Starting phenix.real_space_refine on Fri Jul 25 02:20:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7oh0_12890/07_2025/7oh0_12890.cif Found real_map, /net/cci-nas-00/data/ceres_data/7oh0_12890/07_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_12890/07_2025/7oh0_12890.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7oh0_12890/07_2025/7oh0_12890.map" model { file = "/net/cci-nas-00/data/ceres_data/7oh0_12890/07_2025/7oh0_12890.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7oh0_12890/07_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-5711/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: 4.84, per 1000 atoms: 0.71 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: 1.71 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.94 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: 2.22 Time building geometry restraints manager: 2.09 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: 2.490 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: 0.070 Process input model: 21.120 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.160 ------------------------------------------------------------------------------- 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 6997 Z= 0.246 Angle : 0.917 8.499 9522 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 Details of bonding type rmsd hydrogen bonds : bond 0.29257 ( 136) hydrogen bonds : angle 12.75479 ( 321) SS BOND : bond 0.00581 ( 5) SS BOND : angle 1.44133 ( 10) covalent geometry : bond 0.00470 ( 6992) covalent geometry : angle 0.91614 ( 9512) *********************** 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 : 0.733 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: 0.1955 time to fit residues: 32.3498 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 : 0.719 ------------------------------------------------------------------------------- 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: 5.9990 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: 2.9588 ------------------------------------------------------------------------------- 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 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 227 GLN B 259 GLN ** B 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 432 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.091428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.072772 restraints weight = 20744.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.075624 restraints weight = 11498.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.077636 restraints weight = 7501.862| |-----------------------------------------------------------------------------| r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 6997 Z= 0.243 Angle : 0.784 10.096 9522 Z= 0.415 Chirality : 0.049 0.161 1054 Planarity : 0.007 0.115 1219 Dihedral : 7.526 64.988 949 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 24.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.85 % Favored : 85.15 % Rotamer: Outliers : 3.92 % Allowed : 14.62 % Favored : 81.46 % 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: -4.85 (0.24), residues: 862 helix: -2.69 (0.56), residues: 48 sheet: -3.02 (0.28), residues: 244 loop : -3.58 (0.22), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 955 HIS 0.004 0.001 HIS C 205 PHE 0.037 0.003 PHE C 127 TYR 0.022 0.003 TYR C 34 ARG 0.010 0.001 ARG A1246 Details of bonding type rmsd hydrogen bonds : bond 0.05035 ( 136) hydrogen bonds : angle 9.47121 ( 321) SS BOND : bond 0.00400 ( 5) SS BOND : angle 1.91448 ( 10) covalent geometry : bond 0.00539 ( 6992) covalent geometry : angle 0.78183 ( 9512) *********************** 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 128 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 98 time to evaluate : 1.