_19628_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8s0t_19628/12_2024/8s0t_19628.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8s0t_19628/12_2024/8s0t_19628.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8s0t_19628/12_2024/8s0t_19628.map" model { file = "/net/cci-nas-00/data/ceres_data/8s0t_19628/12_2024/8s0t_19628_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8s0t_19628/12_2024/8s0t_19628_neut_trim.cif" } resolution = 2.3 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= 0.004 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: 7 Type Number sf(0) Gaussians P 1 5.49 5 S 31 5.16 5 C 3297 2.51 5 N 870 2.21 5 O 1059 1.98 5 F 3 1.80 5 H 5404 0.53 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-5532/modules/chem_data/mon_lib" Total number of atoms: 10665 Number of models: 1 Model: "" Number of chains: 7 Chain: "H" Number of atoms: 998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 998 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 5, 'TRANS': 59} Chain: "I" Number of atoms: 4515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 4515 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 13, 'TRANS': 260} Chain breaks: 1 Chain: "J" Number of atoms: 4683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 4683 Classifications: {'peptide': 291} Link IDs: {'PTRANS': 17, 'TRANS': 273} Chain breaks: 2 Chain: "J" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'YNK': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 63 Classifications: {'water': 21} Link IDs: {None: 20} Chain: "I" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 162 Classifications: {'water': 54} Link IDs: {None: 53} Chain: "J" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 210 Classifications: {'water': 70} Link IDs: {None: 69} Time building chain proxies: 4.94, per 1000 atoms: 0.46 Number of scatterers: 10665 At special positions: 0 Unit cell: (85.635, 93.42, 72.66, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 31 16.00 P 1 15.00 F 3 9.00 O 1059 8.00 N 870 7.00 C 3297 6.00 H 5404 1.00 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: 3.24 Conformation dependent library (CDL) restraints added in 710.6 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: 1198 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 3 sheets defined 61.3% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'H' and resid 264 through 269 removed outlier: 4.553A pdb=" N ARG H 268 " --> pdb=" O GLU H 264 " (cutoff:3.500A) Processing helix chain 'H' and resid 270 through 275 removed outlier: 3.601A pdb=" N ASN H 273 " --> pdb=" O GLY H 270 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL H 275 " --> pdb=" O LEU H 272 " (cutoff:3.500A) Processing helix chain 'H' and resid 279 through 285 Processing helix chain 'H' and resid 288 through 302 removed outlier: 3.942A 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 12 removed outlier: 4.076A pdb=" N THR I 12 " --> pdb=" O LYS I 8 " (cutoff:3.500A) Processing helix chain 'I' and resid 15 through 36 Processing helix chain 'I' and resid 49 through 71 Processing helix chain 'I' and resid 76 through 91 removed outlier: 3.542A pdb=" N TYR I 91 " --> pdb=" O PHE I 87 " (cutoff:3.500A) Processing helix chain 'I' and resid 100 through 116 removed outlier: 3.841A pdb=" N LEU I 106 " --> pdb=" O ARG I 102 " (cutoff:3.500A) Processing helix chain 'I' and resid 121 through 127 Processing helix chain 'I' and resid 132 through 154 removed outlier: 4.913A pdb=" N LEU I 148 " --> pdb=" O LEU I 144 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N LEU I 149 " --> pdb=" O GLU I 145 " (cutoff:3.500A) Processing helix chain 'I' and resid 163 through 178 Processing helix chain 'I' and resid 183 through 186 Processing helix chain 'I' and resid 187 through 201 removed outlier: 3.575A pdb=" N LEU I 200 " --> pdb=" O ASN I 196 " (cutoff:3.500A) removed outlier: 3.668A 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: 3.601A pdb=" N LEU I 232 " --> pdb=" O MET I 228 " (cutoff:3.500A) Processing