Starting phenix.real_space_refine on Tue Mar 3 16:13:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7oh0_12890/03_2026/7oh0_12890.cif Found real_map, /net/cci-nas-00/data/ceres_data/7oh0_12890/03_2026/7oh0_12890.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7oh0_12890/03_2026/7oh0_12890.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7oh0_12890/03_2026/7oh0_12890.map" model { file = "/net/cci-nas-00/data/ceres_data/7oh0_12890/03_2026/7oh0_12890.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7oh0_12890/03_2026/7oh0_12890.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 1.52, per 1000 atoms: 0.22 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: 0.61 Conformation dependent library (CDL) restraints added in 210.1 milliseconds 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1624 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 21 sheets defined 8.2% alpha, 25.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 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: 1.17 Time building geometry restraints manager: 0.81 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: 2.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.270 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.090 ------------------------------------------------------------------------------- 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 : 29.20 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.003 0.000 ARG B 433 TYR 0.017 0.002 TYR C 181 PHE 0.019 0.002 PHE B 320 TRP 0.021 0.002 TRP A 955 HIS 0.003 0.001 HIS C 169 Details of bonding type rmsd covalent geometry : bond 0.00470 ( 6992) covalent geometry : angle 0.91614 ( 9512) SS BOND : bond 0.00581 ( 5) SS BOND : angle 1.44133 ( 10) hydrogen bonds : bond 0.29257 ( 136) hydrogen bonds : angle 12.75479 ( 321) *********************** 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 : 0.251 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: 0.7110 (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: 0.0787 time to fit residues: 13.0738 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 : 0.241 ------------------------------------------------------------------------------- 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 49 optimal weight: 0.1980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 0.0870 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 9.9990 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 7.9990 chunk 74 optimal weight: 0.2980 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 919 ASN 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** A1292 ASN ** A1293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 ASN C 202 ASN ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 227 GLN B 259 GLN B 377 GLN B 432 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.099061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.079842 restraints weight = 20473.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.083041 restraints weight = 11190.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.085261 restraints weight = 7211.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.086840 restraints weight = 5180.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.087939 restraints weight = 4035.840| |-----------------------------------------------------------------------------| r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6849 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6997 Z= 0.130 Angle : 0.698 8.533 9522 Z= 0.366 Chirality : 0.046 0.157 1054 Planarity : 0.006 0.102 1219 Dihedral : 6.769 63.412 949 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 17.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.51 % Favored : 90.49 % Rotamer: Outliers : 2.87 % Allowed : 13.97 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.76 % Cis-general : 0.00 % Twisted Proline : 4.88 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.68 (0.23), residues: 862 helix: -2.41 (0.60), residues: 49 sheet: -3.06 (0.27), residues: 247 loop : -3.39 (0.22), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1246 TYR 0.016 0.002 TYR C 54 PHE 0.038 0.002 PHE C 127 TRP 0.022 0.002 TRP A 955 HIS 0.003 0.001 HIS C 205 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 6992) covalent geometry : angle 0.69694 ( 9512) SS BOND : bond 0.00238 ( 5) SS BOND : angle 1.42286 ( 10) hydrogen bonds : bond 0.04349 ( 136) hydrogen bonds : angle 8.93350 ( 321) *********************** 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 141 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 119 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1026 TYR cc_start: 0.7624 (m-10) cc_final: 0.7421 (m-10) REVERT: A 1047 TYR cc_start: 0.8113 (m-80) cc_final: 0.7655 (m-80) REVERT: A 1053 MET cc_start: 0.7202 (mmt) cc_final: 0.6929 (mmt) REVERT: A 1239 LYS cc_start: 0.7708 (tptt) cc_final: 0.7394 (mptt) REVERT: C 176 GLN cc_start: 0.8663 (mm-40) cc_final: 0.8314 (mp10) REVERT: C 202 ASN cc_start: 0.6892 (m110) cc_final: 0.6419 (m110) REVERT: C 204 ASN cc_start: 0.7911 (t0) cc_final: 0.7526 (t0) REVERT: B 256 TRP cc_start: 0.7072 (m100) cc_final: 0.6806 (m100) REVERT: B 299 MET cc_start: 0.7785 (mtm) cc_final: 0.7205 (mtm) REVERT: B 358 LEU cc_start: 0.3394 (OUTLIER) cc_final: 0.3141 (pp) REVERT: B 365 GLU cc_start: 0.8130 (mp0) cc_final: 0.7860 (mp0) REVERT: B 432 ASN cc_start: 0.8759 (t0) cc_final: 0.8297 (p0) outliers start: 22 outliers final: 9 residues processed: 135 average time/residue: 0.0593 time to fit residues: 11.6743 Evaluate side-chains 100 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1046 LEU Chi-restraints excluded: chain A residue 1057 GLU Chi-restraints excluded: chain A residue 1130 LEU Chi-restraints excluded: chain A residue 1268 VAL Chi-restraints excluded: chain A residue 1313 THR Chi-restraints excluded: chain C residue 34 TYR Chi-restraints excluded: chain C residue 59 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 75 optimal weight: 6.9990 chunk 17 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 chunk 67 optimal weight: 10.0000 chunk 36 optimal weight: 8.9990 chunk 83 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 22 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 chunk 74 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 928 ASN ** A 972 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1078 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1163 ASN ** A1293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 311 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.090809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.070777 restraints weight = 21455.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.073704 restraints weight = 11908.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.075775 restraints weight = 7847.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.077260 restraints weight = 5773.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.078328 restraints weight = 4581.448| |-----------------------------------------------------------------------------| r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6984 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 6997 Z= 0.269 Angle : 0.805 10.213 9522 Z= 0.421 Chirality : 0.049 0.181 1054 Planarity : 0.007 0.119 1219 Dihedral : 7.381 65.191 949 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 26.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.34 % Favored : 86.66 % Rotamer: Outliers : 5.09 % Allowed : 16.06 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.76 % Cis-general : 0.00 % Twisted Proline : 4.88 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.52 (0.24), residues: 862 helix: -2.59 (0.55), residues: 56 sheet: -2.84 (0.31), residues: 234 loop : -3.31 (0.22), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1246 TYR 0.027 0.002 TYR C 34 PHE 0.025 0.003 PHE C 127 TRP 0.026 0.003 TRP A 955 HIS 0.004 0.001 HIS C 205 Details of bonding type rmsd covalent geometry : bond 0.00600 ( 6992) covalent geometry : angle 0.80341 ( 9512) SS BOND : bond 0.00305 ( 5) SS BOND : angle 1.54590 ( 10) hydrogen bonds : bond 0.04727 ( 136) hydrogen bonds : angle 8.78424 ( 321) *********************** 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 124 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 85 time to evaluate : 0.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1039 ASP cc_start: 0.8394 (t70) cc_final: 0.8156 (t70) REVERT: A 1239 LYS cc_start: 0.7779 (tptt) cc_final: 0.7105 (mptt) REVERT: A 1305 PHE cc_start: 0.7021 (OUTLIER) cc_final: 0.6610 (m-10) REVERT: C 78 ASN cc_start: 0.7454 (OUTLIER) cc_final: 0.7041 (t0) REVERT: C 204 ASN cc_start: 0.8075 (t0) cc_final: 0.7780 (t0) REVERT: B 254 LEU cc_start: 0.7309 (OUTLIER) cc_final: 0.7053 (pp) REVERT: B 365 GLU cc_start: 0.7903 (mp0) cc_final: 0.7610 (pm20) REVERT: B 432 ASN cc_start: 0.8848 (t0) cc_final: 0.8285 (p0) outliers start: 39 outliers final: 27 residues processed: 116 average time/residue: 0.0682 time to fit residues: 11.2963 Evaluate side-chains 106 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 76 time to evaluate : 0.296 ------------------------------------------------------------------------------- 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 1046 LEU Chi-restraints excluded: chain A residue 1057 GLU Chi-restraints excluded: chain A residue 1091 ILE 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 20 LEU 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 53 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 78 ASN 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 254 LEU Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 327 GLU Chi-restraints excluded: chain B residue 340 PHE Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 418 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 50 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 3 optimal weight: 7.9990 chunk 35 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 30 optimal weight: 7.9990 chunk 19 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 83 optimal weight: 10.0000 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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** ** A1293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 ASN ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.096092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.075449 restraints weight = 20725.