Starting phenix.real_space_refine on Wed Mar 12 00:56:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7oh0_12890/03_2025/7oh0_12890.cif Found real_map, /net/cci-nas-00/data/ceres_data/7oh0_12890/03_2025/7oh0_12890.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7oh0_12890/03_2025/7oh0_12890.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7oh0_12890/03_2025/7oh0_12890.map" model { file = "/net/cci-nas-00/data/ceres_data/7oh0_12890/03_2025/7oh0_12890.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7oh0_12890/03_2025/7oh0_12890.cif" } resolution = 3.9 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= 0.042 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 23 5.16 5 C 4337 2.51 5 N 1138 2.21 5 O 1332 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 43 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 6830 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3516 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 14, 'TRANS': 420} Chain breaks: 1 Chain: "C" Number of atoms: 1665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1665 Classifications: {'peptide': 221} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 205} Chain: "B" Number of atoms: 1649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1649 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 201} Time building chain proxies: 4.81, per 1000 atoms: 0.70 Number of scatterers: 6830 At special positions: 0 Unit cell: (89.316, 80.219, 135.628, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 23 16.00 O 1332 8.00 N 1138 7.00 C 4337 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 97 " distance=2.02 Simple disulfide: pdb=" SG CYS C 145 " - pdb=" SG CYS C 201 " distance=2.03 Simple disulfide: pdb=" SG CYS C 221 " - pdb=" SG CYS B 436 " distance=2.02 Simple disulfide: pdb=" SG CYS B 244 " - pdb=" SG CYS B 309 " distance=2.03 Simple disulfide: pdb=" SG CYS B 356 " - pdb=" SG CYS B 416 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.72 Conformation dependent library (CDL) restraints added in 964.3 milliseconds 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1624 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 21 sheets defined 8.2% alpha, 25.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'A' and resid 876 through 884 Processing helix chain 'A' and resid 962 through 970 Processing helix chain 'A' and resid 1021 through 1025 Processing helix chain 'A' and resid 1097 through 1109 Processing helix chain 'A' and resid 1288 through 1294 removed outlier: 4.049A pdb=" N LEU A1294 " --> pdb=" O PHE A1291 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 92 removed outlier: 3.525A pdb=" N ASP C 91 " --> pdb=" O THR C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 209 Processing helix chain 'B' and resid 300 through 304 Processing helix chain 'B' and resid 343 through 350 removed outlier: 4.005A pdb=" N LEU B 347 " --> pdb=" O SER B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 Processing sheet with id=AA1, first strand: chain 'A' and resid 896 through 898 removed outlier: 6.192A pdb=" N ILE A1091 " --> pdb=" O ILE A 886 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ASN A 888 " --> pdb=" O PHE A1089 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N PHE A1089 " --> pdb=" O ASN A 888 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N ASP A 890 " --> pdb=" O ASP A1087 " (cutoff:3.500A) removed outlier: 9.851A pdb=" N ASP A1087 " --> pdb=" O ASP A 890 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N PHE A1089 " --> pdb=" O SER A 953 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N SER A 953 " --> pdb=" O PHE A1089 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ILE A1091 " --> pdb=" O THR A 951 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N THR A 951 " --> pdb=" O ILE A1091 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL A 952 " --> pdb=" O ILE A1036 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE A1036 " --> pdb=" O VAL A 952 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N PHE A 954 " --> pdb=" O ILE A1034 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE A1034 " --> pdb=" O PHE A 954 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA A1056 " --> pdb=" O ALA A1044 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N GLY A1054 " --> pdb=" O LEU A1046 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N ILE A1048 " --> pdb=" O LEU A1052 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N LEU A1052 " --> pdb=" O ILE A1048 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 914 through 917 removed outlier: 3.544A pdb=" N GLY A 920 " --> pdb=" O GLY A 917 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1011 through 1016 removed outlier: 4.077A pdb=" N ARG A1012 " --> pdb=" O LEU A1004 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU A1004 " --> pdb=" O ARG A1012 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE A1014 " --> pdb=" O TRP A1002 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N TRP A1002 " --> pdb=" O ILE A1014 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LEU A1000 " --> pdb=" O PHE A1016 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N TRP A 991 " --> pdb=" O SER A 978 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N SER A 978 " --> pdb=" O TRP A 991 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N VAL A 993 " --> pdb=" O ILE A 976 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE A 976 " --> pdb=" O VAL A 993 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N TYR A 974 " --> pdb=" O ASP A1075 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N ASP A1075 " --> pdb=" O TYR A 974 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ILE A 976 " --> pdb=" O LYS A1073 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER A 978 " --> pdb=" O THR A1071 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1129 through 1132 Processing sheet with id=AA5, first strand: chain 'A' and resid 1139 through 1142 Processing sheet with id=AA6, first strand: chain 'A' and resid 1156 through 1159 Processing sheet with id=AA7, first strand: chain 'A' and resid 1174 through 1176 removed outlier: 4.068A pdb=" N LYS A1174 " --> pdb=" O SER A1201 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1174 through 1176 removed outlier: 4.068A pdb=" N