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1070 ILE cc_start: 0.8946 (mm) cc_final: 0.8725 (mp) REVERT: A 1239 LYS cc_start: 0.7837 (tptt) cc_final: 0.7408 (mptt) REVERT: A 1240 MET cc_start: 0.8853 (mpp) cc_final: 0.7940 (mpp) REVERT: A 1305 PHE cc_start: 0.6977 (OUTLIER) cc_final: 0.6497 (m-10) REVERT: C 204 ASN cc_start: 0.8110 (t0) cc_final: 0.7697 (t0) REVERT: B 225 MET cc_start: 0.5608 (pmm) cc_final: 0.5111 (tpt) REVERT: B 358 LEU cc_start: 0.3955 (OUTLIER) cc_final: 0.3684 (pp) REVERT: B 365 GLU cc_start: 0.8234 (mp0) cc_final: 0.7785 (pm20) REVERT: B 432 ASN cc_start: 0.8825 (t0) cc_final: 0.8372 (p0) outliers start: 30 outliers final: 17 residues processed: 119 average time/residue: 0.2083 time to fit residues: 35.0163 Evaluate side-chains 101 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 82 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 914 LEU 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 290 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: 6.9990 chunk 26 optimal weight: 1.9990 chunk 1 optimal weight: 9.9990 chunk 25 optimal weight: 0.0060 chunk 71 optimal weight: 9.9990 chunk 85 optimal weight: 7.9990 chunk 49 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 28 optimal weight: 0.8980 chunk 30 optimal weight: 9.9990 overall best weight: 2.3802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 972 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1078 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 311 GLN ** B 377 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 = 0.3822 r_free = 0.3822 target = 0.092879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.073861 restraints weight = 21102.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.076728 restraints weight = 11835.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.078737 restraints weight = 7807.141| |-----------------------------------------------------------------------------| r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7083 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 6997 Z= 0.203 Angle : 0.744 9.164 9522 Z= 0.390 Chirality : 0.048 0.173 1054 Planarity : 0.007 0.125 1219 Dihedral : 7.270 64.967 949 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 23.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.30 % Favored : 87.70 % Rotamer: Outliers : 5.09 % Allowed : 16.32 % Favored : 78.59 % 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: -4.64 (0.24), residues: 862 helix: -2.51 (0.55), residues: 56 sheet: -3.01 (0.28), residues: 256 loop : -3.34 (0.23), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 955 HIS 0.003 0.001 HIS C 205 PHE 0.029 0.002 PHE C 127 TYR 0.020 0.002 TYR A1026 ARG 0.012 0.001 ARG B 364 Details of bonding type rmsd hydrogen bonds : bond 0.04332 ( 136) hydrogen bonds : angle 8.70801 ( 321) SS BOND : bond 0.00462 ( 5) SS BOND : angle 1.29670 ( 10) covalent geometry : bond 0.00450 ( 6992) covalent geometry : angle 0.74310 ( 9512) *********************** 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 131 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 92 time to evaluate : 0.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1047 TYR cc_start: 0.8214 (m-80) cc_final: 0.7807 (m-80) REVERT: A 1053 MET cc_start: 0.6881 (mmt) cc_final: 0.6509 (mmt) REVERT: A 1070 ILE cc_start: 0.8928 (mm) cc_final: 0.8707 (mp) REVERT: A 1100 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.6965 (pm20) REVERT: A 1117 PHE cc_start: 0.7749 (t80) cc_final: 0.7121 (t80) REVERT: A 1131 ILE cc_start: 0.8540 (OUTLIER) cc_final: 0.8257 (mt) REVERT: A 1239 LYS cc_start: 0.7885 (tptt) cc_final: 0.7480 (mptt) REVERT: A 1240 MET cc_start: 0.8913 (mpp) cc_final: 0.8036 (mpp) REVERT: A 1305 PHE cc_start: 0.6971 (OUTLIER) cc_final: 0.6489 (m-10) REVERT: C 204 ASN cc_start: 0.8200 (t0) cc_final: 0.7850 (t0) REVERT: B 225 MET cc_start: 0.5515 (pmm) cc_final: 0.4842 (tpt) REVERT: B 254 LEU cc_start: 0.7476 (OUTLIER) cc_final: 0.7212 (pp) REVERT: B 257 TYR cc_start: 0.7385 (m-80) cc_final: 0.7169 (m-80) REVERT: B 358 LEU cc_start: 0.3829 (OUTLIER) cc_final: 0.3552 (pp) REVERT: B 365 GLU cc_start: 0.7778 (mp0) cc_final: 0.7494 (pm20) REVERT: B 432 ASN cc_start: 0.8852 (t0) cc_final: 0.8244 (p0) outliers start: 39 outliers final: 23 residues processed: 122 average time/residue: 0.1559 time to fit residues: 26.8142 Evaluate side-chains 108 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 80 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 1100 GLU Chi-restraints excluded: chain A residue 1130 LEU Chi-restraints excluded: chain A residue 1131 ILE 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 20 LEU 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 82 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 327 GLU Chi-restraints excluded: chain B residue 340 PHE Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 358 LEU 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: 3.9990 chunk 35 optimal weight: 6.9990 chunk 72 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 75 optimal weight: 7.9990 chunk 3 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 18 optimal weight: 8.