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.078763 restraints weight = 11252.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.081051 restraints weight = 7247.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.082669 restraints weight = 5239.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.083847 restraints weight = 4104.524| |-----------------------------------------------------------------------------| r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6863 moved from start: 0.2901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6997 Z= 0.140 Angle : 0.687 9.836 9522 Z= 0.357 Chirality : 0.046 0.150 1054 Planarity : 0.006 0.120 1219 Dihedral : 6.632 64.257 949 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 18.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.16 % Favored : 90.84 % Rotamer: Outliers : 4.96 % Allowed : 18.28 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.76 % Cis-general : 0.00 % Twisted Proline : 4.88 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.09 (0.25), residues: 862 helix: -1.73 (0.68), residues: 49 sheet: -2.74 (0.32), residues: 219 loop : -2.98 (0.22), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1246 TYR 0.015 0.002 TYR A1026 PHE 0.022 0.002 PHE C 127 TRP 0.024 0.002 TRP A 955 HIS 0.003 0.001 HIS C 205 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 6992) covalent geometry : angle 0.68680 ( 9512) SS BOND : bond 0.00124 ( 5) SS BOND : angle 0.88682 ( 10) hydrogen bonds : bond 0.03658 ( 136) hydrogen bonds : angle 7.88451 ( 321) *********************** 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 136 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 98 time to evaluate : 0.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1047 TYR cc_start: 0.8326 (m-80) cc_final: 0.8115 (m-80) REVERT: A 1053 MET cc_start: 0.6467 (mmt) cc_final: 0.6076 (mmt) REVERT: A 1131 ILE cc_start: 0.8255 (OUTLIER) cc_final: 0.8009 (mt) REVERT: A 1239 LYS cc_start: 0.7820 (tptt) cc_final: 0.7282 (mptt) REVERT: A 1240 MET cc_start: 0.8728 (mpp) cc_final: 0.7766 (mpp) REVERT: A 1305 PHE cc_start: 0.6808 (OUTLIER) cc_final: 0.6424 (m-10) REVERT: C 176 GLN cc_start: 0.8814 (mm-40) cc_final: 0.8383 (mp10) REVERT: C 204 ASN cc_start: 0.8144 (t0) cc_final: 0.7921 (t0) REVERT: B 365 GLU cc_start: 0.7906 (mp0) cc_final: 0.7582 (pm20) REVERT: B 414 TYR cc_start: 0.8638 (m-80) cc_final: 0.8330 (m-80) REVERT: B 432 ASN cc_start: 0.8821 (t0) cc_final: 0.8321 (p0) outliers start: 38 outliers final: 20 residues processed: 129 average time/residue: 0.0566 time to fit residues: 10.5102 Evaluate side-chains 103 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 81 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 1091 ILE Chi-restraints excluded: chain A residue 1130 LEU Chi-restraints excluded: chain A residue 1131 ILE Chi-restraints excluded: chain A residue 1186 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 24 VAL Chi-restraints excluded: chain C residue 34 TYR Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 59 THR 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 290 THR Chi-restraints excluded: chain B residue 340 PHE Chi-restraints excluded: chain B residue 351 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 5 optimal weight: 0.0570 chunk 43 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 chunk 25 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 63 optimal weight: 8.9990 chunk 10 optimal weight: 6.9990 chunk 1 optimal weight: 9.9990 chunk 38 optimal weight: 4.9990 chunk 18 optimal weight: 0.0670 overall best weight: 1.5840 ------------------------------------------------------------------------------- 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** ** A1293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.095095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.074612 restraints weight = 21040.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.077861 restraints weight = 11415.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.080167 restraints weight = 7369.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.081780 restraints weight = 5315.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.082976 restraints weight = 4149.653| |-----------------------------------------------------------------------------| r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6871 moved from start: 0.3197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6997 Z= 0.156 Angle : 0.674 11.026 9522 Z= 0.351 Chirality : 0.046 0.152 1054 Planarity : 0.006 0.132 1219 Dihedral : 6.549 64.683 949 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 18.