Starting phenix.real_space_refine on Mon Jun 9 09:05:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8s0t_19628/06_2025/8s0t_19628_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8s0t_19628/06_2025/8s0t_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_19628/06_2025/8s0t_19628.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8s0t_19628/06_2025/8s0t_19628.map" model { file = "/net/cci-nas-00/data/ceres_data/8s0t_19628/06_2025/8s0t_19628_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8s0t_19628/06_2025/8s0t_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-5710/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: 5.92, per 1000 atoms: 0.56 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: 2.99 Conformation dependent library (CDL) restraints added in 569.7 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: 0.85 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: 3.90 Time building geometry restraints manager: 3.49 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: 0.960 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: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 26.520 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: 0.000 Load rotamer database and sin/cos tables:13.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.060 ------------------------------------------------------------------------------- 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= 0.819 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 Details of bonding type rmsd hydrogen bonds : bond 0.17300 ( 270) hydrogen bonds : angle 7.52015 ( 768) covalent geometry : bond 0.01310 ( 5238) covalent geometry : angle 2.14425 ( 7093) *********************** 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 : 0.813 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: 2.3940 time to fit residues: 265.8528 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 : 0.831 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.178437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.159947 restraints weight = 17247.390| |-----------------------------------------------------------------------------| r_work (start): 0.3916 rms_B_bonded: 1.45 r_work: 0.3828 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3725 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3724 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3724 r_free = 0.3724 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3723 r_free = 0.3723 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3723 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 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= 0.176 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 Details of bonding type rmsd hydrogen bonds : bond 0.05567 ( 270) hydrogen bonds : angle 5.58852 ( 768) covalent geometry : bond 0.00371 ( 5238) covalent geometry : angle 0.70423 ( 7093) *********************** 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 : 0.829 Fit side-chains revert: symmetry clash REVERT: H 251 LEU cc_start: 0.6203 (mt) cc_final: 0.5830 (mp) REVERT: H 276 ARG cc_start: 0.5640 (ttp80) cc_final: 0.4743 (pmt170) REVERT: I 250 ASP cc_start: 0.5591 (OUTLIER) cc_final: 0.5177 (m-30) REVERT: J 172 GLN cc_start: 0.5466 (tp40) cc_final: 0.5111 (mp-120) outliers start: 11 outliers final: 6 residues processed: 90 average time/residue: 2.6199 time to fit residues: 246.1727 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 : 0.880 ------------------------------------------------------------------------------- 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 3 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 31 optimal weight: 0.3980 chunk 6 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 36 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 overall best weight: 2.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 36 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 = 0.4090 r_free = 0.4090 target = 0.175535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.156736 restraints weight = 17529.398| |-----------------------------------------------------------------------------| r_work (start): 0.3876 rms_B_bonded: 1.46 r_work: 0.3787 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3685 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3684 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3684 r_free = 0.3684 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3684 r_free = 0.3684 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3684 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5238 