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 919 ASN A 928 ASN ** A 972 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1078 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 377 GLN ** 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 = 0.3786 r_free = 0.3786 target = 0.090835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.071949 restraints weight = 21561.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.074734 restraints weight = 12135.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.076720 restraints weight = 8018.971| |-----------------------------------------------------------------------------| r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 6997 Z= 0.238 Angle : 0.761 10.859 9522 Z= 0.399 Chirality : 0.048 0.167 1054 Planarity : 0.007 0.133 1219 Dihedral : 7.331 64.695 949 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 24.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.27 % Favored : 85.73 % Rotamer: Outliers : 5.61 % Allowed : 19.71 % Favored : 74.67 % 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: -4.50 (0.25), residues: 862 helix: -2.38 (0.58), residues: 56 sheet: -2.89 (0.29), residues: 257 loop : -3.27 (0.23), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 955 HIS 0.003 0.001 HIS C 205 PHE 0.027 0.002 PHE C 127 TYR 0.026 0.002 TYR C 34 ARG 0.003 0.001 ARG A1281 Details of bonding type rmsd hydrogen bonds : bond 0.04184 ( 136) hydrogen bonds : angle 8.48627 ( 321) SS BOND : bond 0.00331 ( 5) SS BOND : angle 1.25586 ( 10) covalent geometry : bond 0.00528 ( 6992) covalent geometry : angle 0.76074 ( 9512) *********************** 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 127 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 84 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1053 MET cc_start: 0.7082 (mmt) cc_final: 0.6786 (mmt) REVERT: A 1070 ILE cc_start: 0.8969 (mm) cc_final: 0.8740 (mp) REVERT: A 1100 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.6682 (pm20) REVERT: A 1131 ILE cc_start: 0.8543 (OUTLIER) cc_final: 0.8309 (mt) REVERT: A 1239 LYS cc_start: 0.7942 (tptt) cc_final: 0.7561 (mptt) REVERT: A 1240 MET cc_start: 0.8950 (mpp) cc_final: 0.8095 (mpp) REVERT: A 1305 PHE cc_start: 0.7101 (OUTLIER) cc_final: 0.6613 (m-10) REVERT: C 20 LEU cc_start: 0.8031 (OUTLIER) cc_final: 0.7750 (mp) REVERT: C 204 ASN cc_start: 0.8300 (t0) cc_final: 0.8054 (t0) REVERT: B 225 MET cc_start: 0.5809 (pmm) cc_final: 0.4665 (tpt) REVERT: B 254 LEU cc_start: 0.7689 (OUTLIER) cc_final: 0.7463 (pp) REVERT: B 365 GLU cc_start: 0.7971 (mp0) cc_final: 0.7673 (pm20) REVERT: B 432 ASN cc_start: 0.8836 (t0) cc_final: 0.8381 (p0) outliers start: 43 outliers final: 29 residues processed: 119 average time/residue: 0.1786 time to fit residues: 30.4135 Evaluate side-chains 110 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 76 time to evaluate : 0.767 ------------------------------------------------------------------------------- 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 1011 VAL 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 1131 ILE Chi-restraints excluded: chain A residue 1169 LEU Chi-restraints excluded: chain A residue 1186 ILE Chi-restraints excluded: chain A residue 1214 ASP Chi-restraints excluded: chain A residue 1250 THR 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 20 LEU 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 70 THR Chi-restraints excluded: chain C residue 82 LEU 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 238 GLU 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 340 PHE Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 378 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 26 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 60 optimal weight: 0.3980 chunk 66 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 5 optimal weight: 7.9990 chunk 84 optimal weight: 9.9990 chunk 27 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 59 optimal weight: 8.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 972 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 999 ASN ** A1078 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1293 HIS C 103 ASN ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.094912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.075508 restraints weight = 20815.