LYS A1174 " --> pdb=" O SER A1201 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1194 through 1196 removed outlier: 7.251A pdb=" N LEU A1255 " --> pdb=" O LEU A1267 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N LEU A1267 " --> pdb=" O LEU A1255 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N LEU A1257 " --> pdb=" O LEU A1265 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU A1267 " --> pdb=" O SER A1287 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER A1287 " --> pdb=" O LEU A1267 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N HIS A1271 " --> pdb=" O ILE A1283 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE A1283 " --> pdb=" O HIS A1271 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 4 through 7 removed outlier: 3.512A pdb=" N GLN C 5 " --> pdb=" O SER C 23 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER C 23 " --> pdb=" O GLN C 5 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER C 7 " --> pdb=" O THR C 21 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N THR C 21 " --> pdb=" O SER C 7 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 49 through 52 removed outlier: 4.127A pdb=" N GLY C 51 " --> pdb=" O TRP C 38 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N TYR C 35 " --> pdb=" O GLN C 100 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLN C 100 " --> pdb=" O TYR C 35 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA C 37 " --> pdb=" O ALA C 98 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TYR C 95 " --> pdb=" O THR C 112 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N THR C 112 " --> pdb=" O TYR C 95 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 125 through 128 Processing sheet with id=AB4, first strand: chain 'C' and resid 158 through 159 removed outlier: 3.996A pdb=" N VAL C 203 " --> pdb=" O VAL C 212 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL C 212 " --> pdb=" O VAL C 203 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 158 through 159 removed outlier: 3.907A pdb=" N TYR C 199 " --> pdb=" O VAL C 216 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 169 through 170 removed outlier: 3.712A pdb=" N VAL C 186 " --> pdb=" O HIS C 169 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 174 through 176 Processing sheet with id=AB8, first strand: chain 'B' and resid 240 through 242 removed outlier: 3.997A pdb=" N LEU B 294 " --> pdb=" O LEU B 242 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 266 through 270 removed outlier: 6.449A pdb=" N TRP B 256 " --> pdb=" O LEU B 268 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 336 through 337 removed outlier: 3.855A pdb=" N SER B 336 " --> pdb=" O ASN B 359 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN B 359 " --> pdb=" O SER B 336 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N SER B 399 " --> pdb=" O CYS B 356 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 351 through 352 Processing sheet with id=AC3, first strand: chain 'B' and resid 367 through 372 removed outlier: 3.833A pdb=" N LYS B 367 " --> pdb=" O THR B 419 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS B 371 " --> pdb=" O ALA B 415 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA B 415 " --> pdb=" O LYS B 371 " (cutoff:3.500A) 145 hydrogen bonds defined for protein. 321 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: 2.02 Time building geometry restraints manager: 1.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2188 1.34 - 1.46: 1625 1.46 - 1.58: 3146 1.58 - 1.70: 0 1.70 - 1.81: 33 Bond restraints: 6992 Sorted by residual: bond pdb=" C LEU A1027 " pdb=" N ALA A1028 " ideal model delta sigma weight residual 1.334 1.309 0.025 1.24e-02 6.50e+03 3.99e+00 bond pdb=" CA ASN A 892 " pdb=" CB ASN A 892 " ideal model delta sigma weight residual 1.524 1.549 -0.025 1.46e-02 4.69e+03 2.86e+00 bond pdb=" C PRO C 42 " pdb=" N PRO C 43 " ideal model delta sigma weight residual 1.330 1.348 -0.017 1.19e-02 7.06e+03 2.13e+00 bond pdb=" C ASP C 74 " pdb=" N PRO C 75 " ideal model delta sigma weight residual 1.337 1.323 0.013 9.80e-03 1.04e+04 1.85e+00 bond pdb=" N ASP C 106 " pdb=" CA ASP C 106 " ideal model delta sigma weight residual 1.463 1.454 0.009 6.90e-03 2.10e+04 1.85e+00 ... (remaining 6987 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 8868 1.70 - 3.40: 560 3.40 - 5.10: 69 5.10 - 6.80: 11 6.80 - 8.50: 4 Bond angle restraints: 9512 Sorted by residual: angle pdb=" N TRP B 315 " pdb=" CA TRP B 315 " pdb=" C TRP B 315 " ideal model delta sigma weight residual 109.81 101.31 8.50 2.21e+00 2.05e-01 1.48e+01 angle pdb=" CA ALA A1028 " pdb=" C ALA A1028 " pdb=" O ALA A1028 " ideal model delta sigma weight residual 120.15 115.26 4.89 1.29e+00 6.01e-01 1.43e+01 angle pdb=" N GLY A1269 " pdb=" CA GLY A1269 " pdb=" C GLY A1269 " ideal model delta sigma weight residual 111.14 116.28 -5.14 1.46e+00 4.69e-01 1.24e+01 angle pdb=" N SER B 378 " pdb=" CA SER B 378 " pdb=" C SER B 378 " ideal model delta sigma weight residual 112.72 108.27 4.45 1.28e+00 6.10e-01 1.21e+01 angle pdb=" N SER A1156 " pdb=" CA SER A1156 " pdb=" C SER A1156 " ideal model delta sigma weight residual 107.73 112.33 -4.60 1.34e+00 5.57e-01 1.18e+01 ... (remaining 9507 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.11: 3706 17.11 - 34.22: 388 34.22 - 51.33: 57 51.33 - 68.44: 11 68.44 - 85.55: 5 Dihedral angle restraints: 4167 sinusoidal: 1626 harmonic: 2541 Sorted by residual: dihedral pdb=" CA PRO B 316 " pdb=" C PRO B 316 " pdb=" N PRO B 317 " pdb=" CA PRO B 317 " ideal model delta harmonic sigma weight residual 180.00 114.85 65.15 0 5.00e+00 4.00e-02 1.70e+02 dihedral pdb=" CA TRP B 315 " pdb=" C TRP B 315 " pdb=" N PRO B 316 " pdb=" CA PRO B 316 " ideal model delta harmonic sigma weight residual -180.00 -145.40 -34.60 0 5.00e+00 4.00e-02 4.79e+01 dihedral pdb=" CA ASN B 374 " pdb=" C ASN B 374 " pdb=" N ALA B 375 " pdb=" CA ALA B 375 " ideal model delta harmonic sigma weight residual -180.00 -148.01 -31.99 0 5.00e+00 4.00e-02 4.09e+01 ... (remaining 4164 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 625 0.033 - 0.066: 261 0.066 - 0.099: 115 0.099 - 0.132: 47 0.132 - 0.165: 6 Chirality restraints: 1054 Sorted by residual: chirality pdb=" CA VAL A 952 " pdb=" N VAL A 952 " pdb=" C VAL A 952 " pdb=" CB VAL A 952 