Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 15:57:42 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7svr_25452/04_2023/7svr_25452_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7svr_25452/04_2023/7svr_25452.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/7svr_25452/04_2023/7svr_25452.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7svr_25452/04_2023/7svr_25452.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7svr_25452/04_2023/7svr_25452_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7svr_25452/04_2023/7svr_25452_updated.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= 0.002 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: 5 Type Number sf(0) Gaussians S 28 5.16 5 C 5046 2.51 5 N 1375 2.21 5 O 1390 1.98 5 F 2 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 21": "NH1" <-> "NH2" Residue "A ARG 29": "NH1" <-> "NH2" Residue "A ARG 55": "NH1" <-> "NH2" Residue "A ARG 59": "NH1" <-> "NH2" Residue "A PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 104": "NH1" <-> "NH2" Residue "A ARG 134": "NH1" <-> "NH2" Residue "A ASP 173": "OD1" <-> "OD2" Residue "A PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 192": "OD1" <-> "OD2" Residue "A PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 242": "NH1" <-> "NH2" Residue "A GLU 257": "OE1" <-> "OE2" Residue "A ARG 258": "NH1" <-> "NH2" Residue "A GLU 279": "OE1" <-> "OE2" Residue "A ARG 289": "NH1" <-> "NH2" Residue "A GLU 292": "OE1" <-> "OE2" Residue "A ARG 297": "NH1" <-> "NH2" Residue "A ARG 303": "NH1" <-> "NH2" Residue "A PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 334": "NH1" <-> "NH2" Residue "A PHE 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 347": "NH1" <-> "NH2" Residue "A PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 913": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 932": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 933": "NH1" <-> "NH2" Residue "A ASP 993": "OD1" <-> "OD2" Residue "A TYR 1032": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1092": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1166": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 7841 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1134, 7713 Classifications: {'peptide': 1134} Incomplete info: {'truncation_to_alanine': 403} Link IDs: {'PTRANS': 28, 'TRANS': 1105} Chain breaks: 6 Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 1433 Unresolved non-hydrogen angles: 1826 Unresolved non-hydrogen dihedrals: 1188 Unresolved non-hydrogen chiralities: 143 Planarities with less than four sites: {'GLN:plan1': 22, 'HIS:plan': 7, 'TYR:plan': 13, 'ASN:plan1': 14, 'TRP:plan': 6, 'ASP:plan': 22, 'PHE:plan': 21, 'GLU:plan': 35, 'ARG:plan': 21} Unresolved non-hydrogen planarities: 747 Chain: "B" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 95 Classifications: {'peptide': 19} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'TRANS': 18} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'UNK:plan-1': 19} Unresolved non-hydrogen planarities: 19 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'VX8': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.62, per 1000 atoms: 0.59 Number of scatterers: 7841 At special positions: 0 Unit cell: (103, 118.45, 112.27, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 28 16.00 F 2 9.00 O 1390 8.00 N 1375 7.00 C 5046 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 3.01 Conformation dependent library (CDL) restraints added in 1.3 seconds 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2168 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 53 helices and 6 sheets defined 61.9% alpha, 4.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.87 Creating SS restraints... Processing helix chain 'A' and resid 11 through 15 Processing helix chain 'A' and resid 21 through 27 Processing helix chain 'A' and resid 34 through 36 No H-bonds generated for 'chain 'A' and resid 34 through 36' Processing helix chain 'A' and resid 42 through 44 No H-bonds generated for 'chain 'A' and resid 42 through 44' Processing helix chain 'A' and resid 46 through 63 removed outlier: 4.439A pdb=" N SER A 50 " --> pdb=" O ASP A 47 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N GLU A 51 " --> pdb=" O ASN A 48 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASP A 58 " --> pdb=" O