helix chain 'I' and resid 241 through 262 Processing helix chain 'I' and resid 266 through 283 removed outlier: 3.769A pdb=" N VAL I 272 " --> pdb=" O GLU I 268 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 67 Processing helix chain 'J' and resid 98 through 104 Processing helix chain 'J' and resid 110 through 131 Processing helix chain 'J' and resid 139 through 141 No H-bonds generated for 'chain 'J' and resid 139 through 141' Processing helix chain 'J' and resid 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 291 Processing helix chain 'J' and resid 292 through 297 removed outlier: 3.871A 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 12 through 20 removed outlier: 6.664A pdb=" N LYS J 28 " --> pdb=" O LEU J 15 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N PHE J 17 " --> pdb=" O VAL J 26 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N VAL J 26 " --> pdb=" O PHE J 17 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N GLY J 19 " --> pdb=" O ALA J 24 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N ALA J 24 " --> pdb=" O GLY J 19 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ILE J 87 " --> pdb=" O ILE J 43 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ASP J 92 " --> pdb=" O LEU J 77 " (cutoff:3.500A) removed outlier: 7.878A 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 134 270 hydrogen bonds defined for protein. 768 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: 4.11 Time building geometry restraints manager: 3.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.96 - 1.13: 5391 1.13 - 1.30: 822 1.30 - 1.48: 2133 1.48 - 1.65: 2244 1.65 - 1.82: 52 Bond restraints: 10642 Sorted by residual: bond pdb=" O HOH J 525 " pdb=" H1 HOH J 525 " ideal model delta sigma weight residual 0.850 1.027 -0.177 2.00e-02 2.50e+03 7.83e+01 bond pdb=" O HOH J 559 " pdb=" H2 HOH J 559 " ideal model delta sigma weight residual 0.850 1.027 -0.177 2.00e-02 2.50e+03 7.82e+01 bond pdb=" O HOH J 556 " pdb=" H1 HOH J 556 " ideal model delta sigma weight residual 0.850 1.026 -0.176 2.00e-02 2.50e+03 7.75e+01 bond pdb=" O HOH I 412 " pdb=" H2 HOH I 412 " ideal model delta sigma weight residual 0.850 1.026 -0.176 2.00e-02 2.50e+03 7.71e+01 bond pdb=" O HOH H 419 " pdb=" H2 HOH H 419 " ideal model delta sigma weight residual 0.850 1.025 -0.175 2.00e-02 2.50e+03 7.67e+01 ... (remaining 10637 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.75: 14097 2.75 - 5.50: 4247 5.50 - 8.26: 498 8.26 - 11.01: 19 11.01 - 13.76: 13 Bond angle restraints: 18874 Sorted by residual: angle pdb=" CA ASP J 146 " pdb=" CB ASP J 146 " pdb=" CG ASP J 146 " ideal model delta sigma weight residual 112.60 122.82 -10.22 1.00e+00 1.00e+00 1.04e+02 angle pdb=" CA ASP I 192 " pdb=" CB ASP I 192 " pdb=" CG ASP I 192 " ideal model delta sigma weight residual 112.60 121.31 -8.71 1.00e+00 1.00e+00 7.59e+01 angle pdb=" CA ASP I 25 " pdb=" CB ASP I 25 " pdb=" CG ASP I 25 " ideal model delta sigma weight residual 112.60 120.87 -8.27 1.00e+00 1.00e+00 6.85e+01 angle pdb=" CA ASP J 97 " pdb=" CB ASP J 97 " pdb=" CG ASP J 97 " ideal model delta sigma weight residual 112.60 119.97 -7.37 1.00e+00 1.00e+00 5.44e+01 angle pdb=" N LYS J 139 " pdb=" CA LYS J 139 " pdb=" C LYS J 139 " ideal model delta sigma weight residual 108.13 101.81 6.32 9.00e-01 1.23e+00 4.93e+01 ... (remaining 18869 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.89: 4345 20.89 - 41.77: 363 41.77 - 62.66: 161 62.66 - 83.54: 13 83.54 - 104.43: 7 Dihedral angle restraints: 4889 sinusoidal: 2679 harmonic: 2210 Sorted by residual: dihedral pdb=" CA THR J 175 " pdb=" C THR J 175 " pdb=" N ARG J 176 " pdb=" CA ARG J 176 " ideal model delta harmonic sigma weight residual -180.00 -151.77 -28.23 0 5.00e+00 4.00e-02 3.19e+01 dihedral pdb=" CA LYS I 72 " pdb=" C LYS I 72 " pdb=" N PRO I 73 " pdb=" CA PRO I 73 " ideal model delta harmonic sigma weight residual 180.00 153.36 26.64 0 5.00e+00 4.00e-02 2.84e+01 dihedral pdb=" CA ASN J 297 " pdb=" C ASN J 297 " pdb=" N