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.16 2.00e-01 2.50e+01 6.77e-01 chirality pdb=" CA THR A1146 " pdb=" N THR A1146 " pdb=" C THR A1146 " pdb=" CB THR A1146 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.16 2.00e-01 2.50e+01 6.44e-01 chirality pdb=" CA ILE B 339 " pdb=" N ILE B 339 " pdb=" C ILE B 339 " pdb=" CB ILE B 339 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.78e-01 ... (remaining 1051 not shown) Planarity restraints: 1219 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 316 " -0.073 5.00e-02 4.00e+02 1.10e-01 1.95e+01 pdb=" N PRO B 317 " 0.191 5.00e-02 4.00e+02 pdb=" CA PRO B 317 " -0.059 5.00e-02 4.00e+02 pdb=" CD PRO B 317 " -0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 8 " 0.031 5.00e-02 4.00e+02 4.65e-02 3.46e+00 pdb=" N PRO C 9 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO C 9 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 9 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C 151 " 0.030 5.00e-02 4.00e+02 4.57e-02 3.35e+00 pdb=" N PRO C 152 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO C 152 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 152 " 0.024 5.00e-02 4.00e+02 ... (remaining 1216 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 188 2.62 - 3.19: 6888 3.19 - 3.76: 10897 3.76 - 4.33: 14566 4.33 - 4.90: 22510 Nonbonded interactions: 55049 Sorted by model distance: nonbonded pdb=" OG SER A1156 " pdb=" O TYR A1166 " model vdw 2.046 3.040 nonbonded pdb=" O ASN C 103 " pdb=" OH TYR B 318 " model vdw 2.087 3.040 nonbonded pdb=" O SER C 193 " pdb=" OH TYR C 199 " model vdw 2.099 3.040 nonbonded pdb=" N SER A1156 " pdb=" O ASN B 314 " model vdw 2.130 3.120 nonbonded pdb=" OG SER A 979 " pdb=" O SER A 989 " model vdw 2.134 3.040 ... (remaining 55044 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 2.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 20.310 Find NCS groups from input model: 0.070 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7026 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 6992 Z= 0.306 Angle : 0.916 8.499 9512 Z= 0.551 Chirality : 0.047 0.165 1054 Planarity : 0.006 0.110 1219 Dihedral : 13.942 85.548 2528 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 29.13 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.95 % Favored : 87.94 % Rotamer: Outliers : 0.26 % Allowed : 9.01 % Favored : 90.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.76 % Cis-general : 0.00 % Twisted Proline : 4.88 % Twisted General : 0.12 % 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: -5.70 (0.21), residues: 862 helix: -3.99 (0.34), residues: 54 sheet: -3.51 (0.28), residues: 241 loop : -4.15 (0.19), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 955 HIS 0.003 0.001 HIS C 169 PHE 0.019 0.002 PHE B 320 TYR 0.017 0.002 TYR C 181 ARG 0.003 0.000 ARG B 433 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 122 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1039 ASP cc_start: 0.8650 (t0) cc_final: 0.8313 (t70) REVERT: A 1042 SER cc_start: 0.9134 (t) cc_final: 0.8899 (p) REVERT: A 1053 MET cc_start: 0.7312 (mmt) cc_final: 0.7109 (mmt) REVERT: A 1070 ILE cc_start: 0.8894 (mm) cc_final: 0.8657 (mp) REVERT: A 1239 LYS cc_start: 0.7666 (tptt) cc_final: 0.7232 (mptt) REVERT: A 1240 MET cc_start: 0.8894 (mpp) cc_final: 0.8047 (mpp) REVERT: C 204 ASN cc_start: 0.7900 (t0) cc_final: 0.7684 (t0) REVERT: B 224 MET cc_start: 0.4707 (mpp) cc_final: 0.4418 (mmp) REVERT: B 432 ASN cc_start: 0.8861 (t0) cc_final: 0.8272 (p0) outliers start: 2 outliers final: 1 residues processed: 124 average time/residue: 0.1968 time to fit residues: 32.7010 Evaluate side-chains 86 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 85 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 59 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 72 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 43 optimal weight: 0.0980 chunk 34 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 chunk 78 optimal weight: 7.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 936 HIS ** A 972 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 998 ASN A1069 ASN ** A1078 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1163 ASN A1292 ASN ** A1293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 202 ASN ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 227 GLN B 259 GLN B 377 GLN B 432 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.093377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.074469 restraints weight = 20468.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.077425 restraints weight = 11279.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.079489 restraints weight = 7332.299| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 6992 Z= 0.281 Angle : 0.739 9.610 9512 Z= 0.392 Chirality : 0.048 0.159 1054 Planarity : 0.007 0.110 1219 Dihedral : 7.238 64.778 949 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 21.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.88 % Favored : 87.12 % Rotamer: Outliers : 3.52 % Allowed : 14.36 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.76 % Cis-general : 0.00 % Twisted Proline : 4.88 % Twisted General : 0.12 % 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: -4.74 (0.24), residues: 862 helix: -2.57 (0.58), residues: 48 sheet: -2.95 (0.28), residues: 244 loop : -3.51 (0.22), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 955 HIS 0.003 0.001 HIS C 205 PHE 0.035 0.002 PHE C 127 TYR 0.016 0.002 TYR C 34 ARG 0.011 0.001 ARG A1246 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 103 time to evaluate : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1070 ILE cc_start: 0.8922 (mm) cc_final: 0.8697 (mp) REVERT: A 1239 LYS cc_start: 0.7802 (tptt) cc_final: 0.7397 (mptt) REVERT: A 1240 MET cc_start: 0.8779 (mpp) cc_final: 0.8122 (mpp) REVERT: A 1305 PHE cc_start: 0.6838 (OUTLIER) cc_final: 0.6373 (m-10) REVERT: C 176 GLN cc_start: 0.8689 (mm-40) cc_final: 0.8334 (mp10) REVERT: C 202 ASN cc_start: 0.6939 (m110) cc_final: 0.6440 (m110) REVERT: C 204 ASN cc_start: 0.8051 (t0) cc_final: 0.7652 (t0) REVERT: B 225 MET cc_start: 0.5548 (pmm) cc_final: 0.5101 (tpt) REVERT: B 358 LEU cc_start: 0.3860 (OUTLIER) cc_final: 0.3594 (pp) REVERT: B 432 ASN cc_start: 0.8804 (t0) cc_final: 0.8349 (p0) outliers start: 27 outliers final: 15 residues processed: 122 average time/residue: 0.1617 time to fit residues: 27.9876 Evaluate side-chains 100 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 1.