Z= 0.199 Angle : 0.647 4.933 7093 Z= 0.341 Chirality : 0.041 0.152 779 Planarity : 0.005 0.045 900 Dihedral : 8.344 81.169 724 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.59 % Favored : 97.25 % Rotamer: Outliers : 1.98 % Allowed : 11.69 % Favored : 86.33 % 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: -0.70 (0.31), residues: 618 helix: 0.24 (0.26), residues: 352 sheet: -1.67 (1.16), residues: 19 loop : -1.31 (0.36), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP J 132 HIS 0.010 0.002 HIS J 131 PHE 0.016 0.002 PHE I 71 TYR 0.017 0.002 TYR J 178 ARG 0.009 0.001 ARG I 279 Details of bonding type rmsd hydrogen bonds : bond 0.05216 ( 270) hydrogen bonds : angle 5.39241 ( 768) covalent geometry : bond 0.00423 ( 5238) covalent geometry : angle 0.64682 ( 7093) *********************** 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 95 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 0.797 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 251 LEU cc_start: 0.6122 (mt) cc_final: 0.5813 (mp) REVERT: H 276 ARG cc_start: 0.5669 (ttp80) cc_final: 0.4710 (pmt170) REVERT: I 65 LEU cc_start: 0.7694 (OUTLIER) cc_final: 0.7347 (mm) REVERT: I 202 ASP cc_start: 0.7329 (m-30) cc_final: 0.6872 (m-30) REVERT: I 279 ARG cc_start: 0.6782 (mtm110) cc_final: 0.5239 (ptt-90) REVERT: J 172 GLN cc_start: 0.5211 (tp40) cc_final: 0.4985 (mp-120) outliers start: 11 outliers final: 6 residues processed: 90 average time/residue: 2.5228 time to fit residues: 237.6615 Evaluate side-chains 87 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 80 time to evaluate : 0.879 ------------------------------------------------------------------------------- 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 248 THR Chi-restraints excluded: chain J residue 262 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 3 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 11 optimal weight: 6.9990 chunk 52 optimal weight: 0.6980 chunk 17 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 overall best weight: 2.0986 ------------------------------------------------------------------------------- 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 = 0.4094 r_free = 0.4094 target = 0.175902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.157129 restraints weight = 17458.446| |-----------------------------------------------------------------------------| r_work (start): 0.3881 rms_B_bonded: 1.48 r_work: 0.3790 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3688 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3688 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3688 r_free = 0.3688 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3688 r_free = 0.3688 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3688 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5238 Z= 0.185 Angle : 0.603 5.045 7093 Z= 0.315 Chirality : 0.040 0.147 779 Planarity : 0.005 0.069 900 Dihedral : 8.073 78.084 724 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.91 % Favored : 96.93 % Rotamer: Outliers : 2.34 % Allowed : 11.51 % 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: -0.47 (0.32), residues: 618 helix: 0.50 (0.27), residues: 350 sheet: -1.85 (1.12), residues: 19 loop : -1.31 (0.36), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP J 132 HIS 0.008 0.001 HIS J 131 PHE 0.015 0.002 PHE I 71 TYR 0.016 0.002 TYR J 178 ARG 0.009 0.001 ARG I 28 Details of bonding type rmsd hydrogen bonds : bond 0.04819 ( 270) hydrogen bonds : angle 5.24585 ( 768) covalent geometry : bond 0.00402 ( 5238) covalent geometry : angle 0.60297 ( 7093) *********************** 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 94 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 81 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 251 LEU cc_start: 0.6083 (mt) cc_final: 0.5843 (mp) REVERT: H 276 ARG cc_start: 0.5654 (ttp80) cc_final: 0.4702 (pmt170) REVERT: I 49 GLU cc_start: 0.6311 (OUTLIER) cc_final: 0.6026 (mt-10) REVERT: I 131 GLU cc_start: 0.5277 (OUTLIER) cc_final: 0.4793 (mt-10) REVERT: I 202 ASP cc_start: 0.7367 (m-30) cc_final: 0.7147 (m-30) REVERT: I 252 MET cc_start: 0.7659 (mtm) cc_final: 0.7420 (mtp) REVERT: I 279 ARG cc_start: 0.6793 (mtm110) cc_final: 0.5231 (ptt-90) outliers start: 13 outliers final: 7 residues processed: 88 average time/residue: 2.7397 time to fit residues: 251.4425 Evaluate side-chains 90 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 81 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 49 GLU Chi-restraints excluded: chain I residue 131 