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.79 % Favored : 89.21 % Rotamer: Outliers : 5.22 % Allowed : 19.58 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.76 % Cis-general : 0.00 % Twisted Proline : 4.88 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.00 (0.25), residues: 862 helix: -2.05 (0.62), residues: 56 sheet: -2.63 (0.30), residues: 253 loop : -2.87 (0.24), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1168 TYR 0.017 0.002 TYR A1026 PHE 0.016 0.002 PHE C 127 TRP 0.020 0.002 TRP A 955 HIS 0.003 0.001 HIS C 205 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 6992) covalent geometry : angle 0.67376 ( 9512) SS BOND : bond 0.00162 ( 5) SS BOND : angle 0.89954 ( 10) hydrogen bonds : bond 0.03608 ( 136) hydrogen bonds : angle 7.61231 ( 321) *********************** 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 128 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 88 time to evaluate : 0.270 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1033 PHE cc_start: 0.7323 (OUTLIER) cc_final: 0.6262 (t80) REVERT: A 1047 TYR cc_start: 0.8257 (m-80) cc_final: 0.7994 (m-80) REVERT: A 1053 MET cc_start: 0.6674 (mmt) cc_final: 0.6319 (mmt) REVERT: A 1131 ILE cc_start: 0.8212 (OUTLIER) cc_final: 0.7992 (mt) REVERT: A 1239 LYS cc_start: 0.7766 (tptt) cc_final: 0.7289 (mptt) REVERT: A 1240 MET cc_start: 0.8748 (mpp) cc_final: 0.7857 (mpp) REVERT: A 1305 PHE cc_start: 0.6867 (OUTLIER) cc_final: 0.6508 (m-10) REVERT: C 20 LEU cc_start: 0.8146 (OUTLIER) cc_final: 0.7890 (mp) REVERT: C 176 GLN cc_start: 0.8833 (mm-40) cc_final: 0.8394 (mp10) REVERT: C 204 ASN cc_start: 0.8177 (t0) cc_final: 0.7963 (t0) REVERT: B 224 MET cc_start: 0.4961 (OUTLIER) cc_final: 0.4588 (mmp) REVERT: B 365 GLU cc_start: 0.7958 (mp0) cc_final: 0.7641 (pm20) REVERT: B 414 TYR cc_start: 0.8575 (m-80) cc_final: 0.8314 (m-80) REVERT: B 432 ASN cc_start: 0.8794 (t0) cc_final: 0.8310 (p0) outliers start: 40 outliers final: 23 residues processed: 122 average time/residue: 0.0613 time to fit residues: 11.1455 Evaluate side-chains 111 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 83 time to evaluate : 0.205 ------------------------------------------------------------------------------- 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 1033 PHE Chi-restraints excluded: chain A residue 1046 LEU Chi-restraints excluded: chain A residue 1057 GLU Chi-restraints excluded: chain A residue 1091 ILE Chi-restraints excluded: chain A residue 1130 LEU Chi-restraints excluded: chain A residue 1131 ILE Chi-restraints excluded: chain A residue 1169 LEU 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 53 VAL 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 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 290 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 70 optimal weight: 10.0000 chunk 44 optimal weight: 6.9990 chunk 21 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 18 optimal weight: 10.0000 chunk 8 optimal weight: 6.9990 chunk 46 optimal weight: 6.9990 chunk 74 optimal weight: 0.7980 chunk 31 optimal weight: 10.0000 chunk 60 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- 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** A1216 ASN ** A1254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.092593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.072245 restraints weight = 21078.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.075346 restraints weight = 11664.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.077508 restraints weight = 7629.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.079057 restraints weight = 5584.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.080179 restraints weight = 4405.615| |-----------------------------------------------------------------------------| r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6938 moved from start: 0.3396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6997 Z= 0.195 Angle : 0.713 11.087 9522 Z= 0.369 Chirality : 0.047 0.158 1054 Planarity : 0.006 0.130 1219 Dihedral : 6.730 64.551 949 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 22.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.25 % Favored : 88.75 % Rotamer: Outliers : 5.74 % Allowed : 20.50 % Favored : 73.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.76 % Cis-general : 0.00 % Twisted Proline : 4.88 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.01 (0.26), residues: 862 helix: -2.05 (0.62), residues: 57 sheet: -2.73 (0.29), residues: 257 loop : -2.81 (0.24), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1281 TYR 0.018 0.002 TYR A1026 PHE 0.019 0.002 PHE A1089 TRP 0.018 0.002 TRP A 955 HIS 0.003 0.001 HIS C 205 Details of bonding type rmsd covalent geometry : bond 0.00438 ( 6992) covalent geometry : angle 0.71254 ( 9512) SS BOND : bond 0.00329 ( 5) SS BOND : angle 0.97042 ( 10) hydrogen bonds : bond 0.03672 ( 136) hydrogen bonds : angle 7.65582 ( 321) *********************** 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 131 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 87 time to evaluate : 0.