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1046 LEU Chi-restraints excluded: chain A residue 1057 GLU Chi-restraints excluded: chain A residue 1130 LEU Chi-restraints excluded: chain A residue 1169 LEU Chi-restraints excluded: chain A residue 1214 ASP Chi-restraints excluded: chain A residue 1253 VAL Chi-restraints excluded: chain A residue 1268 VAL Chi-restraints excluded: chain A residue 1305 PHE Chi-restraints excluded: chain A residue 1313 THR Chi-restraints excluded: chain C residue 34 TYR Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 340 PHE Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 358 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 40 optimal weight: 10.0000 chunk 26 optimal weight: 2.9990 chunk 1 optimal weight: 0.0020 chunk 25 optimal weight: 5.9990 chunk 71 optimal weight: 7.9990 chunk 85 optimal weight: 0.0870 chunk 49 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 30 optimal weight: 6.9990 overall best weight: 0.7570 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 919 ASN A 972 ASN A1078 ASN A1153 ASN A1293 HIS C 103 ASN ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.098908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.079503 restraints weight = 20378.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.082708 restraints weight = 11145.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.084907 restraints weight = 7198.495| |-----------------------------------------------------------------------------| r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6952 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6992 Z= 0.169 Angle : 0.671 11.064 9512 Z= 0.349 Chirality : 0.046 0.164 1054 Planarity : 0.006 0.114 1219 Dihedral : 6.626 63.523 949 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 16.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.58 % Favored : 91.42 % Rotamer: Outliers : 3.92 % Allowed : 16.06 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.76 % Cis-general : 0.00 % Twisted Proline : 4.88 % Twisted General : 0.12 % 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: -4.29 (0.25), residues: 862 helix: -1.98 (0.66), residues: 49 sheet: -2.97 (0.28), residues: 255 loop : -3.01 (0.23), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 955 HIS 0.004 0.001 HIS C 205 PHE 0.026 0.002 PHE C 127 TYR 0.020 0.001 TYR A1026 ARG 0.005 0.001 ARG A1246 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 108 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1047 TYR cc_start: 0.8076 (m-80) cc_final: 0.7793 (m-80) REVERT: A 1053 MET cc_start: 0.6760 (mmt) cc_final: 0.6383 (mmt) REVERT: A 1100 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.6860 (pm20) REVERT: A 1131 ILE cc_start: 0.8405 (mp) cc_final: 0.8184 (mt) REVERT: A 1239 LYS cc_start: 0.7793 (tptt) cc_final: 0.7452 (mptt) REVERT: A 1305 PHE cc_start: 0.6748 (OUTLIER) cc_final: 0.6251 (m-10) REVERT: C 176 GLN cc_start: 0.8736 (mm-40) cc_final: 0.8448 (mp10) REVERT: C 204 ASN cc_start: 0.8057 (t0) cc_final: 0.7756 (t0) REVERT: B 254 LEU cc_start: 0.7407 (OUTLIER) cc_final: 0.6948 (pp) REVERT: B 256 TRP cc_start: 0.7167 (m100) cc_final: 0.6915 (m100) REVERT: B 320 PHE cc_start: 0.7187 (m-10) cc_final: 0.6932 (m-10) REVERT: B 354 VAL cc_start: 0.8397 (t) cc_final: 0.8166 (t) REVERT: B 414 TYR cc_start: 0.8568 (m-80) cc_final: 0.7830 (m-80) REVERT: B 432 ASN cc_start: 0.8756 (t0) cc_final: 0.8155 (p0) outliers start: 30 outliers final: 17 residues processed: 134 average time/residue: 0.1583 time to fit residues: 30.1582 Evaluate side-chains 105 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 85 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1046 LEU Chi-restraints excluded: chain A residue 1057 GLU Chi-restraints excluded: chain A residue 1100 GLU Chi-restraints excluded: chain A residue 1130 LEU Chi-restraints excluded: chain A residue 1186 ILE Chi-restraints excluded: chain A residue 1268 VAL Chi-restraints excluded: chain A residue 1305 PHE Chi-restraints excluded: chain A residue 1313 THR Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 34 TYR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 105 PHE Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain B residue 224 MET Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 327 GLU Chi-restraints excluded: chain B residue 340 PHE Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 418 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 43 optimal weight: 4.9990 chunk 35 optimal weight: 7.9990 chunk 72 optimal weight: 7.9990 chunk 15 optimal weight: 3.9990 chunk 75 optimal weight: 7.9990 chunk 3 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 18 optimal weight: 0.8980 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 928 ASN ** A1254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 ASN ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 311 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.091228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.072223 restraints weight = 21509.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.074975 restraints weight = 12249.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.076937 restraints weight = 8158.706| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7115 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 6992 Z= 0.371 Angle : 0.776 9.943 9512 Z= 0.406 Chirality : 0.049 0.237 1054 Planarity : 0.007 0.122 1219 Dihedral : 7.164 64.422 949 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 25.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.92 % Favored : 86.08 % Rotamer: Outliers : 5.74 % Allowed : 17.75 % Favored : 76.