Starting phenix.real_space_refine on Tue Sep 24 04:58:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oh0_12890/09_2024/7oh0_12890.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oh0_12890/09_2024/7oh0_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oh0_12890/09_2024/7oh0_12890.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oh0_12890/09_2024/7oh0_12890.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oh0_12890/09_2024/7oh0_12890.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oh0_12890/09_2024/7oh0_12890.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.042 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 23 5.16 5 C 4337 2.51 5 N 1138 2.21 5 O 1332 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 43 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 6830 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3516 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 14, 'TRANS': 420} Chain breaks: 1 Chain: "C" Number of atoms: 1665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1665 Classifications: {'peptide': 221} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 205} Chain: "B" Number of atoms: 1649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1649 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 201} Time building chain proxies: 5.21, per 1000 atoms: 0.76 Number of scatterers: 6830 At special positions: 0 Unit cell: (89.316, 80.219, 135.628, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 23 16.00 O 1332 8.00 N 1138 7.00 C 4337 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 97 " distance=2.02 Simple disulfide: pdb=" SG CYS C 145 " - pdb=" SG CYS C 201 " distance=2.03 Simple disulfide: pdb=" SG CYS C 221 " - pdb=" SG CYS B 436 " distance=2.02 Simple disulfide: pdb=" SG CYS B 244 " - pdb=" SG CYS B 309 " distance=2.03 Simple disulfide: pdb=" SG CYS B 356 " - pdb=" SG CYS B 416 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.79 Conformation dependent library (CDL) restraints added in 1.1 seconds 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1624 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 21 sheets defined 8.2% alpha, 25.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing helix chain 'A' and resid 876 through 884 Processing helix chain 'A' and resid 962 through 970 Processing helix chain 'A' and resid 1021 through 1025 Processing helix chain 'A' and resid 1097 through 1109 Processing helix chain 'A' and resid 1288 through 1294 removed outlier: 4.049A pdb=" N LEU A1294 " --> pdb=" O PHE A1291 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 92 removed outlier: 3.525A pdb=" N ASP C 91 " --> pdb=" O THR C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 209 Processing helix chain 'B' and resid 300 through 304 Processing helix chain 'B' and resid 343 through 350 removed outlier: 4.005A pdb=" N LEU B 347 " --> pdb=" O SER B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 Processing sheet with id=AA1, first strand: chain 'A' and resid 896 through 898 removed outlier: 6.192A pdb=" N ILE A1091 " --> pdb=" O ILE A 886 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ASN A 888 " --> pdb=" O PHE A1089 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N PHE A1089 " --> pdb=" O ASN A 888 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N ASP A 890 " --> pdb=" O ASP A1087 " (cutoff:3.500A) removed outlier: 9.851A pdb=" N ASP A1087 " --> pdb=" O ASP A 890 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N PHE A1089 " --> pdb=" O SER A 953 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N SER A 953 " --> pdb=" O PHE A1089 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ILE A1091 " --> pdb=" O THR A 951 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N THR A 951 " --> pdb=" O ILE A1091 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL A 952 " --> pdb=" O ILE A1036 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE A1036 " --> pdb=" O VAL A 952 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N PHE A 954 " --> pdb=" O ILE A1034 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE A1034 " --> pdb=" O PHE A 954 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA A1056 " --> pdb=" O ALA A1044 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N GLY A1054 " --> pdb=" O LEU A1046 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N ILE A1048 " --> pdb=" O LEU A1052 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N LEU A1052 " --> pdb=" O ILE A1048 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 914 through 917 removed outlier: 3.544A pdb=" N GLY A 920 " --> pdb=" O GLY A 917 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1011 through 1016 removed outlier: 4.077A pdb=" N ARG A1012 " --> pdb=" O LEU A1004 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU A1004 " --> pdb=" O ARG A1012 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE A1014 " --> pdb=" O TRP A1002 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N TRP A1002 " --> pdb=" O ILE A1014 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LEU A1000 " --> pdb=" O