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.078465 restraints weight = 11623.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.080549 restraints weight = 7653.800| |-----------------------------------------------------------------------------| r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7058 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6997 Z= 0.138 Angle : 0.684 11.389 9522 Z= 0.356 Chirality : 0.046 0.186 1054 Planarity : 0.006 0.134 1219 Dihedral : 6.747 63.271 949 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 19.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.32 % Favored : 89.68 % Rotamer: Outliers : 4.57 % Allowed : 22.98 % Favored : 72.45 % 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: -4.17 (0.25), residues: 862 helix: -1.74 (0.68), residues: 50 sheet: -3.01 (0.29), residues: 245 loop : -2.89 (0.23), residues: 567 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 0.022 0.002 PHE C 127 TYR 0.017 0.002 TYR A1026 ARG 0.003 0.000 ARG B 275 Details of bonding type rmsd hydrogen bonds : bond 0.03553 ( 136) hydrogen bonds : angle 7.81869 ( 321) SS BOND : bond 0.00116 ( 5) SS BOND : angle 0.86145 ( 10) covalent geometry : bond 0.00311 ( 6992) covalent geometry : angle 0.68416 ( 9512) *********************** 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 127 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 92 time to evaluate : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1047 TYR cc_start: 0.8045 (m-80) cc_final: 0.7788 (m-80) REVERT: A 1053 MET cc_start: 0.7069 (mmt) cc_final: 0.6805 (mmt) REVERT: A 1131 ILE cc_start: 0.8484 (OUTLIER) cc_final: 0.8210 (mt) REVERT: A 1239 LYS cc_start: 0.7951 (tptt) cc_final: 0.7576 (mptt) REVERT: A 1240 MET cc_start: 0.8792 (mpp) cc_final: 0.8088 (mpp) REVERT: A 1305 PHE cc_start: 0.6789 (OUTLIER) cc_final: 0.6389 (m-10) REVERT: C 16 GLU cc_start: 0.8129 (tt0) cc_final: 0.7562 (tm-30) REVERT: C 55 TYR cc_start: 0.3325 (p90) cc_final: 0.2956 (p90) REVERT: C 204 ASN cc_start: 0.8283 (t0) cc_final: 0.7938 (t0) REVERT: B 225 MET cc_start: 0.5421 (pmm) cc_final: 0.4583 (tpt) REVERT: B 254 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7541 (pp) REVERT: B 358 LEU cc_start: 0.4261 (OUTLIER) cc_final: 0.4029 (pp) REVERT: B 365 GLU cc_start: 0.7948 (mp0) cc_final: 0.7643 (pm20) REVERT: B 432 ASN cc_start: 0.8815 (t0) cc_final: 0.8357 (p0) outliers start: 35 outliers final: 20 residues processed: 122 average time/residue: 0.1813 time to fit residues: 31.6939 Evaluate side-chains 107 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 83 time to evaluate : 1.132 ------------------------------------------------------------------------------- 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 1015 THR 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 1131 ILE 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 70 THR Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain B residue 254 LEU 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 358 LEU 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: 5.9990 chunk 53 optimal weight: 0.9990 chunk 81 optimal weight: 5.9990 chunk 60 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 75 optimal weight: 4.9990 chunk 85 optimal weight: 10.0000 chunk 25 optimal weight: 0.0060 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 972 ASN A 999 ASN A1078 ASN ** A1254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 ASN C 202 ASN ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.097991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.078208 restraints weight = 20616.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.081295 restraints weight = 11464.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.083427 restraints weight = 7496.870| |-----------------------------------------------------------------------------| r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6960 moved from start: 0.3597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6997 Z= 0.118 Angle : 0.662 11.553 9522 Z= 0.341 Chirality : 0.045 0.167 1054 Planarity : 0.006 0.132 1219 Dihedral : 6.313 62.766 949 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 16.