ARG A 55 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N SER A 63 " --> pdb=" O GLU A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 73 Processing helix chain 'A' and resid 78 through 102 removed outlier: 4.310A pdb=" N PHE A 87 " --> pdb=" O PHE A 83 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS A 95 " --> pdb=" O GLY A 91 " (cutoff:3.500A) Proline residue: A 99 - end of helix Processing helix chain 'A' and resid 121 through 137 Processing helix chain 'A' and resid 139 through 166 removed outlier: 3.593A pdb=" N LEU A 165 " --> pdb=" O TYR A 161 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N LYS A 166 " --> pdb=" O LYS A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 174 removed outlier: 4.824A pdb=" N LYS A 174 " --> pdb=" O ARG A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 187 removed outlier: 4.447A pdb=" N VAL A 181 " --> pdb=" O ILE A 177 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ASN A 187 " --> pdb=" O LEU A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 193 No H-bonds generated for 'chain 'A' and resid 190 through 193' Processing helix chain 'A' and resid 199 through 201 No H-bonds generated for 'chain 'A' and resid 199 through 201' Processing helix chain 'A' and resid 203 through 219 removed outlier: 4.240A pdb=" N GLY A 213 " --> pdb=" O ALA A 209 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N TRP A 216 " --> pdb=" O MET A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 275 removed outlier: 3.980A pdb=" N PHE A 229 " --> pdb=" O CYS A 225 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY A 241 " --> pdb=" O GLN A 237 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ARG A 242 " --> pdb=" O ALA A 238 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N MET A 243 " --> pdb=" O GLY A 239 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N TYR A 247 " --> pdb=" O MET A 243 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLY A 253 " --> pdb=" O ASP A 249 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LYS A 254 " --> pdb=" O GLN A 250 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ILE A 261 " --> pdb=" O GLU A 257 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N THR A 262 " --> pdb=" O ARG A 258 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N GLN A 270 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N SER A 271 " --> pdb=" O GLU A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 328 removed outlier: 4.837A pdb=" N THR A 291 " --> pdb=" O ASN A 287 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLU A 292 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE A 310 " --> pdb=" O ASN A 306 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N PHE A 311 " --> pdb=" O SER A 307 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N GLY A 314 " --> pdb=" O PHE A 310 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N PHE A 315 " --> pdb=" O PHE A 311 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N PHE A 316 " --> pdb=" O PHE A 312 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N VAL A 318 " --> pdb=" O GLY A 314 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N SER A 321 " --> pdb=" O VAL A 317 " (cutoff:3.500A) Proline residue: A 324 - end of helix Processing helix chain 'A' and resid 333 through 349 removed outlier: 3.941A pdb=" N PHE A 337 " --> pdb=" O ARG A 334 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N THR A 338 " --> pdb=" O LYS A 335 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR A 339 " --> pdb=" O ILE A 336 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ILE A 340 " --> pdb=" O PHE A 337 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ILE A 344 " --> pdb=" O SER A 341 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU A 346 " --> pdb=" O CYS A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 375 Processing helix chain 'A' and resid 464 through 471 Processing helix chain 'A' and resid 502 through 505 No H-bonds generated for 'chain 'A' and resid 502 through 505' Processing helix chain 'A' and resid 514 through 523 Processing helix chain 'A' and resid 527 through 531 Processing helix chain 'A' and resid 550 through 562 Processing helix chain 'A' and resid 574 through 576 No H-bonds generated for 'chain 'A' and resid 574 through 576' Processing helix chain 'A' and resid 580 