PHE A1016 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N TRP A 991 " --> pdb=" O SER A 978 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N SER A 978 " --> pdb=" O TRP A 991 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N VAL A 993 " --> pdb=" O ILE A 976 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE A 976 " --> pdb=" O VAL A 993 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N TYR A 974 " --> pdb=" O ASP A1075 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N ASP A1075 " --> pdb=" O TYR A 974 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ILE A 976 " --> pdb=" O LYS A1073 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER A 978 " --> pdb=" O THR A1071 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1129 through 1132 Processing sheet with id=AA5, first strand: chain 'A' and resid 1139 through 1142 Processing sheet with id=AA6, first strand: chain 'A' and resid 1156 through 1159 Processing sheet with id=AA7, first strand: chain 'A' and resid 1174 through 1176 removed outlier: 4.068A pdb=" N LYS A1174 " --> pdb=" O SER A1201 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1174 through 1176 removed outlier: 4.068A pdb=" N LYS A1174 " --> pdb=" O SER A1201 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1194 through 1196 removed outlier: 7.251A pdb=" N LEU A1255 " --> pdb=" O LEU A1267 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N LEU A1267 " --> pdb=" O LEU A1255 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N LEU A1257 " --> pdb=" O LEU A1265 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU A1267 " --> pdb=" O SER A1287 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER A1287 " --> pdb=" O LEU A1267 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N HIS A1271 " --> pdb=" O ILE A1283 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE A1283 " --> pdb=" O HIS A1271 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 4 through 7 removed outlier: 3.512A pdb=" N GLN C 5 " --> pdb=" O SER C 23 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER C 23 " --> pdb=" O GLN C 5 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER C 7 " --> pdb=" O THR C 21 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N THR C 21 " --> pdb=" O SER C 7 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 49 through 52 removed outlier: 4.127A pdb=" N GLY C 51 " --> pdb=" O TRP C 38 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N TYR C 35 " --> pdb=" O GLN C 100 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLN C 100 " --> pdb=" O TYR C 35 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA C 37 " --> pdb=" O ALA C 98 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TYR C 95 " --> pdb=" O THR C 112 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N THR C 112 " --> pdb=" O TYR C 95 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 125 through 128 Processing sheet with id=AB4, first strand: chain 'C' and resid 158 through 159 removed outlier: 3.996A pdb=" N VAL C 203 " --> pdb=" O VAL C 212 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL C 212 " --> pdb=" O VAL C 203 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 158 through 159 removed outlier: 3.907A pdb=" N TYR C 199 " --> pdb=" O VAL C 216 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 169 through 170 removed outlier: 3.712A pdb=" N VAL C 186 " --> pdb=" O HIS C 169 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 174 through 176 Processing sheet with id=AB8, first strand: chain 'B' and resid 240 through 242 removed outlier: 3.997A pdb=" N LEU B 294 " --> pdb=" O LEU B 242 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 266 through 270 removed outlier: 6.449A pdb=" N TRP B 256 " --> pdb=" O LEU B 268 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 336 through 337 removed outlier: 3.855A pdb=" N SER B 336 " --> pdb=" O ASN B 359 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN B 359 " --> pdb=" O SER B 336 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N SER B 399 " --> pdb=" O CYS B 356 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 351 through 352 Processing sheet with id=AC3, first strand: chain 'B' and resid 367 through 372 removed outlier: 3.833A pdb=" N LYS B 367 " --> pdb=" O THR B 419 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS B 371 " --> pdb=" O ALA B 415 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA B 415 " --> pdb=" O LYS B 371 " (cutoff:3.500A) 145 hydrogen bonds defined for protein. 321 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.32 Time building geometry restraints manager: 2.11 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: 1.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 21.480 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7026 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 6992 Z= 0.306 Angle : 0.916 8.499 9512 Z= 0.551 Chirality : 0.047 0.165 1054 Planarity : 0.006 0.110 1219 Dihedral : 13.942 85.548 2528 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 29.13 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.95 % Favored : 87.94 % Rotamer: Outliers : 0.26 % Allowed : 9.01 % Favored : 90.