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.76 % Cis-general : 0.00 % Twisted Proline : 4.88 % Twisted General : 0.12 % 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: -4.27 (0.25), residues: 862 helix: -2.47 (0.58), residues: 56 sheet: -2.71 (0.30), residues: 250 loop : -3.10 (0.23), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP A1002 HIS 0.004 0.001 HIS C 205 PHE 0.024 0.002 PHE C 127 TYR 0.028 0.002 TYR C 34 ARG 0.012 0.001 ARG B 364 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 82 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1047 TYR cc_start: 0.8296 (m-80) cc_final: 0.7929 (m-80) REVERT: A 1053 MET cc_start: 0.6984 (mmt) cc_final: 0.6648 (mmt) REVERT: A 1100 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.6995 (pm20) REVERT: A 1131 ILE cc_start: 0.8489 (OUTLIER) cc_final: 0.8239 (mt) REVERT: A 1239 LYS cc_start: 0.7899 (tptt) cc_final: 0.7275 (mptt) REVERT: C 204 ASN cc_start: 0.8227 (t0) cc_final: 0.7870 (t0) REVERT: B 224 MET cc_start: 0.5288 (OUTLIER) cc_final: 0.4963 (mmp) REVERT: B 254 LEU cc_start: 0.7546 (OUTLIER) cc_final: 0.7341 (pp) REVERT: B 432 ASN cc_start: 0.8823 (t0) cc_final: 0.8274 (p0) outliers start: 44 outliers final: 25 residues processed: 119 average time/residue: 0.1658 time to fit residues: 27.6983 Evaluate side-chains 107 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 78 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 891 ILE Chi-restraints excluded: chain A residue 971 THR Chi-restraints excluded: chain A residue 1015 THR Chi-restraints excluded: chain A residue 1046 LEU Chi-restraints excluded: chain A residue 1057 GLU Chi-restraints excluded: chain A residue 1091 ILE Chi-restraints excluded: chain A residue 1100 GLU Chi-restraints excluded: chain A residue 1130 LEU Chi-restraints excluded: chain A residue 1131 ILE Chi-restraints excluded: chain A residue 1150 TYR Chi-restraints excluded: chain A residue 1169 LEU Chi-restraints excluded: chain A residue 1214 ASP Chi-restraints excluded: chain A residue 1253 VAL Chi-restraints excluded: chain A residue 1268 VAL Chi-restraints excluded: chain A residue 1313 THR Chi-restraints excluded: chain C residue 34 TYR Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 105 PHE Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain B residue 224 MET Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 327 GLU Chi-restraints excluded: chain B residue 351 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 26 optimal weight: 4.9990 chunk 47 optimal weight: 0.9990 chunk 58 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 chunk 66 optimal weight: 10.0000 chunk 29 optimal weight: 1.9990 chunk 5 optimal weight: 8.9990 chunk 84 optimal weight: 9.9990 chunk 27 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 59 optimal weight: 8.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 999 ASN ** A1254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 HIS ** 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 = 0.3781 r_free = 0.3781 target = 0.092311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.071992 restraints weight = 21138.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.075029 restraints weight = 11695.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.077120 restraints weight = 7667.351| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6991 moved from start: 0.3115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6992 Z= 0.286 Angle : 0.725 9.369 9512 Z= 0.377 Chirality : 0.048 0.209 1054 Planarity : 0.006 0.126 1219 Dihedral : 7.004 64.062 949 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 22.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.90 % Favored : 89.10 % Rotamer: Outliers : 5.48 % Allowed : 20.10 % Favored : 74.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.76 % Cis-general : 0.00 % Twisted Proline : 4.88 % Twisted General : 0.12 % 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: -4.21 (0.25), residues: 862 helix: -2.28 (0.59), residues: 56 sheet: -2.86 (0.30), residues: 239 loop : -2.97 (0.23), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 955 HIS 0.003 0.001 HIS C 205 PHE 0.021 0.002 PHE C 127 TYR 0.019 0.002 TYR C 34 ARG 0.004 0.001 ARG B 239 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 84 time to evaluate : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1047 TYR cc_start: 0.8321 (m-80) cc_final: 0.8045 (m-80) REVERT: A 1053 MET cc_start: 0.6786 (mmt) cc_final: 0.6446 (mmt) REVERT: A 1100 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.6784 (pm20) REVERT: A 1109 LEU cc_start: 0.8558 (tt) cc_final: 0.7998 (pp) REVERT: A 1131 ILE cc_start: 0.8360 (OUTLIER) cc_final: 0.8149 (mt) REVERT: A 1239 LYS cc_start: 0.7812 (tptt) cc_final: 0.7292 (mptt) REVERT: A 1240 MET cc_start: 0.8856 (mpp) cc_final: 0.7794 (mpp) REVERT: C 16 GLU cc_start: 0.8342 (tt0) cc_final: 0.7704 (tm-30) REVERT: C 78 ASN cc_start: 0.6550 (t0) cc_final: 0.6217 (t0) REVERT: C 204 ASN cc_start: 0.8131 (t0) cc_final: 0.7877 (t0) REVERT: B 432 ASN cc_start: 0.8831 (t0) cc_final: 0.8310 (p0) outliers start: 42 outliers final: 25 residues processed: 119 average time/residue: 0.1653 time to fit residues: 28.0255 Evaluate side-chains 101 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 74 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 891 ILE Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1015 THR Chi-restraints excluded: chain A residue 1046 LEU Chi-restraints excluded: chain A residue 1057 GLU Chi-restraints excluded: chain A residue 1091 ILE Chi-restraints excluded: chain A residue 1100 GLU Chi-restraints excluded: chain A residue 1130 LEU Chi-restraints excluded: chain A residue 1131 ILE Chi-restraints excluded: chain A residue 1150 TYR Chi-restraints excluded: chain A residue 1169 LEU Chi-restraints excluded: chain A residue 1214 ASP Chi-restraints excluded: chain A residue 1253 VAL Chi-restraints excluded: chain A residue 1268 VAL Chi-restraints excluded: chain A residue 1313 THR Chi-restraints excluded: chain C residue 34 TYR Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 105 PHE Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 327 GLU Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 418 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 42 optimal weight: 4.9990 chunk 53 optimal weight: 0.2980 chunk 81 optimal weight: 4.9990 chunk 60 optimal weight: 0.0970 chunk 20 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 4 optimal weight: 8.9990 chunk 75 optimal weight: 0.8980 chunk 85 optimal weight: 0.0370 chunk 25 optimal weight: 4.9990 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 103 ASN ** C 205 HIS ** 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 = 0.3899 r_free = 0.3899 target = 0.098988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.078067 restraints weight = 20131.