ARG J 298 " pdb=" CA ARG J 298 " ideal model delta harmonic sigma weight residual -180.00 -154.73 -25.27 0 5.00e+00 4.00e-02 2.55e+01 ... (remaining 4886 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 383 0.093 - 0.186: 245 0.186 - 0.279: 111 0.279 - 0.372: 32 0.372 - 0.466: 8 Chirality restraints: 779 Sorted by residual: chirality pdb=" CG LEU J 125 " pdb=" CB LEU J 125 " pdb=" CD1 LEU J 125 " pdb=" CD2 LEU J 125 " both_signs ideal model delta sigma weight residual False -2.59 -2.12 -0.47 2.00e-01 2.50e+01 5.42e+00 chirality pdb=" CG LEU I 65 " pdb=" CB LEU I 65 " pdb=" CD1 LEU I 65 " pdb=" CD2 LEU I 65 " both_signs ideal model delta sigma weight residual False -2.59 -2.15 -0.44 2.00e-01 2.50e+01 4.89e+00 chirality pdb=" CA PRO J 238 " pdb=" N PRO J 238 " pdb=" C PRO J 238 " pdb=" CB PRO J 238 " both_signs ideal model delta sigma weight residual False 2.72 2.28 0.44 2.00e-01 2.50e+01 4.80e+00 ... (remaining 776 not shown) Planarity restraints: 1489 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C14 YNK J 401 " 0.070 2.00e-02 2.50e+03 1.46e-01 6.92e+02 pdb=" C16 YNK J 401 " 0.028 2.00e-02 2.50e+03 pdb=" C17 YNK J 401 " 0.198 2.00e-02 2.50e+03 pdb=" C19 YNK J 401 " -0.007 2.00e-02 2.50e+03 pdb=" C20 YNK J 401 " -0.092 2.00e-02 2.50e+03 pdb=" C21 YNK J 401 " -0.066 2.00e-02 2.50e+03 pdb=" C22 YNK J 401 " 0.125 2.00e-02 2.50e+03 pdb=" C24 YNK J 401 " -0.148 2.00e-02 2.50e+03 pdb=" C25 YNK J 401 " -0.166 2.00e-02 2.50e+03 pdb=" C26 YNK J 401 " -0.063 2.00e-02 2.50e+03 pdb=" N18 YNK J 401 " 0.092 2.00e-02 2.50e+03 pdb=" N23 YNK J 401 " 0.281 2.00e-02 2.50e+03 pdb=" P27 YNK J 401 " -0.251 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS I 157 " -0.137 2.00e-02 2.50e+03 9.99e-02 2.24e+02 pdb=" CG HIS I 157 " -0.039 2.00e-02 2.50e+03 pdb=" ND1 HIS I 157 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 HIS I 157 " 0.039 2.00e-02 2.50e+03 pdb=" CE1 HIS I 157 " -0.081 2.00e-02 2.50e+03 pdb=" NE2 HIS I 157 " -0.005 2.00e-02 2.50e+03 pdb=" HD1 HIS I 157 " 0.210 2.00e-02 2.50e+03 pdb=" HD2 HIS I 157 " 0.104 2.00e-02 2.50e+03 pdb=" HE1 HIS I 157 " -0.078 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP J 177 " 0.171 2.00e-02 2.50e+03 7.12e-02 2.03e+02 pdb=" CG TRP J 177 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP J 177 " -0.045 2.00e-02 2.50e+03 pdb=" CD2 TRP J 177 " 0.010 2.00e-02 2.50e+03 pdb=" NE1 TRP J 177 " -0.055 2.00e-02 2.50e+03 pdb=" CE2 TRP J 177 " 0.016 2.00e-02 2.50e+03 pdb=" CE3 TRP J 177 " -0.029 2.00e-02 2.50e+03 pdb=" CZ2 TRP J 177 " 0.064 2.00e-02 2.50e+03 pdb=" CZ3 TRP J 177 " -0.055 2.00e-02 2.50e+03 pdb=" CH2 TRP J 177 " 0.039 2.00e-02 2.50e+03 pdb=" HD1 TRP J 177 " -0.052 2.00e-02 2.50e+03 pdb=" HE1 TRP J 177 " -0.095 2.00e-02 2.50e+03 pdb=" HE3 TRP J 177 " -0.044 2.00e-02 2.50e+03 pdb=" HZ2 TRP J 177 " 0.090 2.00e-02 2.50e+03 pdb=" HZ3 TRP J 177 " -0.105 2.00e-02 2.50e+03 pdb=" HH2 TRP J 177 " 0.053 2.00e-02 2.50e+03 ... (remaining 1486 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.15: 766 2.15 - 2.76: 18737 2.76 - 3.38: 35556 3.38 - 3.99: 47565 3.99 - 4.60: 68701 Nonbonded interactions: 171325 Sorted by model distance: nonbonded pdb=" O GLY H 285 " pdb=" H2 HOH H 401 " model vdw 1.538 2.450 nonbonded pdb=" O PHE J 295 " pdb=" H2 HOH J 501 " model vdw 1.567 2.450 nonbonded pdb=" HE1 TRP I 11 " pdb=" HD1 HIS I 157 " model vdw 1.594 2.100 nonbonded pdb=" O VAL J 194 " pdb=" H2 HOH J 503 " model vdw 1.598 2.450 nonbonded pdb=" H1 HOH J 525 " pdb=" O HOH J 568 " model vdw 1.603 2.450 ... (remaining 171320 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.480 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: 0.190 Extract box with map and model: 0.370 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 25.800 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 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 : 0.013 0.077 5238 Z= 0.848 Angle : 2.144 10.215 7093 Z= 1.481 Chirality : 0.144 0.466 779 Planarity : 0.018 0.146 900 Dihedral : 16.207 104.429 1983 