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.76 % Cis-general : 0.00 % Twisted Proline : 4.88 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.70 (0.21), residues: 862 helix: -3.99 (0.34), residues: 54 sheet: -3.51 (0.28), residues: 241 loop : -4.15 (0.19), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 955 HIS 0.003 0.001 HIS C 169 PHE 0.019 0.002 PHE B 320 TYR 0.017 0.002 TYR C 181 ARG 0.003 0.000 ARG B 433 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 122 time to evaluate : 0.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1039 ASP cc_start: 0.8650 (t0) cc_final: 0.8313 (t70) REVERT: A 1042 SER cc_start: 0.9134 (t) cc_final: 0.8899 (p) REVERT: A 1053 MET cc_start: 0.7312 (mmt) cc_final: 0.7109 (mmt) REVERT: A 1070 ILE cc_start: 0.8894 (mm) cc_final: 0.8657 (mp) REVERT: A 1239 LYS cc_start: 0.7666 (tptt) cc_final: 0.7232 (mptt) REVERT: A 1240 MET cc_start: 0.8894 (mpp) cc_final: 0.8047 (mpp) REVERT: C 204 ASN cc_start: 0.7900 (t0) cc_final: 0.7684 (t0) REVERT: B 224 MET cc_start: 0.4707 (mpp) cc_final: 0.4418 (mmp) REVERT: B 432 ASN cc_start: 0.8861 (t0) cc_final: 0.8272 (p0) outliers start: 2 outliers final: 1 residues processed: 124 average time/residue: 0.1897 time to fit residues: 31.4498 Evaluate side-chains 86 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 85 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 59 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 72 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 43 optimal weight: 0.0980 chunk 34 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 chunk 78 optimal weight: 7.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 936 HIS ** A 972 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 998 ASN A1069 ASN ** A1078 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1163 ASN A1292 ASN ** A1293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 202 ASN ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 227 GLN B 259 GLN B 377 GLN B 432 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7031 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 6992 Z= 0.281 Angle : 0.739 9.610 9512 Z= 0.392 Chirality : 0.048 0.159 1054 Planarity : 0.007 0.110 1219 Dihedral : 7.238 64.778 949 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 21.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.88 % Favored : 87.12 % Rotamer: Outliers : 3.52 % Allowed : 14.36 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.76 % Cis-general : 0.00 % Twisted Proline : 4.88 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.74 (0.24), residues: 862 helix: -2.57 (0.58), residues: 48 sheet: -2.95 (0.28), residues: 244 loop : -3.51 (0.22), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 955 HIS 0.003 0.001 HIS C 205 PHE 0.035 0.002 PHE C 127 TYR 0.016 0.002 TYR C 34 ARG 0.011 0.001 ARG A1246 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 103 time to evaluate : 0.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1070 ILE cc_start: 0.8913 (mm) cc_final: 0.8688 (mp) REVERT: A 1239 LYS cc_start: 0.7743 (tptt) cc_final: 0.7355 (mptt) REVERT: A 1240 MET cc_start: 0.8779 (mpp) cc_final: 0.8096 (mpp) REVERT: A 1305 PHE cc_start: 0.6852 (OUTLIER) cc_final: 0.6390 (m-10) REVERT: C 176 GLN cc_start: 0.8623 (mm-40) cc_final: 0.8312 (mp10) REVERT: C 202 ASN cc_start: 0.6903 (m110) cc_final: 0.6406 (m110) REVERT: C 204 ASN cc_start: 0.8052 (t0) cc_final: 0.7655 (t0) REVERT: B 225 MET cc_start: 0.5599 (pmm) cc_final: 0.5113 (tpt) REVERT: B 358 LEU cc_start: 0.3746 (OUTLIER) cc_final: 0.3486 (pp) REVERT: B 365 GLU cc_start: 0.8198 (mp0) cc_final: 0.7988 (pm20) REVERT: B 432 ASN cc_start: 0.8821 (t0) cc_final: 0.8349 (p0) outliers start: 27 outliers final: 15 residues processed: 122 average time/residue: 0.1542 time to fit residues: 26.5301 Evaluate side-chains 101 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 84 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1046 LEU Chi-restraints excluded: chain A residue 1057 GLU Chi-restraints excluded: chain A residue 1130 LEU Chi-restraints excluded: chain A residue 1169 LEU Chi-restraints excluded: chain A residue 1214 ASP Chi-restraints excluded: chain A residue 1253 VAL Chi-restraints excluded: chain A residue 1268 VAL Chi-restraints excluded: chain A residue 1305 PHE Chi-restraints excluded: chain A residue 1313 THR Chi-restraints excluded: chain C residue 34 TYR Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 340 PHE Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 358 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 43 optimal weight: 0.8980 chunk 24 optimal weight: 5.9990 chunk 64 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 78 optimal weight: 0.5980 chunk 84 optimal weight: 20.0000 chunk 69 optimal weight: 6.9990 chunk 77 optimal weight: 8.9990 chunk 26 optimal weight: 3.9990 chunk 62 optimal weight: 0.0370 overall best weight: 0.9062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 919 ASN A 972 ASN A1078 ASN A1153 ASN A1293 HIS C 103 ASN ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6925 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6992 Z= 0.174 Angle : 0.670 10.917 9512 Z= 0.348 Chirality : 0.046 0.164 1054 Planarity : 0.006 0.114 1219 Dihedral : 6.625 63.608 949 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 16.