Starting phenix.real_space_refine (version: 1.21rc1) on Tue Jul 4 05:43:43 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oh0_12890/07_2023/7oh0_12890.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oh0_12890/07_2023/7oh0_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_12890/07_2023/7oh0_12890.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oh0_12890/07_2023/7oh0_12890.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oh0_12890/07_2023/7oh0_12890.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oh0_12890/07_2023/7oh0_12890.pdb" } 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 ------------------------------------------------------------------------------- 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 Residue "A ASP 890": "OD1" <-> "OD2" Residue "A PHE 902": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 942": "OE1" <-> "OE2" Residue "A GLU 967": "OE1" <-> "OE2" Residue "A TYR 974": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1039": "OD1" <-> "OD2" Residue "A ARG 1040": "NH1" <-> "NH2" Residue "A PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1092": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1127": "OE1" <-> "OE2" Residue "A TYR 1129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1179": "NH1" <-> "NH2" Residue "A TYR 1180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1187": "OD1" <-> "OD2" Residue "A PHE 1189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1222": "OD1" <-> "OD2" Residue "A TYR 1251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1309": "OD1" <-> "OD2" Residue "C ARG 13": "NH1" <-> "NH2" Residue "C GLU 16": "OE1" <-> "OE2" Residue "C ASP 26": "OD1" <-> "OD2" Residue "C TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 99": "NH1" <-> "NH2" Residue "C PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 215": "NH1" <-> "NH2" Residue "B ARG 245": "NH1" <-> "NH2" Residue "B TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 266": "NH1" <-> "NH2" Residue "B PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 303": "OD1" <-> "OD2" Residue "B TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 330": "NH1" <-> "NH2" Residue "B PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 364": "NH1" <-> "NH2" Residue "B ARG 433": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/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: 3.90, per 1000 atoms: 0.57 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.75 Conformation dependent library (CDL) restraints added in 980.4 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: 0.49 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: 2.42 Time building geometry restraints manager: 3.00 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: 100.22 - 107.01: 228 107.01 - 113.80: 3874 113.80 - 120.59: 2520 120.59 - 127.38: 2817 127.38 - 134.17: 73 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 2.440 nonbonded pdb=" O ASN C 103 " pdb=" OH TYR B 318 " model vdw 2.087 2.440 nonbonded pdb=" O SER C 193 " pdb=" OH TYR C 199 " model vdw 2.099 2.440 nonbonded pdb=" N SER A1156 " pdb=" O ASN B 314 " model vdw 2.130 2.520 nonbonded pdb=" OG SER A 979 " pdb=" O SER A 989 " model vdw 2.134 2.440 ... (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 ========== 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: 1.470 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: 6.270 Check model and map are aligned: 0.120 Set scattering table: 0.060 Process input model: 21.690 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.750 ------------------------------------------------------------------------------- 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 % 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 *********************** 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 : 0.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 124 average time/residue: 0.1941 time to fit residues: 32.2947 Evaluate side-chains 82 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 81 time to evaluate : 0.820 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0651 time to fit residues: 1.2031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 72 optimal weight: 0.7980 chunk 65 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 43 optimal weight: 0.0030 chunk 34 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 chunk 26 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 50 optimal weight: 6.9990 chunk 78 optimal weight: 5.9990 overall best weight: 0.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 936 HIS A 998 ASN ** A 999 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1069 ASN A1292 ASN A1293 HIS ** C 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 202 ASN C 204 ASN ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 227 GLN B 259 GLN ** B 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6920 moved from start: 0.1915 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= 0.182 Angle : 0.679 8.263 9512 Z= 0.357 Chirality : 0.046 0.159 1054 Planarity : 0.006 0.101 1219 Dihedral : 6.545 64.845 948 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 21.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.09 % Favored : 89.91 % Rotamer Outliers : 3.66 % 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: -4.72 (0.23), residues: 862 helix: -2.46 (0.58), residues: 48 sheet: -3.02 (0.28), residues: 240 loop : -3.45 (0.21), residues: 574 *********************** 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 fitting. rotamer outliers: 28 poor density : 113 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 17 residues processed: 129 average time/residue: 0.1460 time to fit residues: 27.2707 Evaluate side-chains 100 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 83 time to evaluate : 0.816 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.0890 time to fit residues: 3.5380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 43 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 64 optimal weight: 0.1980 chunk 53 optimal weight: 0.0770 chunk 21 optimal weight: 1.9990 chunk 78 optimal weight: 10.0000 chunk 84 optimal weight: 20.0000 chunk 69 optimal weight: 0.9980 chunk 77 optimal weight: 6.9990 chunk 26 optimal weight: 0.9990 chunk 62 optimal weight: 7.9990 overall best weight: 0.8542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 927 ASN ** A 999 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 311 GLN ** B 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6895 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 6992 Z= 0.176 Angle : 0.657 10.337 9512 Z= 0.341 Chirality : 0.045 0.161 1054 Planarity : 0.006 0.115 1219 Dihedral : 6.136 64.285 948 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 21.