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.51 % Favored : 90.49 % Rotamer: Outliers : 4.96 % Allowed : 22.06 % Favored : 72.98 % 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: -3.66 (0.26), residues: 862 helix: -1.54 (0.68), residues: 51 sheet: -2.35 (0.32), residues: 229 loop : -2.71 (0.23), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 955 HIS 0.003 0.001 HIS C 205 PHE 0.022 0.002 PHE A1089 TYR 0.016 0.001 TYR A1026 ARG 0.005 0.000 ARG B 275 Details of bonding type rmsd hydrogen bonds : bond 0.03380 ( 136) hydrogen bonds : angle 7.30890 ( 321) SS BOND : bond 0.00455 ( 5) SS BOND : angle 0.72594 ( 10) covalent geometry : bond 0.00262 ( 6992) covalent geometry : angle 0.66201 ( 9512) *********************** 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 143 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 105 time to evaluate : 0.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 903 ASN cc_start: 0.8075 (p0) cc_final: 0.7869 (p0) REVERT: A 1053 MET cc_start: 0.6891 (mmt) cc_final: 0.6638 (mmt) REVERT: A 1236 LEU cc_start: 0.8825 (pp) cc_final: 0.8238 (tt) REVERT: A 1239 LYS cc_start: 0.7854 (tptt) cc_final: 0.7541 (mptt) REVERT: A 1240 MET cc_start: 0.8719 (mpp) cc_final: 0.8330 (mpp) REVERT: C 16 GLU cc_start: 0.8202 (tt0) cc_final: 0.7608 (tm-30) REVERT: C 20 LEU cc_start: 0.8045 (OUTLIER) cc_final: 0.7768 (mp) REVERT: C 55 TYR cc_start: 0.3415 (p90) cc_final: 0.3039 (p90) REVERT: C 78 ASN cc_start: 0.6689 (t0) cc_final: 0.6146 (m-40) REVERT: C 176 GLN cc_start: 0.8757 (mm-40) cc_final: 0.8438 (mp10) REVERT: C 204 ASN cc_start: 0.8316 (t0) cc_final: 0.8025 (t0) REVERT: B 225 MET cc_start: 0.5457 (pmm) cc_final: 0.4669 (tpt) REVERT: B 254 LEU cc_start: 0.7728 (OUTLIER) cc_final: 0.7375 (pp) REVERT: B 354 VAL cc_start: 0.8256 (OUTLIER) cc_final: 0.8032 (t) REVERT: B 365 GLU cc_start: 0.7913 (mp0) cc_final: 0.7700 (pm20) REVERT: B 432 ASN cc_start: 0.8753 (t0) cc_final: 0.8254 (p0) outliers start: 38 outliers final: 19 residues processed: 134 average time/residue: 0.1851 time to fit residues: 36.4238 Evaluate side-chains 111 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 89 time to evaluate : 0.922 ------------------------------------------------------------------------------- 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 1046 LEU Chi-restraints excluded: chain A residue 1057 GLU Chi-restraints excluded: chain A residue 1130 LEU 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 20 LEU 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 70 THR Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain B residue 254 LEU 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 354 VAL 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: 0.8980 chunk 0 optimal weight: 10.0000 chunk 82 optimal weight: 5.9990 chunk 6 optimal weight: 0.0970 chunk 53 optimal weight: 0.0270 chunk 63 optimal weight: 0.8980 chunk 84 optimal weight: 0.8980 chunk 9 optimal weight: 7.9990 chunk 72 optimal weight: 9.9990 chunk 65 optimal weight: 0.9980 chunk 76 optimal weight: 4.9990 overall best weight: 0.5636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 999 ASN A1216 ASN C 103 ASN ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 311 GLN ** B 377 GLN ** 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 = 0.3939 r_free = 0.3939 target = 0.099860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.080049 restraints weight = 20155.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.083264 restraints weight = 11096.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.085497 restraints weight = 7207.168| |-----------------------------------------------------------------------------| r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6937 moved from start: 0.4014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6997 Z= 0.113 Angle : 0.668 11.279 9522 Z= 0.340 Chirality : 0.045 0.148 1054 Planarity : 0.006 0.126 1219 Dihedral : 6.096 63.088 949 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 15.