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer: Outliers : 4.05 % Allowed : 15.93 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.76 % Cis-general : 0.00 % Twisted Proline : 4.88 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.26 (0.25), residues: 862 helix: -1.97 (0.65), residues: 49 sheet: -2.95 (0.29), residues: 255 loop : -2.99 (0.23), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 955 HIS 0.004 0.001 HIS C 205 PHE 0.025 0.002 PHE C 127 TYR 0.019 0.002 TYR A1026 ARG 0.005 0.001 ARG A1246 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 108 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1047 TYR cc_start: 0.8129 (m-80) cc_final: 0.7845 (m-80) REVERT: A 1053 MET cc_start: 0.6608 (mmt) cc_final: 0.6218 (mmt) REVERT: A 1100 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.6956 (pm20) REVERT: A 1131 ILE cc_start: 0.8377 (mp) cc_final: 0.8158 (mt) REVERT: A 1239 LYS cc_start: 0.7761 (tptt) cc_final: 0.7424 (mptt) REVERT: A 1305 PHE cc_start: 0.6795 (OUTLIER) cc_final: 0.6303 (m-10) REVERT: C 55 TYR cc_start: 0.3090 (p90) cc_final: 0.2848 (p90) REVERT: C 176 GLN cc_start: 0.8672 (mm-40) cc_final: 0.8428 (mp10) REVERT: C 204 ASN cc_start: 0.8069 (t0) cc_final: 0.7617 (t0) REVERT: B 254 LEU cc_start: 0.7361 (OUTLIER) cc_final: 0.6883 (pp) REVERT: B 256 TRP cc_start: 0.7209 (m100) cc_final: 0.6865 (m100) REVERT: B 257 TYR cc_start: 0.7061 (m-80) cc_final: 0.6855 (m-80) REVERT: B 320 PHE cc_start: 0.7226 (m-10) cc_final: 0.6924 (m-10) REVERT: B 354 VAL cc_start: 0.8389 (t) cc_final: 0.8152 (t) REVERT: B 358 LEU cc_start: 0.3760 (OUTLIER) cc_final: 0.3542 (pp) REVERT: B 365 GLU cc_start: 0.8157 (mp0) cc_final: 0.7864 (mp0) REVERT: B 414 TYR cc_start: 0.8658 (m-80) cc_final: 0.7932 (m-80) REVERT: B 432 ASN cc_start: 0.8785 (t0) cc_final: 0.8189 (p0) outliers start: 31 outliers final: 17 residues processed: 135 average time/residue: 0.1509 time to fit residues: 29.0519 Evaluate side-chains 107 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 86 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1046 LEU Chi-restraints excluded: chain A residue 1057 GLU Chi-restraints excluded: chain A residue 1100 GLU Chi-restraints excluded: chain A residue 1130 LEU Chi-restraints excluded: chain A residue 1186 ILE Chi-restraints excluded: chain A residue 1268 VAL Chi-restraints excluded: chain A residue 1305 PHE Chi-restraints excluded: chain A residue 1313 THR Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 34 TYR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 105 PHE Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain B residue 224 MET Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 327 GLU Chi-restraints excluded: chain B residue 340 PHE Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 418 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 77 optimal weight: 9.9990 chunk 58 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 chunk 8 optimal weight: 6.9990 chunk 37 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 83 optimal weight: 9.9990 chunk 41 optimal weight: 0.9980 chunk 74 optimal weight: 0.4980 chunk 22 optimal weight: 0.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 928 ASN A 999 ASN C 103 ASN ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 311 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6913 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6992 Z= 0.178 Angle : 0.657 10.355 9512 Z= 0.338 Chirality : 0.045 0.157 1054 Planarity : 0.006 0.114 1219 Dihedral : 6.267 62.762 949 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 16.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.98 % Favored : 90.02 % Rotamer: Outliers : 4.57 % Allowed : 17.62 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.76 % Cis-general : 0.00 % Twisted Proline : 4.88 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.83 (0.26), residues: 862 helix: -1.68 (0.68), residues: 49 sheet: -2.56 (0.31), residues: 241 loop : -2.77 (0.23), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 955 HIS 0.003 0.001 HIS C 205 PHE 0.022 0.002 PHE C 127 TYR 0.019 0.001 TYR A1026 ARG 0.009 0.001 ARG B 364 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 103 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1047 TYR cc_start: 0.8053 (m-80) cc_final: 0.7835 (m-80) REVERT: A 1053 MET cc_start: 0.6732 (mmt) cc_final: 0.6349 (mmt) REVERT: A 1131 ILE cc_start: 0.8350 (mp) cc_final: 0.8114 (mt) REVERT: A 1236 LEU cc_start: 0.8918 (pp) cc_final: 0.8343 (tt) REVERT: A 1239 LYS cc_start: 0.7858 (tptt) cc_final: 0.7171 (mptt) REVERT: A 1240 MET cc_start: 0.8626 (mpp) cc_final: 0.7791 (mpp) REVERT: A 1305 PHE cc_start: 0.6771 (OUTLIER) cc_final: 0.6277 (m-10) REVERT: C 78 ASN cc_start: 0.6394 (t0) cc_final: 