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.63 % Favored : 90.37 % Rotamer Outliers : 1.70 % 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: -4.14 (0.25), residues: 862 helix: -1.68 (0.70), residues: 47 sheet: -2.84 (0.28), residues: 258 loop : -2.94 (0.23), residues: 557 *********************** 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 125 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 112 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 4 residues processed: 124 average time/residue: 0.1593 time to fit residues: 28.1016 Evaluate side-chains 91 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 87 time to evaluate : 0.787 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0751 time to fit residues: 1.6481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 77 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 40 optimal weight: 9.9990 chunk 8 optimal weight: 0.4980 chunk 37 optimal weight: 10.0000 chunk 52 optimal weight: 6.9990 chunk 78 optimal weight: 5.9990 chunk 83 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 chunk 74 optimal weight: 0.8980 chunk 22 optimal weight: 5.9990 overall best weight: 2.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 999 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1163 ASN ** B 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7028 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 6992 Z= 0.280 Angle : 0.713 9.797 9512 Z= 0.371 Chirality : 0.046 0.165 1054 Planarity : 0.006 0.119 1219 Dihedral : 6.426 64.954 948 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 26.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.11 % Favored : 86.89 % Rotamer Outliers : 6.01 % 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: -4.10 (0.25), residues: 862 helix: -2.13 (0.59), residues: 54 sheet: -2.54 (0.30), residues: 252 loop : -3.02 (0.23), residues: 556 *********************** 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 130 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 84 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 27 residues processed: 120 average time/residue: 0.1684 time to fit residues: 28.6204 Evaluate side-chains 105 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 78 time to evaluate : 0.786 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.0720 time to fit residues: 4.6473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 69 optimal weight: 3.9990 chunk 47 optimal weight: 0.0570 chunk 1 optimal weight: 8.9990 chunk 61 optimal weight: 5.9990 chunk 34 optimal weight: 6.9990 chunk 70 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 42 optimal weight: 4.9990 chunk 74 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 overall best weight: 1.3302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 999 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6963 moved from start: 0.3145 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= 0.200 Angle : 0.659 10.875 9512 Z= 0.341 Chirality : 0.045 0.200 1054 Planarity : 0.006 0.120 1219 Dihedral : 6.151 64.609 948 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 22.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.32 % Favored : 89.68 % Rotamer Outliers : 1.31 % 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: -3.81 (0.26), residues: 862 helix: -1.51 (0.66), residues: 48 sheet: -2.49 (0.31), residues: 243 loop : -2.79 (0.23), residues: 571 *********************** 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 110 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 100 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 4 residues processed: 108 average time/residue: 0.1448 time to fit residues: 23.2018 Evaluate side-chains 86 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 82 time to evaluate : 0.820 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0745 time to fit residues: 1.6063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.2980 chunk 48 optimal weight: 7.9990 chunk 20 optimal weight: 6.9990 chunk 83 optimal weight: 10.0000 chunk 69 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 chunk 6 optimal weight: 10.0000 chunk 43 optimal weight: 5.9990 chunk 80 optimal weight: 8.9990 overall best weight: 3.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 999 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** 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: 0.7121 moved from start: 0.3275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.058 6992 Z= 0.392 Angle : 0.794 10.763 9512 Z= 0.417 Chirality : 0.049 0.203 1054 Planarity : 0.007 0.131 1219 Dihedral : 7.082 66.184 948 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 35.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.85 % Favored : 85.15 % Rotamer Outliers : 3.52 % 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: -4.12 (0.25), residues: 862 helix: -2.30 (0.54), residues: 55 sheet: -2.57 (0.30), residues: 259 loop : -3.02 (0.23), residues: 548 *********************** 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 104 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 77 time to evaluate : 0.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 17 residues processed: 99 average time/residue: 0.1485 time to fit residues: 21.9516 Evaluate side-chains 86 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 69 time to evaluate : 0.875 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1008 time to fit residues: 3.6625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 9 optimal weight: 0.3980 chunk 47 optimal weight: 0.4980 chunk 60 optimal weight: 0.7980 chunk 70 optimal weight: 5.9990 chunk 46 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 38 optimal weight: 0.4980 chunk 33 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 999 ASN ** B 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6955 moved from start: 0.3591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 6992 Z= 0.175 Angle : 0.706 13.245 9512 Z= 0.357 Chirality : 0.046 0.164 1054 Planarity : 0.006 0.128 1219 Dihedral : 6.291 65.472 948 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 23.