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.081502 restraints weight = 10781.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.083871 restraints weight = 6883.834| |-----------------------------------------------------------------------------| r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6821 moved from start: 0.3686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6992 Z= 0.158 Angle : 0.676 11.564 9512 Z= 0.346 Chirality : 0.046 0.172 1054 Planarity : 0.006 0.122 1219 Dihedral : 6.287 63.824 949 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 15.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.58 % Favored : 91.42 % Rotamer: Outliers : 3.52 % Allowed : 22.06 % Favored : 74.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.76 % Cis-general : 0.00 % Twisted Proline : 4.88 % Twisted General : 0.12 % 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: -3.76 (0.26), residues: 862 helix: -1.53 (0.67), residues: 51 sheet: -2.53 (0.29), residues: 259 loop : -2.69 (0.24), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 955 HIS 0.003 0.001 HIS C 205 PHE 0.032 0.002 PHE B 340 TYR 0.013 0.001 TYR A1026 ARG 0.006 0.001 ARG B 364 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 102 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 939 MET cc_start: 0.8935 (mtm) cc_final: 0.8477 (tmm) REVERT: A 1047 TYR cc_start: 0.8172 (m-80) cc_final: 0.7525 (m-80) REVERT: A 1053 MET cc_start: 0.6807 (mmt) cc_final: 0.6492 (mmt) REVERT: A 1236 LEU cc_start: 0.8856 (pp) cc_final: 0.8232 (tt) REVERT: A 1239 LYS cc_start: 0.7697 (tptt) cc_final: 0.7235 (mptt) REVERT: A 1240 MET cc_start: 0.8648 (mpp) cc_final: 0.7854 (mpp) REVERT: C 78 ASN cc_start: 0.6543 (t0) cc_final: 0.6160 (t0) REVERT: C 176 GLN cc_start: 0.8833 (mm-40) cc_final: 0.8419 (mp10) REVERT: B 354 VAL cc_start: 0.8201 (t) cc_final: 0.7991 (t) REVERT: B 432 ASN cc_start: 0.8739 (t0) cc_final: 0.8211 (p0) outliers start: 27 outliers final: 18 residues processed: 123 average time/residue: 0.1582 time to fit residues: 27.9336 Evaluate side-chains 107 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 89 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 891 ILE Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1057 GLU Chi-restraints excluded: chain A residue 1130 LEU Chi-restraints excluded: chain A residue 1268 VAL Chi-restraints excluded: chain A residue 1313 THR Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 34 TYR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain B residue 224 MET Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 340 PHE Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 418 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 14 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 82 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 84 optimal weight: 0.7980 chunk 9 optimal weight: 6.9990 chunk 72 optimal weight: 9.9990 chunk 65 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1292 ASN ** C 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 HIS ** 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 = 0.3809 r_free = 0.3809 target = 0.093851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.073537 restraints weight = 20586.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.076629 restraints weight = 11385.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.078833 restraints weight = 7449.879| |-----------------------------------------------------------------------------| r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6961 moved from start: 0.3760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6992 Z= 0.275 Angle : 0.714 10.681 9512 Z= 0.371 Chirality : 0.046 0.165 1054 Planarity : 0.006 0.122 1219 Dihedral : 6.600 64.051 949 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 20.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.14 % Favored : 88.86 % Rotamer: Outliers : 4.18 % Allowed : 23.11 % Favored : 72.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.76 % Cis-general : 0.00 % Twisted Proline : 4.88 % Twisted General : 0.12 % 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: -3.84 (0.26), residues: 862 helix: -1.81 (0.63), residues: 57 sheet: -2.52 (0.28), residues: 271 loop : -2.75 (0.24), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 955 HIS 0.003 0.001 HIS C 205 PHE 0.047 0.002 PHE C 127 TYR 0.021 0.002 TYR C 54 ARG 0.009 0.001 ARG B 364 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 88 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 903 ASN cc_start: 0.8281 (p0) cc_final: 0.8081 (p0) REVERT: A 1033 PHE cc_start: 0.7637 (OUTLIER) cc_final: 0.6794 (t80) REVERT: A 1047 TYR cc_start: 0.8124 (m-80) cc_final: 0.7920 (m-80) REVERT: A 1053 MET cc_start: 0.6893 (mmt) cc_final: 0.6555 (mmt) REVERT: A 1239 LYS cc_start: 0.7728 (tptt) cc_final: 0.7265 (mptt) REVERT: A 1240 MET cc_start: 0.8808 (mpp) cc_final: 0.7767 (mpp) REVERT: B 432 ASN cc_start: 0.8775 (t0) cc_final: 0.8288 (p0) outliers start: 32 outliers final: 25 residues processed: 113 average time/residue: 0.1485 time to fit residues: 24.4779 Evaluate side-chains 105 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 79 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 891 ILE Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1033 PHE Chi-restraints excluded: chain A residue 1046 LEU Chi-restraints excluded: chain A residue 1057 GLU Chi-restraints excluded: chain A residue 1130 LEU Chi-restraints excluded: chain A residue 1150 TYR Chi-restraints excluded: chain A residue 1214 ASP Chi-restraints excluded: chain A residue 1268 VAL Chi-restraints excluded: chain A residue 1305 PHE Chi-restraints excluded: chain A residue 1313 THR Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 34 TYR Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 105 PHE Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain B residue 224 MET Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 288 SER Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 418 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 32 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 73 optimal weight: 0.7980 chunk 23 optimal weight: 0.5980 chunk 56 optimal weight: 6.9990 chunk 2 optimal weight: 6.9990 chunk 64 optimal weight: 6.9990 chunk 46 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 chunk 38 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1292 ASN C 176 GLN ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.093666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.073212 restraints weight = 20780.