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1033 PHE cc_start: 0.7481 (OUTLIER) cc_final: 0.6482 (t80) REVERT: A 1047 TYR cc_start: 0.8283 (m-80) cc_final: 0.8044 (m-80) REVERT: A 1053 MET cc_start: 0.6879 (mmt) cc_final: 0.6570 (mmt) REVERT: A 1100 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.6851 (pm20) REVERT: A 1239 LYS cc_start: 0.7796 (tptt) cc_final: 0.7365 (mptt) REVERT: A 1240 MET cc_start: 0.8834 (mpp) cc_final: 0.7825 (mpp) REVERT: A 1305 PHE cc_start: 0.6939 (OUTLIER) cc_final: 0.6595 (m-10) REVERT: C 16 GLU cc_start: 0.8336 (tt0) cc_final: 0.7740 (tm-30) REVERT: C 20 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7879 (mp) REVERT: C 176 GLN cc_start: 0.8812 (mm-40) cc_final: 0.8379 (mp10) REVERT: C 204 ASN cc_start: 0.8242 (t0) cc_final: 0.8014 (t0) REVERT: B 238 GLU cc_start: 0.7786 (tm-30) cc_final: 0.7105 (tm-30) REVERT: B 432 ASN cc_start: 0.8797 (t0) cc_final: 0.8301 (p0) outliers start: 44 outliers final: 30 residues processed: 123 average time/residue: 0.0637 time to fit residues: 11.3260 Evaluate side-chains 114 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 80 time to evaluate : 0.227 ------------------------------------------------------------------------------- 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 1057 GLU Chi-restraints excluded: chain A residue 1091 ILE Chi-restraints excluded: chain A residue 1100 GLU Chi-restraints excluded: chain A residue 1130 LEU Chi-restraints excluded: chain A residue 1150 TYR Chi-restraints excluded: chain A residue 1169 LEU Chi-restraints excluded: chain A residue 1214 ASP Chi-restraints excluded: chain A residue 1253 VAL Chi-restraints excluded: chain A residue 1268 VAL Chi-restraints excluded: chain A residue 1305 PHE 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 39 ILE Chi-restraints excluded: chain C residue 53 VAL 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 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 245 ARG 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 418 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 74 optimal weight: 0.6980 chunk 26 optimal weight: 5.9990 chunk 25 optimal weight: 0.0670 chunk 24 optimal weight: 0.8980 chunk 43 optimal weight: 6.9990 chunk 34 optimal weight: 0.8980 chunk 66 optimal weight: 9.9990 chunk 46 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 972 ASN A1078 ASN A1216 ASN A1293 HIS ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.098042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.077386 restraints weight = 20099.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.080741 restraints weight = 10873.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.083100 restraints weight = 7019.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.084696 restraints weight = 5053.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.085944 restraints weight = 3970.522| |-----------------------------------------------------------------------------| r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6785 moved from start: 0.3829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6997 Z= 0.114 Angle : 0.659 11.740 9522 Z= 0.336 Chirality : 0.045 0.145 1054 Planarity : 0.006 0.127 1219 Dihedral : 6.185 65.397 949 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 16.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer: Outliers : 4.18 % Allowed : 22.45 % Favored : 73.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.76 % Cis-general : 0.00 % Twisted Proline : 4.88 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.58 (0.26), residues: 862 helix: -1.79 (0.62), residues: 58 sheet: -2.29 (0.31), residues: 231 loop : -2.62 (0.24), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1246 TYR 0.017 0.001 TYR C 199 PHE 0.020 0.001 PHE A1089 TRP 0.015 0.001 TRP A 955 HIS 0.003 0.001 HIS B 411 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 6992) covalent geometry : angle 0.65856 ( 9512) SS BOND : bond 0.00542 ( 5) SS BOND : angle 0.72791 ( 10) hydrogen bonds : bond 0.03242 ( 136) hydrogen bonds : angle 7.11096 ( 321) *********************** 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 132 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 100 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 903 ASN cc_start: 0.8155 (p0) cc_final: 0.7942 (p0) REVERT: A 939 MET cc_start: 0.8931 (mtm) cc_final: 0.8461 (tmm) REVERT: A 1033 PHE cc_start: 0.7244 (OUTLIER) cc_final: 0.6241 (t80) REVERT: A 1053 MET cc_start: 0.6891 (mmt) cc_final: 0.6640 (mmt) REVERT: A 1100 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.6833 (pm20) REVERT: A 1230 ASN cc_start: 0.9195 (t0) cc_final: 0.8939 (m-40) REVERT: A 1236 LEU cc_start: 0.8850 (pp) cc_final: 0.8252 (tt) REVERT: A 1239 LYS cc_start: 0.7745 (tptt) cc_final: 0.7408 (mptt) REVERT: A 1240 MET cc_start: 0.8649 (mpp) cc_final: 0.8206 (mpp) REVERT: A 1305 PHE cc_start: 0.6804 (OUTLIER) cc_final: 0.6450 (m-10) REVERT: B 238 GLU cc_start: 0.7500 (tm-30) cc_final: 0.6807 (tm-30) REVERT: B 354 VAL cc_start: 0.8152 (t) cc_final: 0.7923 (t) REVERT: B 365 GLU cc_start: 0.8248 (mp0) cc_final: 0.7724 (pm20) REVERT: B 417 GLU cc_start: 0.4459 (pm20) cc_final: 0.4242 (pm20) REVERT: B 432 ASN cc_start: 0.8766 (t0) cc_final: 0.8246 (p0) outliers start: 32 outliers final: 21 residues processed: 125 average time/residue: 0.0652 time to fit residues: 11.8264 Evaluate side-chains 116 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 92 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 891 ILE Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1033 PHE Chi-restraints excluded: chain A residue 1046 LEU Chi-restraints excluded: chain A residue 1057 GLU Chi-restraints excluded: chain A residue 1100 GLU Chi-restraints excluded: chain A residue 1130 LEU Chi-restraints excluded: chain A residue 1268 VAL Chi-restraints excluded: chain A residue 1305 PHE Chi-restraints excluded: chain A residue 1313 THR Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 34 TYR Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 105 PHE 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 277 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 20 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 79 optimal weight: 0.0170 chunk 47 optimal weight: 0.0670 chunk 19 optimal weight: 4.9990 chunk 69 optimal weight: 7.9990 chunk 43 optimal weight: 6.9990 chunk 68 optimal weight: 4.9990 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 overall best weight: 1.8162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1216 ASN ** A1254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1292 ASN C 176 GLN ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.095847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.075096 restraints weight = 20659.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.078372 restraints weight = 11296.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.080626 restraints weight = 7368.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.082274 restraints weight = 5389.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.083453 restraints weight = 4245.321| |-----------------------------------------------------------------------------| r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6891 moved from start: 0.3914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6997 Z= 0.167 Angle : 0.696 9.912 9522 Z= 0.359 Chirality : 0.046 0.158 1054 Planarity : 0.006 0.128 1219 Dihedral : 6.387 64.288 949 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 20.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.09 % Favored : 89.91 % Rotamer: Outliers : 4.70 % Allowed : 22.85 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.66 (0.26), residues: 862 helix: -1.79 (0.62), residues: 58 sheet: -2.50 (0.29), residues: 259 loop : -2.56 (0.24), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 245 TYR 0.018 0.002 TYR C 34 PHE 0.020 0.002 PHE A1089 TRP 0.015 0.002 TRP A 955 HIS 0.002 0.001 HIS C 205 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 6992) covalent geometry : angle 0.69615 ( 9512) SS BOND : bond 0.00258 ( 5) SS BOND : angle 0.86476 ( 10) hydrogen bonds : bond 0.03405 ( 136) hydrogen bonds : angle 7.16497 ( 321) *********************** 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 124 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 88 time to evaluate : 0.265 Fit side-chains revert: symmetry clash REVERT: A 939 MET cc_start: 0.8964 (mtm) cc_final: 0.8470 (tmm) REVERT: A 1033 PHE cc_start: 0.7396 (OUTLIER) cc_final: 0.6393 (t80) REVERT: A 1047 TYR cc_start: 0.8155 (m-80) cc_final: 0.7691 (m-80) REVERT: A 1053 MET cc_start: 0.7007 (mmt) cc_final: 0.6761 (mmt) REVERT: A 1100 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.6791 (pm20) REVERT: A 1236 LEU cc_start: 0.8891 (pp) cc_final: 0.8277 (tt) REVERT: A 1239 LYS cc_start: 0.7756 (tptt) cc_final: 0.7397 (mptt) REVERT: A 1240 MET cc_start: 0.8764 (mpp) cc_final: 0.7932 (mpp) REVERT: A 1305 PHE cc_start: 0.6943 (OUTLIER) cc_final: 0.6580 (m-10) REVERT: C 20 LEU cc_start: 0.8079 (OUTLIER) cc_final: 0.7808 (mp) REVERT: B 238 GLU cc_start: 0.7816 (tm-30) cc_final: 0.7187 (tm-30) REVERT: B 257 TYR cc_start: 0.7521 (m-80) cc_final: 0.7259 (m-80) REVERT: B 365 GLU cc_start: 0.8314 (mp0) cc_final: 0.7950 (pm20) REVERT: B 417 GLU cc_start: 0.4457 (pm20) cc_final: 0.4221 (pm20) REVERT: B 432 ASN cc_start: 0.8780 (t0) cc_final: 0.8294 (p0) outliers start: 36 outliers final: 26 residues processed: 116 average time/residue: 0.0571 time to fit residues: 9.9314 Evaluate side-chains 114 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 84 time to evaluate : 0.257 ------------------------------------------------------------------------------- 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 1057 GLU Chi-restraints excluded: chain A residue 1091 ILE Chi-restraints excluded: chain A residue 1100 GLU Chi-restraints excluded: chain A residue 1130 LEU Chi-restraints