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 26 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 39 optimal weight: 0.7980 chunk 55 optimal weight: 4.9990 chunk 32 optimal weight: 7.9990 chunk 37 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 overall best weight: 1.6986 ------------------------------------------------------------------------------- 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 = 0.4095 r_free = 0.4095 target = 0.176138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.157562 restraints weight = 17387.020| |-----------------------------------------------------------------------------| r_work (start): 0.3886 rms_B_bonded: 1.46 r_work: 0.3797 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3696 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3696 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3696 r_free = 0.3696 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3696 r_free = 0.3696 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3696 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5238 Z= 0.163 Angle : 0.583 5.030 7093 Z= 0.301 Chirality : 0.039 0.139 779 Planarity : 0.004 0.042 900 Dihedral : 7.775 76.866 721 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.07 % Favored : 96.76 % Rotamer: Outliers : 2.34 % Allowed : 11.87 % 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: -0.14 (0.33), residues: 618 helix: 0.80 (0.28), residues: 350 sheet: -1.84 (1.11), residues: 19 loop : -1.20 (0.37), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP J 132 HIS 0.006 0.001 HIS J 131 PHE 0.016 0.002 PHE I 110 TYR 0.015 0.002 TYR J 178 ARG 0.007 0.000 ARG I 28 Details of bonding type rmsd hydrogen bonds : bond 0.04578 ( 270) hydrogen bonds : angle 5.13566 ( 768) covalent geometry : bond 0.00359 ( 5238) covalent geometry : angle 0.58291 ( 7093) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 251 LEU cc_start: 0.6171 (mt) cc_final: 0.5959 (mp) REVERT: I 49 GLU cc_start: 0.6307 (OUTLIER) cc_final: 0.6069 (mt-10) REVERT: I 279 ARG cc_start: 0.6773 (mtm110) cc_final: 0.5191 (ptt-90) outliers start: 13 outliers final: 7 residues processed: 90 average time/residue: 3.2677 time to fit residues: 307.2785 Evaluate side-chains 87 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 79 time to evaluate : 0.847 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 8 optimal weight: 8.9990 chunk 9 optimal weight: 0.8980 chunk 41 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.178176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.159774 restraints weight = 17594.102| |-----------------------------------------------------------------------------| r_work (start): 0.3910 rms_B_bonded: 1.47 r_work: 0.3822 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3721 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3721 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3721 r_free = 0.3721 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3721 r_free = 0.3721 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3721 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.3118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5238 Z= 0.120 Angle : 0.533 4.507 7093 Z= 0.274 Chirality : 0.038 0.142 779 Planarity : 0.005 0.077 900 Dihedral : 7.531 74.774 721 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.75 % Favored : 97.09 % Rotamer: Outliers : 1.26 % Allowed : 13.13 % Favored : 85.61 % 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: 0.18 (0.33), residues: 618 helix: 0.99 (0.28), residues: 356 sheet: -1.83 (1.11), residues: 19 loop : -0.97 (0.38), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J 132 HIS 0.005 0.001 HIS J 131 PHE 0.017 0.001 PHE I 110 TYR 0.011 0.001 TYR H 248 ARG 0.010 0.000 ARG I 28 Details of bonding type rmsd hydrogen bonds : bond 0.04096 ( 270) hydrogen bonds : angle 4.89607 ( 768) covalent geometry : bond 0.00264 ( 5238) covalent geometry : angle 0.53283 ( 7093) *********************** 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: 7 poor density : 86 time to evaluate : 0.706 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 276 ARG cc_start: 0.5654 (tmm160) cc_final: 0.4635 (pmt170) REVERT: I 202 ASP cc_start: 0.7242 (m-30) cc_final: 0.6893 (m-30) REVERT: I 260 LYS cc_start: 0.6841 (ttmp) cc_final: 0.6311 (tttp) REVERT: I 279 ARG cc_start: 0.6764 (mtm110) cc_final: 0.5196 (ptt-90) outliers start: 7 outliers final: 3 residues processed: 88 average time/residue: 2.6378 time to fit residues: 242.2961 Evaluate side-chains 80 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 