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.076300 restraints weight = 11526.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.078490 restraints weight = 7521.368| |-----------------------------------------------------------------------------| r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6965 moved from start: 0.3913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6992 Z= 0.261 Angle : 0.708 9.897 9512 Z= 0.368 Chirality : 0.046 0.166 1054 Planarity : 0.006 0.124 1219 Dihedral : 6.636 64.468 949 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 20.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.37 % Favored : 88.63 % Rotamer: Outliers : 4.31 % Allowed : 23.50 % Favored : 72.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.76 % Cis-general : 0.00 % Twisted Proline : 4.88 % 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: -3.75 (0.26), residues: 862 helix: -1.76 (0.64), residues: 57 sheet: -2.42 (0.29), residues: 258 loop : -2.72 (0.24), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 955 HIS 0.003 0.001 HIS B 411 PHE 0.037 0.002 PHE C 127 TYR 0.017 0.002 TYR C 34 ARG 0.008 0.001 ARG B 364 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 87 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 939 MET cc_start: 0.8958 (mtm) cc_final: 0.8460 (tmm) REVERT: A 1033 PHE cc_start: 0.7548 (OUTLIER) cc_final: 0.6709 (t80) REVERT: A 1053 MET cc_start: 0.6918 (mmt) cc_final: 0.6576 (mmt) REVERT: A 1236 LEU cc_start: 0.8886 (pp) cc_final: 0.8255 (tt) REVERT: A 1239 LYS cc_start: 0.7738 (tptt) cc_final: 0.7313 (mptt) REVERT: A 1240 MET cc_start: 0.8842 (mpp) cc_final: 0.7744 (mpp) REVERT: C 16 GLU cc_start: 0.8442 (tt0) cc_final: 0.7812 (tm-30) REVERT: B 299 MET cc_start: 0.8627 (mpp) cc_final: 0.8294 (mmt) REVERT: B 417 GLU cc_start: 0.4707 (pm20) cc_final: 0.4424 (pm20) REVERT: B 432 ASN cc_start: 0.8821 (t0) cc_final: 0.8345 (p0) outliers start: 33 outliers final: 28 residues processed: 113 average time/residue: 0.1532 time to fit residues: 25.3062 Evaluate side-chains 107 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 78 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 891 ILE Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1033 PHE Chi-restraints excluded: chain A residue 1046 LEU Chi-restraints excluded: chain A residue 1057 GLU Chi-restraints excluded: chain A residue 1130 LEU Chi-restraints excluded: chain A residue 1150 TYR Chi-restraints excluded: chain A residue 1169 LEU Chi-restraints excluded: chain A residue 1214 ASP Chi-restraints excluded: chain A residue 1268 VAL Chi-restraints excluded: chain A residue 1305 PHE Chi-restraints excluded: chain A residue 1313 THR Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 34 TYR Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 105 PHE Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 197 GLN Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain B residue 224 MET Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 288 SER Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 340 PHE Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 418 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 5 optimal weight: 9.9990 chunk 16 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 82 optimal weight: 10.0000 chunk 48 optimal weight: 6.9990 chunk 13 optimal weight: 0.1980 chunk 84 optimal weight: 7.9990 chunk 46 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 20 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1292 ASN ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 311 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.096377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.075663 restraints weight = 20330.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.078902 restraints weight = 11149.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.081177 restraints weight = 7252.494| |-----------------------------------------------------------------------------| r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6889 moved from start: 0.4199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6992 Z= 0.193 Angle : 0.683 9.724 9512 Z= 0.350 Chirality : 0.045 0.145 1054 Planarity : 0.006 0.122 1219 Dihedral : 6.288 64.047 949 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 17.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.86 % Favored : 90.14 % Rotamer: Outliers : 3.66 % Allowed : 24.28 % Favored : 72.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.76 % Cis-general : 0.00 % Twisted Proline : 4.88 % 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: -3.50 (0.26), residues: 862 helix: -1.65 (0.65), residues: 57 sheet: -2.22 (0.31), residues: 245 loop : -2.57 (0.24), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 955 HIS 0.002 0.001 HIS B 411 PHE 0.032 0.002 PHE C 127 TYR 0.013 0.002 TYR A1150 ARG 0.007 0.001 ARG B 364 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 91 time to evaluate : 0.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 939 MET cc_start: 0.8969 (mtm) cc_final: 0.8441 (tmm) REVERT: A 1012 ARG cc_start: 0.8572 (mmt-90) cc_final: 0.8254 (mmp80) REVERT: A 1047 TYR cc_start: 0.8111 (m-80) cc_final: 0.7706 (m-80) REVERT: A 1053 MET cc_start: 0.6888 (mmt) cc_final: 0.6593 (mmt) REVERT: A 1236 LEU cc_start: 0.8857 (pp) cc_final: 0.8236 (tt) REVERT: A 1239 LYS cc_start: 0.7700 (tptt) cc_final: 0.7335 (mptt) REVERT: A 1240 MET cc_start: 0.8751 (mpp) cc_final: 0.7946 (mpp) REVERT: C 209 ASN cc_start: 0.8429 (t0) cc_final: 0.8186 (t0) REVERT: B 256 TRP cc_start: 0.7221 (m100) cc_final: 0.6881 (m100) REVERT: B 299 MET cc_start: 0.8538 (mpp) cc_final: 0.8083 (mmm) REVERT: B 417 GLU cc_start: 0.4947 (pm20) cc_final: 0.4650 (pm20) REVERT: B 432 ASN cc_start: 0.8815 (t0) cc_final: 0.8295 (p0) outliers start: 28 outliers final: 26 residues processed: 112 average time/residue: 0.1532 time to fit residues: 24.6667 Evaluate side-chains 110 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 84 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 891 