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.65 % Allowed : 3.56 % Favored : 95.79 % Rotamer: Outliers : 3.24 % Allowed : 7.55 % Favored : 89.21 % Cbeta Deviations : 0.67 % Peptide Plane: Cis-proline : 0.00 % 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: -2.68 (0.29), residues: 618 helix: -1.90 (0.22), residues: 346 sheet: -0.73 (1.03), residues: 27 loop : -1.45 (0.37), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.103 0.029 TRP J 177 HIS 0.039 0.010 HIS I 157 PHE 0.110 0.025 PHE I 47 TYR 0.138 0.031 TYR I 2 ARG 0.009 0.002 ARG J 309 *********************** 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 113 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 95 time to evaluate : 0.851 Fit side-chains revert: symmetry clash REVERT: H 276 ARG cc_start: 0.5779 (ttp80) cc_final: 0.4970 (pmt170) REVERT: I 65 LEU cc_start: 0.7707 (OUTLIER) cc_final: 0.7443 (mm) REVERT: I 131 GLU cc_start: 0.4709 (OUTLIER) cc_final: 0.4299 (mt-10) REVERT: I 279 ARG cc_start: 0.6363 (ttm110) cc_final: 0.5807 (ttt180) outliers start: 18 outliers final: 5 residues processed: 106 average time/residue: 2.5632 time to fit residues: 284.5763 Evaluate side-chains 81 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 74 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 49 GLU Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain I residue 131 GLU Chi-restraints excluded: chain J residue 95 GLU Chi-restraints excluded: chain J residue 164 SER Chi-restraints excluded: chain J residue 248 THR Chi-restraints excluded: chain J residue 277 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 249 GLN I 124 GLN J 22 GLN J 86 ASN ** J 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 5238 Z= 0.241 Angle : 0.704 6.192 7093 Z= 0.374 Chirality : 0.043 0.171 779 Planarity : 0.005 0.046 900 Dihedral : 9.618 84.198 731 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.10 % Favored : 97.73 % Rotamer: Outliers : 1.98 % Allowed : 10.07 % Favored : 87.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.21 (0.30), residues: 618 helix: -0.22 (0.25), residues: 349 sheet: -1.59 (1.14), residues: 19 loop : -1.47 (0.35), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP J 132 HIS 0.009 0.002 HIS J 131 PHE 0.022 0.002 PHE I 30 TYR 0.015 0.002 TYR J 178 ARG 0.004 0.001 ARG I 28 *********************** 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 94 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 0.840 Fit side-chains revert: symmetry clash REVERT: H 276 ARG cc_start: 0.5616 (ttp80) cc_final: 0.4903 (pmt170) REVERT: I 250 ASP cc_start: 0.5452 (OUTLIER) cc_final: 0.4996 (m-30) REVERT: J 172 GLN cc_start: 0.5423 (tp40) cc_final: 0.5191 (mp-120) outliers start: 11 outliers final: 6 residues processed: 90 average time/residue: 2.7541 time to fit residues: 258.6861 Evaluate side-chains 84 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 77 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain I residue 250 ASP Chi-restraints excluded: chain I residue 272 VAL Chi-restraints excluded: chain J residue 88 SER Chi-restraints excluded: chain J residue 95 GLU Chi-restraints excluded: chain J residue 164 SER Chi-restraints excluded: chain J residue 277 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 31 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 56 optimal weight: 0.0970 chunk 60 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 130 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5238 Z= 0.206 Angle : 0.602 4.969 7093 Z= 0.315 Chirality : 0.040 0.144 779 Planarity : 0.005 0.047 900 Dihedral : 8.197 81.683 724 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.10 % Favored : 97.73 % Rotamer: Outliers : 1.62 % Allowed : 11.51 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.42 (0.32), residues: 618 helix: 0.51 (0.27), residues: 350 sheet: -1.64 (1.14), residues: 19 loop : -1.23 (0.36), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP J 132 HIS 0.007 0.001 HIS J 131 PHE 0.015 0.002 PHE I 30 TYR 0.016 0.002 TYR J 