0.6119 (t0) REVERT: C 176 GLN cc_start: 0.8696 (mm-40) cc_final: 0.8416 (mp10) REVERT: B 254 LEU cc_start: 0.7375 (OUTLIER) cc_final: 0.7012 (pp) REVERT: B 256 TRP cc_start: 0.7172 (m100) cc_final: 0.6864 (m100) REVERT: B 354 VAL cc_start: 0.8308 (t) cc_final: 0.8089 (t) REVERT: B 365 GLU cc_start: 0.7764 (mp0) cc_final: 0.7395 (pm20) REVERT: B 414 TYR cc_start: 0.8564 (m-80) cc_final: 0.7765 (m-80) REVERT: B 432 ASN cc_start: 0.8765 (t0) cc_final: 0.8298 (p0) outliers start: 35 outliers final: 18 residues processed: 134 average time/residue: 0.1663 time to fit residues: 31.1677 Evaluate side-chains 111 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 91 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 891 ILE Chi-restraints excluded: chain A residue 1046 LEU Chi-restraints excluded: chain A residue 1057 GLU Chi-restraints excluded: chain A residue 1130 LEU Chi-restraints excluded: chain A residue 1268 VAL Chi-restraints excluded: chain A residue 1305 PHE Chi-restraints excluded: chain A residue 1313 THR Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 34 TYR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 105 PHE Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain B residue 224 MET Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 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 69 optimal weight: 0.9990 chunk 47 optimal weight: 0.0670 chunk 1 optimal weight: 9.9990 chunk 61 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 70 optimal weight: 20.0000 chunk 57 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 42 optimal weight: 6.9990 chunk 74 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 overall best weight: 1.9524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 999 ASN C 103 ASN ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 6992 Z= 0.253 Angle : 0.686 10.409 9512 Z= 0.356 Chirality : 0.046 0.190 1054 Planarity : 0.006 0.117 1219 Dihedral : 6.423 62.852 949 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 19.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.67 % Favored : 89.33 % Rotamer: Outliers : 5.48 % Allowed : 18.28 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.76 % Cis-general : 0.00 % Twisted Proline : 4.88 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.89 (0.25), residues: 862 helix: -2.06 (0.60), residues: 56 sheet: -2.54 (0.30), residues: 251 loop : -2.79 (0.24), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 955 HIS 0.003 0.001 HIS C 205 PHE 0.019 0.002 PHE A1089 TYR 0.019 0.002 TYR C 34 ARG 0.007 0.001 ARG B 364 *********************** 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 137 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 95 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1047 TYR cc_start: 0.8167 (m-80) cc_final: 0.7829 (m-80) REVERT: A 1053 MET cc_start: 0.6824 (mmt) cc_final: 0.6449 (mmt) REVERT: A 1131 ILE cc_start: 0.8377 (OUTLIER) cc_final: 0.8113 (mt) REVERT: A 1239 LYS cc_start: 0.7827 (tptt) cc_final: 0.7245 (mptt) REVERT: A 1240 MET cc_start: 0.8718 (mpp) cc_final: 0.7795 (mpp) REVERT: A 1305 PHE cc_start: 0.6889 (OUTLIER) cc_final: 0.6465 (m-10) REVERT: C 78 ASN cc_start: 0.6448 (t0) cc_final: 0.6137 (t0) REVERT: C 176 GLN cc_start: 0.8650 (mm-40) cc_final: 0.8368 (mp10) REVERT: B 365 GLU cc_start: 0.7525 (mp0) cc_final: 0.7274 (pm20) REVERT: B 432 ASN cc_start: 0.8757 (t0) cc_final: 0.8272 (p0) outliers start: 42 outliers final: 29 residues processed: 126 average time/residue: 0.1785 time to fit residues: 32.5900 Evaluate side-chains 115 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 84 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 891 ILE Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1046 LEU Chi-restraints excluded: chain A residue 1057 GLU Chi-restraints excluded: chain A residue 1130 LEU Chi-restraints excluded: chain A residue 1131 ILE Chi-restraints excluded: chain A residue 1150 TYR Chi-restraints excluded: chain A residue 1169 LEU Chi-restraints excluded: chain A residue 1214 ASP Chi-restraints excluded: chain A residue 1250 THR Chi-restraints excluded: chain A residue 1253 VAL Chi-restraints excluded: chain A residue 1268 VAL Chi-restraints excluded: chain A residue 1305 PHE Chi-restraints excluded: chain A residue 1313 THR Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 34 TYR Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 340 PHE Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 418 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 27 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 48 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 38 optimal weight: 0.0980 chunk 6 optimal weight: 2.9990 chunk 43 optimal weight: 6.9990 chunk 80 optimal weight: 3.9990 overall best weight: 1.4188 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6970 moved from start: 0.3548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6992 Z= 0.205 Angle : 0.658 9.711 9512 Z= 0.341 Chirality : 0.045 0.176 1054 Planarity : 0.006 0.117 1219 Dihedral : 6.271 63.515 949 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 17.