through 589 Processing helix chain 'A' and resid 610 through 612 No H-bonds generated for 'chain 'A' and resid 610 through 612' Processing helix chain 'A' and resid 630 through 633 No H-bonds generated for 'chain 'A' and resid 630 through 633' Processing helix chain 'A' and resid 638 through 644 Processing helix chain 'A' and resid 846 through 853 Processing helix chain 'A' and resid 859 through 885 Processing helix chain 'A' and resid 911 through 920 removed outlier: 4.481A pdb=" N TYR A 917 " --> pdb=" O TYR A 913 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N ILE A 918 " --> pdb=" O TYR A 914 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N TYR A 919 " --> pdb=" O VAL A 915 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N VAL A 920 " --> pdb=" O PHE A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 927 removed outlier: 3.748A pdb=" N LEU A 927 " --> pdb=" O ALA A 923 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 923 through 927' Processing helix chain 'A' and resid 935 through 956 Processing helix chain 'A' and resid 961 through 964 No H-bonds generated for 'chain 'A' and resid 961 through 964' Processing helix chain 'A' and resid 969 through 975 removed outlier: 3.553A pdb=" N ILE A 972 " --> pdb=" O ALA A 969 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N LEU A 973 " --> pdb=" O GLY A 970 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N ASN A 974 " --> pdb=" O GLY A 971 " (cutoff:3.500A) Processing helix chain 'A' and resid 979 through 1011 removed outlier: 5.055A pdb=" N LEU A 987 " --> pdb=" O LEU A 983 " (cutoff:3.500A) Proline residue: A 988 - end of helix removed outlier: 3.608A pdb=" N LEU A1011 " --> pdb=" O VAL A1007 " (cutoff:3.500A) Processing helix chain 'A' and resid 1015 through 1047 Proline residue: A1021 - end of helix removed outlier: 4.027A pdb=" N ALA A1025 " --> pdb=" O PRO A1021 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLN A1035 " --> pdb=" O ALA A1031 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N THR A1036 " --> pdb=" O TYR A1032 " (cutoff:3.500A) Processing helix chain 'A' and resid 1049 through 1060 Processing helix chain 'A' and resid 1062 through 1068 Processing helix chain 'A' and resid 1071 through 1119 removed outlier: 3.993A pdb=" N ASN A1088 " --> pdb=" O LEU A1084 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1167 removed outlier: 4.138A pdb=" N ASN A1138 " --> pdb=" O THR A1134 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N MET A1140 " --> pdb=" O ALA A1136 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N SER A1141 " --> pdb=" O MET A1137 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N THR A1142 " --> pdb=" O ASN A1138 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ARG A1158 " --> pdb=" O ASP A1154 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N SER A1159 " --> pdb=" O SER A1155 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N VAL A1160 " --> pdb=" O LEU A1156 " (cutoff:3.500A) Processing helix chain 'A' and resid 1251 through 1258 removed outlier: 3.812A pdb=" N LEU A1258 " --> pdb=" O LEU A1254 " (cutoff:3.500A) Processing helix chain 'A' and resid 1279 through 1282 No H-bonds generated for 'chain 'A' and resid 1279 through 1282' Processing helix chain 'A' and resid 1300 through 1304 Processing helix chain 'A' and resid 1312 through 1320 Processing helix chain 'A' and resid 1325 through 1329 Processing helix chain 'A' and resid 1340 through 1343 No H-bonds generated for 'chain 'A' and resid 1340 through 1343' Processing helix chain 'A' and resid 1348 through 1361 Processing helix chain 'A' and resid 1372 through 1375 No H-bonds generated for 'chain 'A' and resid 1372 through 1375' Processing helix chain 'A' and resid 1378 through 1390 removed outlier: 3.588A pdb=" N GLN A1390 " --> pdb=" O ARG A1386 " (cutoff:3.500A) Processing helix chain 'A' and resid 1404 through 1407 No H-bonds generated for 'chain 'A' and resid 1404 through 1407' Processing helix chain 'A' and resid 1430 through 1433 No H-bonds generated for 'chain 'A' and resid 1430 through 1433' Processing helix chain 'B' and resid 10 through 17 removed outlier: 3.557A pdb=" N UNK B 15 " --> pdb=" O UNK B 11 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N UNK B 16 " --> pdb=" O UNK B 12 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 446 through 448 