178 ARG 0.008 0.001 ARG I 279 *********************** 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 93 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 84 time to evaluate : 0.832 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 276 ARG cc_start: 0.5694 (ttp80) cc_final: 0.4931 (pmt170) REVERT: I 65 LEU cc_start: 0.7569 (OUTLIER) cc_final: 0.7318 (mm) REVERT: I 202 ASP cc_start: 0.6881 (m-30) cc_final: 0.6453 (m-30) REVERT: I 279 ARG cc_start: 0.6855 (mtm110) cc_final: 0.5506 (ptt-90) REVERT: J 96 THR cc_start: 0.7483 (p) cc_final: 0.7200 (t) outliers start: 9 outliers final: 4 residues processed: 89 average time/residue: 2.8247 time to fit residues: 262.5121 Evaluate side-chains 82 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 77 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain J residue 88 SER Chi-restraints excluded: chain J residue 95 GLU Chi-restraints excluded: chain J residue 164 SER Chi-restraints excluded: chain J residue 277 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 55 optimal weight: 5.9990 chunk 42 optimal weight: 6.9990 chunk 29 optimal weight: 6.9990 chunk 6 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 49 optimal weight: 0.5980 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 36 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5238 Z= 0.247 Angle : 0.590 5.828 7093 Z= 0.308 Chirality : 0.040 0.142 779 Planarity : 0.005 0.063 900 Dihedral : 8.015 79.345 724 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.27 % Favored : 97.57 % Rotamer: Outliers : 2.16 % Allowed : 11.69 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.26 (0.32), residues: 618 helix: 0.65 (0.27), residues: 350 sheet: -1.72 (1.14), residues: 19 loop : -1.19 (0.36), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP J 132 HIS 0.007 0.001 HIS J 131 PHE 0.014 0.002 PHE I 30 TYR 0.014 0.002 TYR H 248 ARG 0.009 0.001 ARG I 28 *********************** 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 95 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 83 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 276 ARG cc_start: 0.5674 (ttp80) cc_final: 0.4920 (pmt170) REVERT: I 49 GLU cc_start: 0.6170 (OUTLIER) cc_final: 0.5844 (mt-10) REVERT: I 202 ASP cc_start: 0.6932 (m-30) cc_final: 0.6559 (m-30) outliers start: 12 outliers final: 5 residues processed: 89 average time/residue: 2.8916 time to fit residues: 268.2437 Evaluate side-chains 87 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 81 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 49 GLU Chi-restraints excluded: chain J residue 88 SER Chi-restraints excluded: chain J residue 95 GLU Chi-restraints excluded: chain J residue 248 THR Chi-restraints excluded: chain J residue 262 SER Chi-restraints excluded: chain J residue 277 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 34 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 130 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5238 Z= 0.268 Angle : 0.604 4.940 7093 Z= 0.313 Chirality : 0.040 0.143 779 Planarity : 0.005 0.047 900 Dihedral : 7.852 78.177 721 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.75 % Favored : 97.09 % Rotamer: Outliers : 1.80 % Allowed : 12.41 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.23 (0.32), residues: 618 helix: 0.70 (0.27), residues: 350 sheet: -1.77 (1.13), residues: 19 loop : -1.20 (0.36), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP J 132 HIS 0.007 0.001 HIS J 131 PHE 0.014 0.002 PHE I 125 TYR 0.015 0.002 TYR J 178 ARG 0.009 0.001 ARG I 279 *********************** 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 90 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 80 time to evaluate : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 276 ARG cc_start: 0.5650 (ttp80) cc_final: 0.4904 (pmt170) REVERT: I 49 GLU cc_start: 0.6186 (OUTLIER) cc_final: 0.5909 (mt-10) REVERT: I 202 ASP cc_start: 0.7022 (m-30) cc_final: 0.6674 (m-30) REVERT: I 279 ARG cc_start: 0.6786 (mtm110) cc_final: 0.5525 (ptt-90) outliers start: 10 outliers final: 6 residues processed: 85 average time/residue: 2.9091 time to fit residues: 258.7024 Evaluate side-chains 86 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 79 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 49 GLU Chi-restraints excluded: chain J residue 88 SER Chi-restraints excluded: chain J residue 95 GLU Chi-restraints excluded: chain J residue 189 MET Chi-restraints excluded: chain J residue 248 THR Chi-restraints excluded: chain J residue 262 SER Chi-restraints excluded: chain J residue 277 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 35 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 27 optimal weight: 8.9990 chunk 4 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 chunk 57 optimal weight: 6.9990 chunk 6 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 22 GLN J 130 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 5238 Z= 0.278 Angle : 0.608 4.777 7093 Z= 0.316 Chirality : 0.040 0.144 779 Planarity : 0.005 0.038 900 Dihedral : 7.810 77.108 721 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.75 % Favored : 97.09 % Rotamer: Outliers : 1.98 % Allowed : 12.23 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.27 (0.32), residues: 618 helix: 0.66 (0.27), residues: 350 sheet: -1.82 (1.10), residues: 19 loop : -1.20 (0.36), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP J 132 HIS 0.007 0.001 HIS J 131 PHE 0.017 0.002 PHE I 125 TYR 0.015 0.002 TYR J 178 ARG 0.005 0.001 ARG I 279 *********************** 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 93 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 82 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 49 GLU cc_start: 0.6205 (OUTLIER) cc_final: 0.5931 (mt-10) outliers start: 11 outliers final: 8 residues processed: 88 average time/residue: 2.8640 time to fit residues: 262.8139 Evaluate side-chains 88 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 79 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 49 GLU Chi-restraints excluded: chain I residue 105 MET Chi-restraints excluded: chain J residue 88 SER Chi-restraints excluded: chain J residue 95 GLU Chi-restraints excluded: chain J residue 189 MET Chi-restraints excluded: chain J residue 216 ASP Chi-restraints excluded: chain J residue 248 THR Chi-restraints excluded: chain J residue 262 SER Chi-restraints excluded: chain J residue 277 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 43 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 27 optimal weight: 8.9990 chunk 23 optimal weight: 0.1980 chunk 35 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 overall best weight: 1.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 22 GLN ** J 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5238 Z= 0.241 Angle : 0.585 4.851 7093 Z= 0.303 Chirality : 0.040 0.139 779 Planarity : 0.005 0.058 900 Dihedral : 7.712 75.863 721 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.59 % Favored : 97.25 % Rotamer: Outliers : 1.80 % Allowed : 13.31 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.07 (0.32), residues: 618 helix: 0.82 (0.27), residues: 350 sheet: -1.84 (1.10), residues: 19 loop : -1.11 (0.36), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP J 132 HIS 0.007 0.001 HIS J 131 PHE 0.017 0.002 PHE I 125 TYR 0.014 0.002 TYR J 178 ARG 0.010 0.001 ARG I 279 *********************** 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 90 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 80 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 276 ARG cc_start: 0.5710 (tmm160) cc_final: 0.4855 (pmt170) REVERT: I 49 GLU cc_start: 0.6177 (OUTLIER) cc_final: 0.5890 (mt-10) REVERT: I 202 ASP cc_start: 0.7150 (m-30) cc_final: 0.6876 (m-30) REVERT: I 279 ARG cc_start: 0.6749 (mtm110) cc_final: 0.5535 (ptt-90) outliers start: 10 outliers final: 8 residues processed: 86 average time/residue: 3.0026 time to fit residues: 269.6358 Evaluate side-chains 86 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 77 