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.86 % Favored : 90.14 % Rotamer: Outliers : 4.18 % Allowed : 20.89 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.76 % Cis-general : 0.00 % Twisted Proline : 4.88 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.72 (0.26), residues: 862 helix: -1.89 (0.61), residues: 56 sheet: -2.40 (0.30), residues: 267 loop : -2.67 (0.24), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 955 HIS 0.002 0.001 HIS C 205 PHE 0.020 0.002 PHE A1089 TYR 0.016 0.002 TYR A1026 ARG 0.005 0.001 ARG B 364 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 96 time to evaluate : 1.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1047 TYR cc_start: 0.8107 (m-80) cc_final: 0.7883 (m-80) REVERT: A 1053 MET cc_start: 0.7060 (mmt) cc_final: 0.6724 (mmt) REVERT: A 1131 ILE cc_start: 0.8407 (mp) cc_final: 0.8158 (mt) REVERT: A 1236 LEU cc_start: 0.8868 (pp) cc_final: 0.8281 (tt) REVERT: A 1239 LYS cc_start: 0.7824 (tptt) cc_final: 0.7304 (mptt) REVERT: A 1240 MET cc_start: 0.8684 (mpp) cc_final: 0.8044 (mpp) REVERT: A 1305 PHE cc_start: 0.6847 (OUTLIER) cc_final: 0.6465 (m-10) REVERT: C 78 ASN cc_start: 0.6250 (t0) cc_final: 0.6027 (t0) REVERT: C 176 GLN cc_start: 0.8627 (mm-40) cc_final: 0.8377 (mp10) REVERT: B 257 TYR cc_start: 0.7304 (m-80) cc_final: 0.7010 (m-80) REVERT: B 365 GLU cc_start: 0.7453 (mp0) cc_final: 0.7242 (pm20) REVERT: B 432 ASN cc_start: 0.8761 (t0) cc_final: 0.8270 (p0) outliers start: 32 outliers final: 23 residues processed: 120 average time/residue: 0.1548 time to fit residues: 26.9478 Evaluate side-chains 111 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 87 time to evaluate : 0.725 ------------------------------------------------------------------------------- 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 1046 LEU Chi-restraints excluded: chain A residue 1057 GLU Chi-restraints excluded: chain A residue 1130 LEU Chi-restraints excluded: chain A residue 1169 LEU Chi-restraints excluded: chain A residue 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 59 THR Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 105 PHE Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 358 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 9 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 70 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 chunk 82 optimal weight: 4.9990 chunk 51 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 33 optimal weight: 8.9990 chunk 49 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6952 moved from start: 0.3826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6992 Z= 0.184 Angle : 0.649 10.825 9512 Z= 0.334 Chirality : 0.045 0.164 1054 Planarity : 0.006 0.118 1219 Dihedral : 6.033 63.314 949 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.16 % Favored : 90.84 % Rotamer: Outliers : 4.05 % Allowed : 21.54 % Favored : 74.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.76 % Cis-general : 0.00 % Twisted Proline : 4.88 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.53 (0.26), residues: 862 helix: -1.83 (0.61), residues: 57 sheet: -2.15 (0.31), residues: 256 loop : -2.61 (0.24), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 955 HIS 0.002 0.001 HIS C 205 PHE 0.020 0.002 PHE A1089 TYR 0.015 0.001 TYR A1026 ARG 0.005 0.000 ARG B 275 *********************** 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 124 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 93 time to evaluate : 0.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1033 PHE cc_start: 0.7519 (OUTLIER) cc_final: 0.6469 (t80) REVERT: A 1053 MET cc_start: 0.7122 (mmt) cc_final: 0.6828 (mmt) REVERT: A 1131 ILE cc_start: 0.8329 (OUTLIER) cc_final: 0.8068 (mt) REVERT: A 1236 LEU cc_start: 0.8867 (pp) cc_final: 0.8082 (tt) REVERT: A 1239 LYS cc_start: 0.7790 (tptt) cc_final: 0.7327 (mptt) REVERT: A 1240 MET cc_start: 0.8655 (mpp) cc_final: 0.8212 (mpp) REVERT: C 78 ASN cc_start: 0.6572 (t0) cc_final: 0.6246 (t0) REVERT: C 176 GLN cc_start: 0.8634 (mm-40) cc_final: 0.8401 (mp10) REVERT: B 365 GLU cc_start: 0.7501 (mp0) cc_final: 0.7260 (pm20) REVERT: B 432 ASN cc_start: 0.8769 (t0) cc_final: 0.8249 (p0) outliers start: 31 outliers final: 22 residues processed: 114 average time/residue: 0.1397 time to fit residues: 23.1911 Evaluate side-chains 114 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 90 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 891 ILE Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1033 PHE Chi-restraints excluded: chain A residue 1046 LEU Chi-restraints excluded: chain A residue 1057 GLU Chi-restraints excluded: chain A residue 1130 LEU Chi-restraints excluded: chain A residue 1131 ILE Chi-restraints excluded: chain A residue 1268 VAL Chi-restraints excluded: chain A residue 1313 THR Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 34 TYR Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 105 PHE Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain B residue 224 MET Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 358 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 24 optimal weight: 0.8980 chunk 16 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 chunk 40 optimal weight: 0.1980 chunk 7 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 75 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 72 optimal weight: 9.9990 chunk 77 optimal weight: 6.