77 time to evaluate : 0.914 ------------------------------------------------------------------------------- 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 277 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 45 optimal weight: 4.9990 chunk 32 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 31 optimal weight: 0.0970 chunk 43 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 46 optimal weight: 0.6980 chunk 58 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 4 optimal weight: 7.9990 overall best weight: 2.5584 ------------------------------------------------------------------------------- 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** J 236 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.175230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.156531 restraints weight = 17740.255| |-----------------------------------------------------------------------------| r_work (start): 0.3873 rms_B_bonded: 1.48 r_work: 0.3784 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3684 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3682 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3682 r_free = 0.3682 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3682 r_free = 0.3682 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3682 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 5238 Z= 0.209 Angle : 0.611 4.890 7093 Z= 0.316 Chirality : 0.041 0.141 779 Planarity : 0.005 0.050 900 Dihedral : 7.704 76.167 721 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.75 % Favored : 97.09 % Rotamer: Outliers : 1.80 % Allowed : 13.67 % 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: -0.08 (0.32), residues: 618 helix: 0.80 (0.27), residues: 350 sheet: -1.83 (1.08), residues: 19 loop : -1.09 (0.36), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP I 11 HIS 0.008 0.002 HIS J 131 PHE 0.014 0.002 PHE I 71 TYR 0.014 0.002 TYR H 248 ARG 0.008 0.001 ARG I 28 Details of bonding type rmsd hydrogen bonds : bond 0.04751 ( 270) hydrogen bonds : angle 5.08598 ( 768) covalent geometry : bond 0.00461 ( 5238) covalent geometry : angle 0.61052 ( 7093) *********************** 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 89 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 276 ARG cc_start: 0.5695 (tmm160) cc_final: 0.4650 (pmt170) REVERT: I 49 GLU cc_start: 0.6381 (OUTLIER) cc_final: 0.6134 (mt-10) outliers start: 10 outliers final: 7 residues processed: 86 average time/residue: 2.7858 time to fit residues: 249.8376 Evaluate side-chains 86 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 78 time to evaluate : 0.805 ------------------------------------------------------------------------------- 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 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 52 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 27 optimal weight: 9.9990 chunk 51 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 chunk 20 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.176977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.158481 restraints weight = 17481.188| |-----------------------------------------------------------------------------| r_work (start): 0.3896 rms_B_bonded: 1.46 r_work: 0.3808 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3707 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3705 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3705 r_free = 0.3705 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3705 r_free = 0.3705 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3705 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5238 Z= 0.143 Angle : 0.568 4.959 7093 Z= 0.292 Chirality : 0.039 0.138 779 Planarity : 0.005 0.062 900 Dihedral : 7.590 74.918 721 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.27 % Favored : 97.57 % Rotamer: Outliers : 1.80 % Allowed : 13.49 % Favored : 84.71 % 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: 0.15 (0.33), residues: 618 helix: 0.93 (0.28), residues: 356 sheet: -1.86 (1.10), residues: 19 loop : -0.91 (0.38), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP J 132 HIS 0.005 0.001 HIS J 131 PHE 0.017 0.002 PHE I 30 TYR 0.013 0.001 TYR H 248 ARG 0.012 0.001 ARG I 279 Details of bonding type rmsd hydrogen bonds : bond 0.04299 ( 270) hydrogen bonds : angle 4.96260 ( 768) covalent geometry : bond 0.00316 ( 5238) covalent geometry : angle 0.56810 ( 7093) *********************** 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 89 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 276 ARG cc_start: 0.5668 (tmm160) cc_final: 0.4629 (pmt170) REVERT: I 202 ASP cc_start: 0.7296 (m-30) cc_final: 0.7006 (m-30) REVERT: I 260 LYS cc_start: 0.6836 (ttmp) cc_final: 0.6287 (tttp) REVERT: I 279 ARG cc_start: 0.6604 (mtm110) cc_final: 0.5218 (ptt-90) REVERT: J 172 GLN cc_start: 0.4641 (mp-120) cc_final: 0.4282 (tp-100) outliers start: 10 outliers final: 6 residues processed: 85 average time/residue: 2.7099 time to fit residues: 241.1709 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 : 0.884 ------------------------------------------------------------------------------- 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 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 11 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 52 optimal weight: 0.4980 chunk 15 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 28 optimal weight: 7.9990 chunk 44 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 22 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.175268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.156635 restraints weight = 17671.631| |-----------------------------------------------------------------------------| r_work (start): 0.3873 rms_B_bonded: 1.47 r_work: 0.3786 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3685 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3684 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3684 r_free = 0.3684 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3684 r_free = 0.3684 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3684 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.3156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 5238 Z= 0.204 Angle : 0.617 4.649 7093 Z= 0.319 Chirality : 0.040 0.142 779 Planarity : 0.005 0.046 900 Dihedral : 7.686 75.671 721 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.07 % Favored : 96.76 % 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: -0.06 (0.32), residues: 618 helix: 0.79 (0.27), residues: 350 sheet: -1.85 (1.07), residues: 19 loop : -1.03 (0.37), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP I 11 HIS 0.007 0.001 HIS J 131 PHE 0.019 0.002 PHE I 30 TYR 0.013 0.002 TYR J 178 ARG 0.010 0.001 ARG I 279 Details of bonding type rmsd hydrogen bonds : bond 0.04725 ( 270) hydrogen bonds : angle 5.08960 ( 768) covalent geometry : bond 0.00448 ( 5238) covalent geometry : angle 0.61689 ( 7093) *********************** 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 85 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 276 ARG cc_start: 0.5705 (tmm160) cc_final: 0.4644 (pmt170) REVERT: I 49 GLU cc_start: 0.6445 (OUTLIER) cc_final: 0.6194 (mt-10) REVERT: I 202 ASP cc_start: 0.7449 (OUTLIER) cc_final: 0.7167 (m-30) REVERT: I 279 ARG cc_start: 0.6631 (mtm110) cc_final: 0.5251 (ptt-90) outliers start: 9 outliers final: 6 residues processed: 81 average time/residue: 2.8253 time to fit residues: 239.2986 Evaluate side-chains 82 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 49 GLU Chi-restraints excluded: chain I residue 202 ASP Chi-restraints excluded: chain J residue 88 SER Chi-restraints excluded: chain J residue 95 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 67.8113 > 50: distance: 142 - 154: 20.289 distance: 154 - 155: 23.596 distance: 154 - 165: 37.776 distance: 155 - 156: 30.572 distance: 155 - 158: 24.971 distance: 155 - 166: 28.493 distance: 156 - 157: 31.820 distance: 156 - 174: 29.351 distance: 158 - 159: 10.404 distance: 158 - 167: 21.163 distance: 158 - 168: 12.672 distance: 159 - 160: 4.319 distance: 159 - 161: 6.634 distance: 160 - 162: 23.212 distance: 160 - 169: 11.624 distance: 161 - 163: 5.850 distance: 161 - 170: 6.308 distance: 162 - 164: 14.762 distance: 162 - 171: 12.437 distance: 163 - 164: 10.870 distance: 163 - 172: 19.211 distance: 164 - 173: 4.179 distance: 174 - 175: 32.851 distance: 174 - 183: 9.131 distance: 175 - 176: 26.453 distance: 175 - 178: 19.051 distance: 175 - 184: 19.342 distance: 176 - 196: 52.518 distance: 178 - 179: 26.371 distance: 178 - 185: 17.556 distance: 178 - 186: 26.963 distance: 179 - 180: 23.183 distance: 179 - 187: 15.555 distance: 179 - 188: 8.736 distance: 180 - 181: 6.856 distance: 180 - 189: 19.128 distance: 180 - 190: 12.486 distance: 181 - 182: 15.172 distance: 181 - 191: 5.345 distance: 181 - 192: 3.098 distance: 182 - 193: 9.032 distance: 182 - 194: 20.015 distance: 182 - 195: 8.518 distance: 196 - 197: 7.028 distance: 196 - 202: 56.212 distance: 197 - 198: 60.250 distance: 197 - 200: 42.617 distance: 197 - 203: 27.114 distance: 198 - 199: 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