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 4.18 % Allowed : 23.76 % 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: -3.39 (0.26), residues: 862 helix: -1.37 (0.68), residues: 51 sheet: -2.22 (0.32), residues: 223 loop : -2.48 (0.24), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 955 HIS 0.003 0.001 HIS C 205 PHE 0.035 0.002 PHE B 340 TYR 0.015 0.001 TYR A1026 ARG 0.004 0.000 ARG B 275 Details of bonding type rmsd hydrogen bonds : bond 0.03286 ( 136) hydrogen bonds : angle 6.98499 ( 321) SS BOND : bond 0.00092 ( 5) SS BOND : angle 0.64034 ( 10) covalent geometry : bond 0.00257 ( 6992) covalent geometry : angle 0.66770 ( 9512) *********************** 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 133 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 101 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 903 ASN cc_start: 0.8022 (p0) cc_final: 0.7814 (p0) REVERT: A 1033 PHE cc_start: 0.7601 (OUTLIER) cc_final: 0.6693 (t80) REVERT: A 1047 TYR cc_start: 0.7653 (m-80) cc_final: 0.7430 (m-80) REVERT: A 1236 LEU cc_start: 0.8791 (pp) cc_final: 0.8263 (tt) REVERT: A 1239 LYS cc_start: 0.7878 (tptt) cc_final: 0.6775 (mptt) REVERT: C 78 ASN cc_start: 0.6826 (t0) cc_final: 0.6505 (t0) REVERT: C 204 ASN cc_start: 0.8253 (t0) cc_final: 0.7994 (t0) REVERT: B 254 LEU cc_start: 0.7785 (OUTLIER) cc_final: 0.7388 (pp) REVERT: B 256 TRP cc_start: 0.7201 (m100) cc_final: 0.6886 (m100) REVERT: B 354 VAL cc_start: 0.8360 (t) cc_final: 0.8136 (t) REVERT: B 365 GLU cc_start: 0.7953 (mp0) cc_final: 0.7742 (pm20) REVERT: B 432 ASN cc_start: 0.8730 (t0) cc_final: 0.8274 (p0) outliers start: 32 outliers final: 22 residues processed: 126 average time/residue: 0.2586 time to fit residues: 48.1553 Evaluate side-chains 115 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 91 time to evaluate : 1.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 1057 GLU Chi-restraints excluded: chain A residue 1130 LEU Chi-restraints excluded: chain A residue 1216 ASN 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 70 THR Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain B residue 254 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 32 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 73 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 56 optimal weight: 0.8980 chunk 2 optimal weight: 7.9990 chunk 64 optimal weight: 10.0000 chunk 46 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 38 optimal weight: 9.9990 chunk 24 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 999 ASN C 52 ASN C 103 ASN C 176 GLN ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 377 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.099051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.079227 restraints weight = 20245.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.082369 restraints weight = 11240.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.084557 restraints weight = 7337.412| |-----------------------------------------------------------------------------| r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6954 moved from start: 0.4258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6997 Z= 0.120 Angle : 0.677 10.586 9522 Z= 0.342 Chirality : 0.045 0.143 1054 Planarity : 0.006 0.126 1219 Dihedral : 6.024 62.606 949 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 15.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.93 % Favored : 91.07 % Rotamer: Outliers : 4.31 % Allowed : 25.07 % Favored : 70.63 % 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: -3.21 (0.27), residues: 862 helix: -1.27 (0.69), residues: 51 sheet: -2.10 (0.31), residues: 243 loop : -2.34 (0.24), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 955 HIS 0.003 0.001 HIS C 205 PHE 0.041 0.002 PHE C 127 TYR 0.025 0.002 TYR C 55 ARG 0.003 0.000 ARG B 275 Details of bonding type rmsd hydrogen bonds : bond 0.03346 ( 136) hydrogen bonds : angle 7.02827 ( 321) SS BOND : bond 0.00165 ( 5) SS BOND : angle 0.55506 ( 10) covalent geometry : bond 0.00276 ( 6992) covalent geometry : angle 0.67680 ( 9512) *********************** 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 128 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 95 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 903 ASN cc_start: 0.8073 (p0) cc_final: 0.7866 (p0) REVERT: A 939 MET cc_start: 0.8918 (mtm) cc_final: 0.8448 (tmm) REVERT: A 1033 PHE cc_start: 0.7713 (OUTLIER) cc_final: 0.6652 (t80) REVERT: A 1047 TYR cc_start: 0.7873 (m-80) cc_final: 0.7334 (m-80) REVERT: A 1236 LEU cc_start: 0.8784 (pp) cc_final: 0.8128 (tt) REVERT: A 1239 LYS cc_start: 0.7920 (tptt) cc_final: 0.7393 (mptt) REVERT: C 78 ASN cc_start: 0.6834 (t0) cc_final: 0.6513 (t0) REVERT: C 204 ASN cc_start: 0.8266 (t0) cc_final: 0.8035 (t0) REVERT: B 254 LEU cc_start: 0.7659 (OUTLIER) cc_final: 0.7315 (pp) REVERT: B 256 TRP cc_start: 0.7219 (m100) cc_final: 