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1292 ASN ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6924 moved from start: 0.4074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6992 Z= 0.169 Angle : 0.643 10.229 9512 Z= 0.328 Chirality : 0.045 0.161 1054 Planarity : 0.006 0.117 1219 Dihedral : 5.944 63.196 949 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 16.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.16 % Favored : 90.84 % Rotamer: Outliers : 4.18 % Allowed : 22.32 % Favored : 73.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.76 % Cis-general : 0.00 % Twisted Proline : 4.88 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.39 (0.26), residues: 862 helix: -1.71 (0.61), residues: 57 sheet: -2.10 (0.31), residues: 258 loop : -2.48 (0.24), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 955 HIS 0.002 0.001 HIS A1271 PHE 0.032 0.002 PHE B 340 TYR 0.012 0.001 TYR A1026 ARG 0.004 0.000 ARG B 275 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 96 time to evaluate : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 903 ASN cc_start: 0.8065 (p0) cc_final: 0.7833 (p0) REVERT: A 939 MET cc_start: 0.8956 (mtm) cc_final: 0.8448 (tmm) REVERT: A 1033 PHE cc_start: 0.7427 (OUTLIER) cc_final: 0.6420 (t80) REVERT: A 1047 TYR cc_start: 0.7814 (m-80) cc_final: 0.7371 (m-80) REVERT: A 1131 ILE cc_start: 0.8332 (OUTLIER) cc_final: 0.8119 (mt) REVERT: A 1236 LEU cc_start: 0.8846 (pp) cc_final: 0.8148 (tt) REVERT: A 1239 LYS cc_start: 0.7753 (tptt) cc_final: 0.7322 (mptt) REVERT: A 1240 MET cc_start: 0.8602 (mpp) cc_final: 0.8348 (mpp) REVERT: B 365 GLU cc_start: 0.7550 (mp0) cc_final: 0.7331 (pm20) REVERT: B 432 ASN cc_start: 0.8758 (t0) cc_final: 0.8234 (p0) outliers start: 32 outliers final: 23 residues processed: 118 average time/residue: 0.1433 time to fit residues: 24.5713 Evaluate side-chains 117 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 92 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 891 ILE Chi-restraints excluded: chain A residue 1003 THR Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1033 PHE Chi-restraints excluded: chain A residue 1046 LEU Chi-restraints excluded: chain A residue 1130 LEU Chi-restraints excluded: chain A residue 1131 ILE Chi-restraints excluded: chain A residue 1268 VAL Chi-restraints excluded: chain A residue 1313 THR Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 34 TYR Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 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 238 GLU Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 351 THR 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 79 optimal weight: 5.9990 chunk 46 optimal weight: 6.9990 chunk 33 optimal weight: 0.0980 chunk 60 optimal weight: 0.6980 chunk 23 optimal weight: 0.0980 chunk 69 optimal weight: 6.9990 chunk 73 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 50 optimal weight: 0.0870 chunk 81 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 overall best weight: 0.3558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1216 ASN C 169 HIS ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6823 moved from start: 0.4502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 6992 Z= 0.146 Angle : 0.641 9.823 9512 Z= 0.325 Chirality : 0.044 0.161 1054 Planarity : 0.005 0.115 1219 Dihedral : 5.647 63.154 949 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 3.13 % Allowed : 23.24 % Favored : 73.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.76 % Cis-general : 0.00 % Twisted Proline : 4.88 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.15 (0.27), residues: 862 helix: -1.62 (0.61), residues: 57 sheet: -1.95 (0.31), residues: 258 loop : -2.30 (0.25), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 955 HIS 0.002 0.001 HIS A1271 PHE 0.032 0.002 PHE C 127 TYR 0.031 0.001 TYR C 54 ARG 0.004 0.000 ARG B 275 *********************** 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 131 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 107 time to evaluate : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 903 ASN cc_start: 0.7991 (p0) cc_final: 0.7753 (p0) REVERT: A 939 MET cc_start: 0.8941 (mtm) cc_final: 0.8383 (tmm) REVERT: A 1033 PHE cc_start: 0.7389 (OUTLIER) cc_final: 0.6392 (t80) REVERT: A 1047 TYR cc_start: 0.7611 (m-80) cc_final: 0.7225 (m-80) REVERT: A 1236 LEU cc_start: 0.8805 (pp) cc_final: 0.8125 (tt) REVERT: A 1239 LYS cc_start: 0.7657 (tptt) cc_final: 0.6546 (mptt) REVERT: C 49 TRP cc_start: 0.4127 (p90) cc_final: 0.3535 (p-90) REVERT: C 202 ASN cc_start: 0.6965 (m110) cc_final: 0.6527 (m110) REVERT: B 267 LEU cc_start: 0.8231 (pt) cc_final: 0.7743 (tt) REVERT: B 354 VAL cc_start: 0.8323 (t) cc_final: 0.8118 (t) REVERT: B 365 GLU cc_start: 