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 49 GLU Chi-restraints excluded: chain I residue 105 MET Chi-restraints excluded: chain J residue 88 SER Chi-restraints excluded: chain J residue 95 GLU Chi-restraints excluded: chain J residue 189 MET Chi-restraints excluded: chain J residue 216 ASP Chi-restraints excluded: chain J residue 248 THR Chi-restraints excluded: chain J residue 262 SER Chi-restraints excluded: chain J residue 277 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 11 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 54 optimal weight: 0.3980 chunk 57 optimal weight: 5.9990 chunk 52 optimal weight: 0.9990 chunk 55 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 22 GLN ** J 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 0.3127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5238 Z= 0.213 Angle : 0.565 4.793 7093 Z= 0.292 Chirality : 0.039 0.141 779 Planarity : 0.005 0.046 900 Dihedral : 7.618 74.963 721 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.27 % Favored : 97.57 % Rotamer: Outliers : 1.62 % Allowed : 14.21 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.08 (0.33), residues: 618 helix: 0.88 (0.27), residues: 356 sheet: -1.87 (1.10), residues: 19 loop : -0.96 (0.37), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP J 132 HIS 0.005 0.001 HIS J 131 PHE 0.016 0.002 PHE I 110 TYR 0.013 0.001 TYR J 178 ARG 0.009 0.001 ARG I 279 *********************** 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 88 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 79 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 276 ARG cc_start: 0.5693 (tmm160) cc_final: 0.4849 (pmt170) REVERT: I 49 GLU cc_start: 0.6137 (OUTLIER) cc_final: 0.5850 (mt-10) REVERT: I 202 ASP cc_start: 0.7184 (m-30) cc_final: 0.6909 (m-30) REVERT: I 260 LYS cc_start: 0.6727 (ttmp) cc_final: 0.6236 (tttp) REVERT: I 279 ARG cc_start: 0.6743 (mtm110) cc_final: 0.5519 (ptt-90) outliers start: 9 outliers final: 7 residues processed: 84 average time/residue: 2.7141 time to fit residues: 238.0101 Evaluate side-chains 85 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 77 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 49 GLU Chi-restraints excluded: chain J residue 88 SER Chi-restraints excluded: chain J residue 95 GLU Chi-restraints excluded: chain J residue 189 MET Chi-restraints excluded: chain J residue 216 ASP Chi-restraints excluded: chain J residue 248 THR Chi-restraints excluded: chain J residue 262 SER Chi-restraints excluded: chain J residue 277 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 24 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 17 optimal weight: 0.2980 chunk 50 optimal weight: 5.9990 chunk 52 optimal weight: 0.9990 chunk 55 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 58 optimal weight: 0.9980 chunk 35 optimal weight: 0.0570 chunk 27 optimal weight: 7.9990 chunk 40 optimal weight: 0.9980 overall best weight: 0.6700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 22 GLN ** J 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7104 moved from start: 0.3291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5238 Z= 0.167 Angle : 0.528 4.748 7093 Z= 0.271 Chirality : 0.038 0.145 779 Planarity : 0.004 0.049 900 Dihedral : 7.403 73.740 721 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.59 % Favored : 97.25 % Rotamer: Outliers : 1.08 % Allowed : 14.39 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.43 (0.34), residues: 618 helix: 1.20 (0.28), residues: 355 sheet: -1.81 (1.11), residues: 19 loop : -0.86 (0.38), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP J 132 HIS 0.004 0.001 HIS J 258 PHE 0.018 0.001 PHE I 110 TYR 0.012 0.001 TYR I 60 ARG 0.008 0.001 ARG I 279 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 86 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 276 ARG cc_start: 0.5672 (tmm160) cc_final: 0.4819 (pmt170) REVERT: I 260 LYS cc_start: 0.6807 (ttmp) cc_final: 0.6398 (tttp) REVERT: I 279 ARG cc_start: 0.6680 (mtm110) cc_final: 0.5472 (ptt-90) REVERT: J 96 THR cc_start: 0.7379 (p) cc_final: 0.7171 (t) REVERT: J 172 GLN cc_start: 0.4615 (mp-120) cc_final: 0.4362 (tp-100) outliers start: 6 outliers final: 4 residues processed: 88 average time/residue: 2.7386 time to fit residues: 251.6465 Evaluate side-chains 84 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 80 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 88 SER Chi-restraints excluded: chain J residue 95 GLU Chi-restraints excluded: chain J residue 248 THR Chi-restraints excluded: chain J residue 277 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 61 optimal weight: 0.9990 chunk 56 optimal weight: 8.9990 chunk 49 optimal weight: 0.7980 chunk 5 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 22 GLN ** J 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7161 moved from start: 0.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5238 Z= 0.268 Angle : 0.592 5.316 7093 Z= 0.305 Chirality : 0.040 0.141 779 Planarity : 0.005 0.038 900 Dihedral : 7.541 75.428 721 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.59 % Favored : 97.25 % Rotamer: Outliers : 1.08 % Allowed : 15.65 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.23 (0.33), residues: 618 helix: 0.98 (0.27), residues: 356 sheet: -1.77 (1.10), residues: 19 loop : -0.86 (0.37), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP I 11 HIS 0.007 0.001 HIS J 131 PHE 0.015 0.002 PHE I 30 TYR 0.015 0.002 TYR J 178 ARG 0.008 0.001 ARG I 279 ********************** 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 84 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 78 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 276 ARG cc_start: 0.5705 (tmm160) cc_final: 0.4841 (pmt170) REVERT: I 260 LYS cc_start: 0.6764 (ttmp) cc_final: 0.6314 (tttp) REVERT: I 279 ARG cc_start: 0.6712 (mtm110) cc_final: 0.5501 (ptt-90) outliers start: 6 outliers final: 4 residues processed: 82 average time/residue: 2.8070 time to fit residues: 240.3377 Evaluate side-chains 79 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 75 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 88 SER Chi-restraints excluded: chain J residue 95 GLU Chi-restraints excluded: chain J residue 248 THR Chi-restraints excluded: chain J residue 277 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 13 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 9 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 chunk 56 optimal weight: 0.0270 chunk 33 optimal weight: 4.9990 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 22 GLN ** J 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.179009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.160548 restraints weight = 17437.572| |-----------------------------------------------------------------------------| r_work (start): 0.3918 rms_B_bonded: 1.47 r_work: 0.3832 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3732 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3731 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3731 r_free = 0.3731 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3730 r_free = 0.3730 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3730 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.3367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5238 Z= 0.169 Angle : 0.541 4.904 7093 Z= 0.277 Chirality : 0.038 0.143 779 Planarity : 0.004 0.044 900 Dihedral : 7.394 73.706 721 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.59 % Favored : 97.25 % Rotamer: Outliers : 1.08 % Allowed : 15.65 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.52 (0.34), residues: 618 helix: 1.24 (0.28), residues: 355 sheet: -1.69 (1.05), residues: 20 loop : -0.78 (0.38), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 132 HIS 0.005 0.001 HIS J 131 PHE 0.017 0.001 PHE I 110 TYR 0.012 0.001 TYR I 60 ARG 0.007 0.000 ARG I 279 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5330.46 seconds wall clock time: 96 minutes 38.38 seconds (5798.38 seconds total)