excluded: chain A residue 1150 TYR 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 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 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 277 THR Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 358 LEU 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 82 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 72 optimal weight: 10.0000 chunk 53 optimal weight: 0.0020 chunk 66 optimal weight: 5.9990 chunk 67 optimal weight: 0.2980 chunk 30 optimal weight: 0.6980 chunk 12 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 54 optimal weight: 7.9990 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1216 ASN A1292 ASN C 5 GLN ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.101019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.079919 restraints weight = 20013.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.083520 restraints weight = 10699.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.085990 restraints weight = 6844.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.087746 restraints weight = 4910.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.089036 restraints weight = 3817.648| |-----------------------------------------------------------------------------| r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6748 moved from start: 0.4364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6997 Z= 0.111 Angle : 0.658 9.963 9522 Z= 0.335 Chirality : 0.045 0.146 1054 Planarity : 0.006 0.125 1219 Dihedral : 5.964 65.109 949 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 3.79 % Allowed : 24.15 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.43 (0.26), residues: 862 helix: -1.58 (0.63), residues: 58 sheet: -2.37 (0.30), residues: 249 loop : -2.40 (0.24), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 245 TYR 0.015 0.001 TYR A1150 PHE 0.032 0.002 PHE B 340 TRP 0.014 0.001 TRP A 955 HIS 0.002 0.001 HIS A1271 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 6992) covalent geometry : angle 0.65797 ( 9512) SS BOND : bond 0.00204 ( 5) SS BOND : angle 0.60418 ( 10) hydrogen bonds : bond 0.03210 ( 136) hydrogen bonds : angle 6.82219 ( 321) *********************** 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 130 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 101 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 939 MET cc_start: 0.8933 (mtm) cc_final: 0.8426 (tmm) REVERT: A 1012 ARG cc_start: 0.8577 (mmt-90) cc_final: 0.8189 (mmp80) REVERT: A 1033 PHE cc_start: 0.7248 (OUTLIER) cc_final: 0.6282 (t80) REVERT: A 1047 TYR cc_start: 0.8135 (m-80) cc_final: 0.7749 (m-80) REVERT: A 1067 ASP cc_start: 0.6733 (OUTLIER) cc_final: 0.6259 (m-30) REVERT: A 1100 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.6843 (pm20) REVERT: A 1236 LEU cc_start: 0.8810 (pp) cc_final: 0.8220 (tt) REVERT: A 1239 LYS cc_start: 0.7712 (tptt) cc_final: 0.6675 (mptt) REVERT: A 1305 PHE cc_start: 0.6766 (OUTLIER) cc_final: 0.6457 (m-10) REVERT: C 16 GLU cc_start: 0.8277 (tt0) cc_final: 0.7697 (tm-30) REVERT: B 238 GLU cc_start: 0.7573 (tm-30) cc_final: 0.7032 (tm-30) REVERT: B 299 MET cc_start: 0.8580 (mpp) cc_final: 0.8356 (mmt) REVERT: B 365 GLU cc_start: 0.8302 (mp0) cc_final: 0.7717 (pm20) REVERT: B 432 ASN cc_start: 0.8752 (t0) cc_final: 0.8271 (p0) outliers start: 29 outliers final: 21 residues processed: 122 average time/residue: 0.0635 time to fit residues: 11.4090 Evaluate side-chains 120 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 95 time to evaluate : 0.253 ------------------------------------------------------------------------------- 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 1033 PHE Chi-restraints excluded: chain A residue 1057 GLU Chi-restraints excluded: chain A residue 1067 ASP Chi-restraints excluded: chain A residue 1100 GLU Chi-restraints excluded: chain A residue 1130 LEU Chi-restraints excluded: chain A residue 1268 VAL Chi-restraints excluded: chain A residue 1305 PHE Chi-restraints excluded: chain A residue 1313 THR Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 34 TYR Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 70 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 277 THR Chi-restraints excluded: chain B residue 290 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 49 optimal weight: 0.1980 chunk 32 optimal weight: 0.8980 chunk 9 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 chunk 30 optimal weight: 6.9990 chunk 47 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 74 optimal weight: 0.2980 chunk 67 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 311 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.101800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.080921 restraints weight = 20018.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.084460 restraints weight = 10771.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.086920 restraints weight = 6932.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.088677 restraints weight = 4978.