0.6946 (m100) REVERT: B 432 ASN cc_start: 0.8735 (t0) cc_final: 0.8291 (p0) outliers start: 33 outliers final: 20 residues processed: 120 average time/residue: 0.2340 time to fit residues: 40.7420 Evaluate side-chains 113 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 91 time to evaluate : 0.707 ------------------------------------------------------------------------------- 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 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 70 THR Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain B residue 254 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 5 optimal weight: 0.6980 chunk 16 optimal weight: 6.9990 chunk 64 optimal weight: 5.9990 chunk 82 optimal weight: 10.0000 chunk 48 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- 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 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 = 0.3830 r_free = 0.3830 target = 0.095018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.074614 restraints weight = 20681.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.077701 restraints weight = 11494.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.079880 restraints weight = 7556.328| |-----------------------------------------------------------------------------| r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6965 moved from start: 0.4232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6997 Z= 0.175 Angle : 0.721 9.602 9522 Z= 0.370 Chirality : 0.046 0.150 1054 Planarity : 0.006 0.128 1219 Dihedral : 6.373 63.316 949 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 21.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.56 % Favored : 89.44 % Rotamer: Outliers : 3.79 % Allowed : 25.46 % Favored : 70.76 % 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: -3.48 (0.26), residues: 862 helix: -1.65 (0.64), residues: 57 sheet: -2.35 (0.30), residues: 246 loop : -2.47 (0.24), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP C 104 HIS 0.003 0.001 HIS C 205 PHE 0.033 0.002 PHE C 127 TYR 0.026 0.002 TYR C 55 ARG 0.002 0.000 ARG A1012 Details of bonding type rmsd hydrogen bonds : bond 0.03616 ( 136) hydrogen bonds : angle 7.23631 ( 321) SS BOND : bond 0.00314 ( 5) SS BOND : angle 0.79065 ( 10) covalent geometry : bond 0.00390 ( 6992) covalent geometry : angle 0.72113 ( 9512) *********************** 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 110 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 81 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 939 MET cc_start: 0.8963 (mtm) cc_final: 0.8413 (tmm) REVERT: A 1033 PHE cc_start: 0.7749 (OUTLIER) cc_final: 0.6667 (t80) REVERT: A 1236 LEU cc_start: 0.8828 (pp) cc_final: 0.8273 (tt) REVERT: A 1239 LYS cc_start: 0.7941 (tptt) cc_final: 0.7398 (mptt) REVERT: C 78 ASN cc_start: 0.6705 (t0) cc_final: 0.6254 (t0) REVERT: B 365 GLU cc_start: 0.8323 (mp0) cc_final: 0.7827 (pm20) REVERT: B 432 ASN cc_start: 0.8798 (t0) cc_final: 0.8344 (p0) outliers start: 29 outliers final: 22 residues processed: 105 average time/residue: 0.2168 time to fit residues: 34.2679 Evaluate side-chains 98 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 75 time to evaluate : 0.899 ------------------------------------------------------------------------------- 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 1033 PHE Chi-restraints excluded: chain A residue 1046 LEU Chi-restraints excluded: chain A residue 1130 LEU Chi-restraints excluded: chain A residue 1169 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 39 ILE Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain B residue 245 ARG 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 1 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 chunk 62 optimal weight: 10.0000 chunk 19 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 43 optimal weight: 5.9990 chunk 64 optimal weight: 7.9990 chunk 55 optimal weight: 0.0770 chunk 58 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 overall best weight: 1.7744 ------------------------------------------------------------------------------- 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 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 = 0.3839 r_free = 0.3839 target = 0.095558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.075026 restraints weight = 20855.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.078207 restraints weight = 11461.