ILE Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1033 PHE Chi-restraints excluded: chain A residue 1046 LEU Chi-restraints excluded: chain A residue 1057 GLU Chi-restraints excluded: chain A residue 1130 LEU Chi-restraints excluded: chain A residue 1268 VAL Chi-restraints excluded: chain A residue 1305 PHE Chi-restraints excluded: chain A residue 1313 THR Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 34 TYR Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 105 PHE Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain B residue 224 MET Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 288 SER Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 340 PHE Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 378 SER Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 418 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 1 optimal weight: 10.0000 chunk 83 optimal weight: 5.9990 chunk 62 optimal weight: 0.4980 chunk 19 optimal weight: 0.0270 chunk 27 optimal weight: 0.8980 chunk 17 optimal weight: 7.9990 chunk 43 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 overall best weight: 1.2842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 205 HIS ** 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 = 0.3859 r_free = 0.3859 target = 0.096495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.075685 restraints weight = 20710.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.078903 restraints weight = 11381.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.081140 restraints weight = 7408.164| |-----------------------------------------------------------------------------| r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6916 moved from start: 0.4327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6992 Z= 0.204 Angle : 0.694 10.530 9512 Z= 0.358 Chirality : 0.045 0.146 1054 Planarity : 0.006 0.121 1219 Dihedral : 6.260 64.012 949 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 16.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.09 % Favored : 89.91 % Rotamer: Outliers : 3.66 % Allowed : 24.41 % Favored : 71.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.76 % Cis-general : 0.00 % Twisted Proline : 4.88 % 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: -3.44 (0.26), residues: 862 helix: -1.67 (0.64), residues: 58 sheet: -2.17 (0.31), residues: 247 loop : -2.52 (0.24), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 955 HIS 0.002 0.001 HIS B 411 PHE 0.030 0.002 PHE C 127 TYR 0.016 0.002 TYR A1150 ARG 0.011 0.001 ARG B 364 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 89 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 939 MET cc_start: 0.8969 (mtm) cc_final: 0.8442 (tmm) REVERT: A 1012 ARG cc_start: 0.8634 (mmt-90) cc_final: 0.8280 (mmp80) REVERT: A 1047 TYR cc_start: 0.8076 (m-80) cc_final: 0.7571 (m-80) REVERT: A 1053 MET cc_start: 0.6852 (mmt) cc_final: 0.6534 (mmt) REVERT: A 1236 LEU cc_start: 0.8840 (pp) cc_final: 0.8244 (tt) REVERT: A 1239 LYS cc_start: 0.7695 (tptt) cc_final: 0.7322 (mptt) REVERT: A 1240 MET cc_start: 0.8770 (mpp) cc_final: 0.7900 (mpp) REVERT: B 256 TRP cc_start: 0.7229 (m100) cc_final: 0.6835 (m100) REVERT: B 299 MET cc_start: 0.8554 (mpp) cc_final: 0.8188 (mmt) REVERT: B 417 GLU cc_start: 0.4963 (pm20) cc_final: 0.4399 (pm20) REVERT: B 432 ASN cc_start: 0.8798 (t0) cc_final: 0.8280 (p0) outliers start: 28 outliers final: 27 residues processed: 109 average time/residue: 0.1470 time to fit residues: 23.5354 Evaluate side-chains 112 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 85 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 891 ILE Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1033 PHE Chi-restraints excluded: chain A residue 1046 LEU Chi-restraints excluded: chain A residue 1091 ILE Chi-restraints excluded: chain A residue 1130 LEU Chi-restraints excluded: chain A residue 1268 VAL Chi-restraints excluded: chain A residue 1305 PHE Chi-restraints excluded: chain A residue 1313 THR Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 34 TYR Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 105 PHE Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain B residue 224 MET Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 288 SER Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 340 PHE Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 378 SER Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 418 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 6 optimal weight: 10.0000 chunk 71 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 84 optimal weight: 20.0000 chunk 60 optimal weight: 0.0870 chunk 67 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 72 optimal weight: 9.9990 chunk 36 optimal weight: 10.0000 overall best weight: 2.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 ASN ** C 205 HIS ** 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 = 0.3798 r_free = 0.3798 target = 0.093150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.072738 restraints weight = 21021.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.075776 restraints weight = 11684.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.077954 restraints weight = 7665.548| |-----------------------------------------------------------------------------| r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6989 moved from start: 0.4337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 6992 Z= 0.294 Angle : 0.747 10.932 9512 Z= 0.386 Chirality : 0.047 0.174 1054 Planarity : 0.006 0.122 1219 Dihedral : 6.652 64.668 949 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 22.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.18 % Favored : 87.82 % Rotamer: Outliers : 4.18 % Allowed : 25.07 % Favored : 70.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.76 % Cis-general : 0.00 % Twisted Proline : 2.44 % 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: -3.53 (0.26), residues: 862 helix: -1.86 (0.62), residues: 57 sheet: -2.29 (0.31), residues: 247 loop : -2.54 (0.24), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 955 HIS 0.003 0.001 HIS B 411 PHE 0.029 0.002 PHE C 127 TYR 0.021 0.002 TYR A1150 ARG 0.010 0.001 ARG B 364 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2531.20 seconds wall clock time: 44 minutes 48.88 seconds (2688.88 seconds total)