0.7531 (mp0) cc_final: 0.7316 (pm20) REVERT: B 432 ASN cc_start: 0.8702 (t0) cc_final: 0.8221 (p0) outliers start: 24 outliers final: 18 residues processed: 124 average time/residue: 0.1536 time to fit residues: 26.9453 Evaluate side-chains 114 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 95 time to evaluate : 0.779 ------------------------------------------------------------------------------- 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 1130 LEU Chi-restraints excluded: chain A residue 1268 VAL Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 34 TYR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 105 PHE Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain B residue 224 MET Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 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 38 optimal weight: 6.9990 chunk 56 optimal weight: 8.9990 chunk 85 optimal weight: 10.0000 chunk 78 optimal weight: 6.9990 chunk 68 optimal weight: 4.9990 chunk 7 optimal weight: 7.9990 chunk 52 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 72 optimal weight: 9.9990 chunk 20 optimal weight: 1.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 0.4211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 6992 Z= 0.427 Angle : 0.809 9.546 9512 Z= 0.424 Chirality : 0.049 0.177 1054 Planarity : 0.007 0.115 1219 Dihedral : 6.780 64.847 949 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 26.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.18 % Favored : 87.82 % Rotamer: Outliers : 3.52 % Allowed : 23.24 % Favored : 73.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.76 % Cis-general : 0.00 % Twisted Proline : 2.44 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.39 (0.26), residues: 862 helix: -2.00 (0.59), residues: 57 sheet: -2.06 (0.31), residues: 259 loop : -2.48 (0.24), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.004 TRP B 256 HIS 0.003 0.001 HIS C 169 PHE 0.033 0.003 PHE C 127 TYR 0.026 0.003 TYR A1150 ARG 0.010 0.001 ARG B 364 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 83 time to evaluate : 0.787 Fit side-chains revert: symmetry clash REVERT: A 903 ASN cc_start: 0.8272 (p0) cc_final: 0.8070 (p0) REVERT: A 939 MET cc_start: 0.8987 (mtm) cc_final: 0.8477 (tmm) REVERT: A 1033 PHE cc_start: 0.7681 (OUTLIER) cc_final: 0.6807 (t80) REVERT: A 1239 LYS cc_start: 0.8069 (tptt) cc_final: 0.7436 (mptt) REVERT: C 54 TYR cc_start: 0.4467 (t80) cc_final: 0.4252 (t80) REVERT: B 365 GLU cc_start: 0.7680 (mp0) cc_final: 0.7254 (pm20) REVERT: B 432 ASN cc_start: 0.8805 (t0) cc_final: 0.8262 (p0) outliers start: 27 outliers final: 18 residues processed: 103 average time/residue: 0.1445 time to fit residues: 21.9242 Evaluate side-chains 95 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 76 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 891 ILE Chi-restraints excluded: chain A residue 933 VAL Chi-restraints excluded: chain A residue 1003 THR Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1033 PHE Chi-restraints excluded: chain A residue 1130 LEU Chi-restraints excluded: chain A residue 1150 TYR Chi-restraints excluded: chain A residue 1214 ASP Chi-restraints excluded: chain A residue 1268 VAL Chi-restraints excluded: chain 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 187 VAL Chi-restraints excluded: chain B residue 224 MET Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 418 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 62 optimal weight: 2.9990 chunk 10 optimal weight: 0.0370 chunk 18 optimal weight: 4.9990 chunk 68 optimal weight: 0.5980 chunk 28 optimal weight: 0.6980 chunk 70 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 103 ASN ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.099526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.079532 restraints weight = 19962.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.082742 restraints weight = 11178.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.085026 restraints weight = 7316.416| |-----------------------------------------------------------------------------| r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6905 moved from start: 0.4629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6992 Z= 0.175 Angle : 0.708 9.791 9512 Z= 0.361 Chirality : 0.046 0.264 1054 Planarity : 0.006 0.118 1219 Dihedral : 6.071 64.349 949 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 16.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 2.48 % Allowed : 25.07 % Favored : 72.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.76 % Cis-general : 0.00 % Twisted Proline : 4.88 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.21 (0.26), residues: 862 helix: -1.62 (0.63), residues: 57 sheet: -2.02 (0.31), residues: 253 loop : -2.33 (0.24), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.077 0.003 TRP B 256 HIS 0.002 0.001 HIS A1271 PHE 0.032 0.002 PHE C 127 TYR 0.021 0.002 TYR C 54 ARG 0.007 0.001 ARG B 364 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1713.36 seconds wall clock time: 31 minutes 48.05 seconds (1908.05 seconds total)