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.080468 restraints weight = 7487.878| |-----------------------------------------------------------------------------| r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6951 moved from start: 0.4358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6997 Z= 0.163 Angle : 0.721 9.614 9522 Z= 0.368 Chirality : 0.046 0.146 1054 Planarity : 0.006 0.128 1219 Dihedral : 6.356 63.704 949 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 20.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.74 % Favored : 90.26 % Rotamer: Outliers : 3.13 % Allowed : 26.50 % Favored : 70.37 % 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: -3.49 (0.26), residues: 862 helix: -1.65 (0.64), residues: 57 sheet: -2.24 (0.30), residues: 257 loop : -2.53 (0.24), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 104 HIS 0.002 0.001 HIS B 411 PHE 0.031 0.002 PHE C 127 TYR 0.030 0.002 TYR C 55 ARG 0.002 0.000 ARG A1246 Details of bonding type rmsd hydrogen bonds : bond 0.03467 ( 136) hydrogen bonds : angle 7.24386 ( 321) SS BOND : bond 0.00256 ( 5) SS BOND : angle 0.70772 ( 10) covalent geometry : bond 0.00366 ( 6992) covalent geometry : angle 0.72104 ( 9512) ********************** 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 105 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 81 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 939 MET cc_start: 0.8963 (mtm) cc_final: 0.8416 (tmm) REVERT: A 1012 ARG cc_start: 0.8633 (mmt-90) cc_final: 0.8251 (mmp80) REVERT: A 1033 PHE cc_start: 0.7832 (OUTLIER) cc_final: 0.6754 (t80) REVERT: A 1239 LYS cc_start: 0.7847 (tptt) cc_final: 0.7353 (mptt) REVERT: B 365 GLU cc_start: 0.8304 (mp0) cc_final: 0.7777 (pm20) REVERT: B 432 ASN cc_start: 0.8798 (t0) cc_final: 0.8341 (p0) outliers start: 24 outliers final: 21 residues processed: 101 average time/residue: 0.1744 time to fit residues: 25.5119 Evaluate side-chains 102 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 80 time to evaluate : 0.756 ------------------------------------------------------------------------------- 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 1033 PHE Chi-restraints excluded: chain A residue 1046 LEU Chi-restraints excluded: chain A residue 1130 LEU Chi-restraints excluded: chain A residue 1150 TYR 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 39 ILE Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain B residue 245 ARG 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 6 optimal weight: 8.9990 chunk 71 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 84 optimal weight: 5.9990 chunk 60 optimal weight: 0.1980 chunk 67 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 36 optimal weight: 0.2980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 5 GLN ** 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 = 0.3907 r_free = 0.3907 target = 0.099515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.078729 restraints weight = 20169.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.082176 restraints weight = 10851.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.084634 restraints weight = 6935.245| |-----------------------------------------------------------------------------| r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6825 moved from start: 0.4686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6997 Z= 0.116 Angle : 0.689 9.888 9522 Z= 0.347 Chirality : 0.045 0.139 1054 Planarity : 0.006 0.125 1219 Dihedral : 5.973 63.622 949 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 15.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 2.61 % Allowed : 27.42 % Favored : 69.97 % 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: -3.26 (0.26), residues: 862 helix: -1.45 (0.65), residues: 57 sheet: -1.99 (0.31), residues: 240 loop : -2.44 (0.24), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 104 HIS 0.002 0.001 HIS A1271 PHE 0.028 0.002 PHE C 127 TYR 0.028 0.002 TYR C 55 ARG 0.003 0.000 ARG B 275 Details of bonding type rmsd hydrogen bonds : bond 0.03241 ( 136) hydrogen bonds : angle 6.87565 ( 321) SS BOND : bond 0.00163 ( 5) SS BOND : angle 0.50775 ( 10) covalent geometry : bond 0.00264 ( 6992) covalent geometry : angle 0.68946 ( 9512) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3217.53 seconds wall clock time: 61 minutes 39.31 seconds (3699.31 seconds total)