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.089866 restraints weight = 3870.663| |-----------------------------------------------------------------------------| r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6749 moved from start: 0.4613 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= 0.114 Angle : 0.676 10.805 9522 Z= 0.341 Chirality : 0.045 0.147 1054 Planarity : 0.006 0.121 1219 Dihedral : 5.878 64.033 949 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer: Outliers : 3.00 % Allowed : 25.07 % Favored : 71.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.76 % Cis-general : 0.00 % Twisted Proline : 4.88 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.17 (0.27), residues: 862 helix: -1.39 (0.65), residues: 57 sheet: -2.14 (0.30), residues: 254 loop : -2.24 (0.25), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 245 TYR 0.017 0.001 TYR A1150 PHE 0.033 0.002 PHE C 127 TRP 0.014 0.001 TRP A1002 HIS 0.002 0.001 HIS A1271 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 6992) covalent geometry : angle 0.67641 ( 9512) SS BOND : bond 0.00246 ( 5) SS BOND : angle 0.43606 ( 10) hydrogen bonds : bond 0.03347 ( 136) hydrogen bonds : angle 6.71933 ( 321) ********************** 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 125 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 102 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 939 MET cc_start: 0.8913 (mtm) cc_final: 0.8413 (tmm) REVERT: A 1012 ARG cc_start: 0.8634 (mmt-90) cc_final: 0.8258 (mmp80) REVERT: A 1033 PHE cc_start: 0.7155 (OUTLIER) cc_final: 0.6249 (t80) REVERT: A 1047 TYR cc_start: 0.8000 (m-80) cc_final: 0.7655 (m-80) REVERT: A 1100 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.6833 (pm20) REVERT: A 1236 LEU cc_start: 0.8835 (pp) cc_final: 0.8110 (tt) REVERT: A 1305 PHE cc_start: 0.6711 (OUTLIER) cc_final: 0.6402 (m-10) REVERT: B 299 MET cc_start: 0.8593 (mpp) cc_final: 0.8382 (mmt) REVERT: B 365 GLU cc_start: 0.8318 (mp0) cc_final: 0.7748 (pm20) REVERT: B 432 ASN cc_start: 0.8768 (t0) cc_final: 0.8283 (p0) outliers start: 23 outliers final: 19 residues processed: 119 average time/residue: 0.0590 time to fit residues: 10.1814 Evaluate side-chains 116 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 94 time to evaluate : 0.182 ------------------------------------------------------------------------------- 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 1033 PHE Chi-restraints excluded: chain A residue 1100 GLU Chi-restraints excluded: chain A residue 1130 LEU Chi-restraints excluded: chain A residue 1268 VAL Chi-restraints excluded: chain A residue 1305 PHE Chi-restraints excluded: chain 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 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 277 THR Chi-restraints excluded: chain B residue 290 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 82 optimal weight: 0.3980 chunk 56 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 37 optimal weight: 8.9990 chunk 44 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 35 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 81 optimal weight: 0.6980 chunk 7 optimal weight: 9.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.099061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.078356 restraints weight = 20209.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.081725 restraints weight = 11067.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.084087 restraints weight = 7205.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.085786 restraints weight = 5236.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.087031 restraints weight = 4094.111| |-----------------------------------------------------------------------------| r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6845 moved from start: 0.4611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6997 Z= 0.147 Angle : 0.705 10.131 9522 Z= 0.360 Chirality : 0.046 0.152 1054 Planarity : 0.006 0.125 1219 Dihedral : 5.995 64.021 949 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 17.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.93 % Favored : 91.07 % Rotamer: Outliers : 3.66 % Allowed : 24.93 % Favored : 71.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.76 % Cis-general : 0.00 % Twisted Proline : 4.88 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.23 (0.27), residues: 862 helix: -1.42 (0.64), residues: 57 sheet: -2.17 (0.29), residues: 272 loop : -2.28 (0.25), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 275 TYR 0.018 0.002 TYR A1150 PHE 0.030 0.002 PHE C 127 TRP 0.025 0.002 TRP A1002 HIS 0.002 0.001 HIS A1271 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 6992) covalent geometry : angle 0.70506 ( 9512) SS BOND : bond 0.00237 ( 5) SS BOND : angle 0.58095 ( 10) hydrogen bonds : bond 0.03303 ( 136) hydrogen bonds : angle 6.75356 ( 321) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1333.99 seconds wall clock time: 23 minutes 51.15 seconds (1431.15 seconds total)