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.16 % Favored : 90.84 % Rotamer Outliers : 2.22 % 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: -3.75 (0.26), residues: 862 helix: -1.25 (0.67), residues: 48 sheet: -2.57 (0.29), residues: 249 loop : -2.69 (0.24), residues: 565 *********************** 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 113 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 96 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 5 residues processed: 107 average time/residue: 0.1456 time to fit residues: 23.8875 Evaluate side-chains 86 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 81 time to evaluate : 0.828 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0732 time to fit residues: 1.8200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 24 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 56 optimal weight: 0.1980 chunk 40 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 72 optimal weight: 7.9990 chunk 77 optimal weight: 8.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6995 moved from start: 0.3766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 6992 Z= 0.215 Angle : 0.725 13.089 9512 Z= 0.364 Chirality : 0.046 0.163 1054 Planarity : 0.006 0.133 1219 Dihedral : 6.288 66.030 948 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 24.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.48 % Favored : 88.52 % Rotamer Outliers : 1.70 % 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: -3.63 (0.26), residues: 862 helix: -1.28 (0.66), residues: 49 sheet: -2.46 (0.30), residues: 240 loop : -2.63 (0.24), residues: 573 *********************** 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 101 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 88 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 9 residues processed: 96 average time/residue: 0.1335 time to fit residues: 19.5747 Evaluate side-chains 94 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 85 time to evaluate : 0.807 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0765 time to fit residues: 2.2539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 79 optimal weight: 4.9990 chunk 46 optimal weight: 5.9990 chunk 33 optimal weight: 9.9990 chunk 60 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 69 optimal weight: 0.1980 chunk 73 optimal weight: 0.7980 chunk 76 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6971 moved from start: 0.3993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 6992 Z= 0.208 Angle : 0.712 12.855 9512 Z= 0.361 Chirality : 0.046 0.158 1054 Planarity : 0.006 0.135 1219 Dihedral : 6.137 66.043 948 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 23.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.98 % Favored : 90.02 % Rotamer Outliers : 1.31 % 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: -3.51 (0.26), residues: 862 helix: -1.17 (0.67), residues: 49 sheet: -2.37 (0.31), residues: 238 loop : -2.55 (0.24), residues: 575 *********************** 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 103 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 93 time to evaluate : 0.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 8 residues processed: 100 average time/residue: 0.1412 time to fit residues: 21.3491 Evaluate side-chains 90 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 82 time to evaluate : 0.817 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0712 time to fit residues: 2.1072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 38 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 68 optimal weight: 0.1980 chunk 7 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 overall best weight: 2.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1292 ASN ** C 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7047 moved from start: 0.4052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 6992 Z= 0.278 Angle : 0.767 13.338 9512 Z= 0.390 Chirality : 0.047 0.169 1054 Planarity : 0.007 0.137 1219 Dihedral : 6.561 66.171 948 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 28.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.53 % Favored : 87.47 % Rotamer Outliers : 0.91 % 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: -3.73 (0.25), residues: 862 helix: -1.71 (0.61), residues: 56 sheet: -2.50 (0.30), residues: 241 loop : -2.68 (0.23), residues: 565 ********************** 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 86 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 79 time to evaluate : 0.846 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 83 average time/residue: 0.1348 time to fit residues: 17.2175 Evaluate side-chains 82 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 77 time to evaluate : 0.752 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0775 time to fit residues: 1.6735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 62 optimal weight: 0.1980 chunk 10 optimal weight: 4.9990 chunk 18 optimal weight: 9.9990 chunk 68 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 70 optimal weight: 7.9990 chunk 8 optimal weight: 3.9990 chunk 12 optimal weight: 0.0170 chunk 59 optimal weight: 0.1980 chunk 3 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 overall best weight: 0.6620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1292 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.098133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.077393 restraints weight = 20116.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.080812 restraints weight = 10928.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.083217 restraints weight = 7038.013| |-----------------------------------------------------------------------------| r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6838 moved from start: 0.4324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 6992 Z= 0.175 Angle : 0.726 12.830 9512 Z= 0.362 Chirality : 0.045 0.153 1054 Planarity : 0.006 0.134 1219 Dihedral : 6.031 66.481 948 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 23.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.93 % Favored : 91.07 % Rotamer Outliers : 0.26 % 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: -3.35 (0.26), residues: 862 helix: -1.04 (0.69), residues: 49 sheet: -2.36 (0.31), residues: 240 loop : -2.39 (0.24), residues: 573 =============================================================================== Job complete usr+sys time: 1592.32 seconds wall clock time: 29 minutes 50.79 seconds (1790.79 seconds total)