Processing sheet with id= B, first strand: chain 'A' and resid 600 through 603 removed outlier: 3.625A pdb=" N LEU A 602 " --> pdb=" O LEU A 454 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N LYS A 615 " --> pdb=" O ALA A 455 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N ALA A 457 " --> pdb=" O LYS A 615 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N LEU A 617 " --> pdb=" O ALA A 457 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILE A 616 " --> pdb=" O GLY A 628 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY A 628 " --> pdb=" O ILE A 616 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N PHE A 626 " --> pdb=" O ILE A 618 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N HIS A 620 " --> pdb=" O SER A 624 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N SER A 624 " --> pdb=" O HIS A 620 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 488 through 491 removed outlier: 6.340A pdb=" N LEU A 568 " --> pdb=" O SER A 489 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N CYS A 491 " --> pdb=" O LEU A 568 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N LEU A 570 " --> pdb=" O CYS A 491 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 1232 through 1234 Processing sheet with id= E, first strand: chain 'A' and resid 1216 through 1218 Processing sheet with id= F, first strand: chain 'A' and resid 1286 through 1289 removed outlier: 6.022A pdb=" N ILE A1366 " --> pdb=" O GLY A1287 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N ILE A1289 " --> pdb=" O ILE A1366 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N LEU A1368 " --> pdb=" O ILE A1289 " (cutoff:3.500A) No H-bonds generated for sheet with id= F 446 hydrogen bonds defined for protein. 1248 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: 2.82 Time building geometry restraints manager: 3.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1283 1.31 - 1.44: 2064 1.44 - 1.56: 4571 1.56 - 1.68: 0 1.68 - 1.81: 50 Bond restraints: 7968 Sorted by residual: bond pdb=" C12 VX8 A1501 " pdb=" N2 VX8 A1501 " ideal model delta sigma weight residual 1.359 1.468 -0.109 2.00e-02 2.50e+03 2.96e+01 bond pdb=" C11 VX8 A1501 " pdb=" N2 VX8 A1501 " ideal model delta sigma weight residual 1.397 1.467 -0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" C3 VX8 A1501 " pdb=" C4 VX8 A1501 " ideal model delta sigma weight residual 1.482 1.548 -0.066 2.00e-02 2.50e+03 1.10e+01 bond pdb=" C13 VX8 A1501 " pdb=" C14 VX8 A1501 " ideal model delta sigma weight residual 1.494 1.544 -0.050 2.00e-02 2.50e+03 6.19e+00 bond pdb=" C16 VX8 A1501 " pdb=" O5 VX8 A1501 " ideal model delta sigma weight residual 1.368 1.416 -0.048 2.00e-02 2.50e+03 5.88e+00 ... (remaining 7963 not shown) Histogram of bond angle deviations from ideal: 59.85 - 75.85: 3 75.85 - 91.84: 0 91.84 - 107.84: 211 107.84 - 123.84: 10525 123.84 - 139.83: 138 Bond angle restraints: 10877 Sorted by residual: angle pdb=" C14 VX8 A1501 " pdb=" C13 VX8 A1501 " pdb=" C22 VX8 A1501 " ideal model delta sigma weight residual 117.72 139.83 -22.11 3.00e+00 1.11e-01 5.43e+01 angle pdb=" C11 VX8 A1501 " pdb=" N2 VX8 A1501 " pdb=" C12 VX8 A1501 " ideal model delta sigma weight residual 127.44 115.04 12.40 3.00e+00 1.11e-01 1.71e+01 angle pdb=" N ARG A 104 " pdb=" CA ARG A 104 " pdb=" C ARG A 104 " ideal model delta sigma weight residual 114.31 109.71 4.60 1.29e+00 6.01e-01 1.27e+01 angle pdb=" C12 VX8 A1501 " pdb=" C13 VX8 A1501 " pdb=" C14 VX8 A1501 " ideal model delta sigma weight residual 117.71 107.49 10.22 3.00e+00 1.11e-01 1.16e+01 angle pdb=" N VAL A 956 " pdb=" CA VAL A 956 " pdb=" C VAL A 956 " ideal model delta sigma weight residual 112.90 109.82 3.08 9.60e-01 1.09e+00 1.03e+01 ... (remaining 10872 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.27: 4566 30.27 - 60.54: 94 60.54 - 90.81: 7 90.81 - 121.08: 3 121.08 - 151.35: 3 Dihedral angle restraints: 4673 sinusoidal: 1337 harmonic: 3336 Sorted by residual: dihedral pdb=" C12 VX8 A1501 " pdb=" C13 VX8 A1501 " pdb=" C21 VX8 A1501 " pdb=" C22 VX8 A1501 " ideal model delta sinusoidal sigma weight residual 253.58 102.23 151.35 1 3.00e+01 1.11e-03 2.00e+01 dihedral pdb=" C16 VX8 A1501 " pdb=" C20 VX8 A1501 " pdb=" O5 VX8 A1501 " pdb=" F2 VX8 A1501 " ideal model delta sinusoidal sigma weight residual 236.98 101.86 135.12 1 3.00e+01 1.11e-03 1.82e+01 dihedral pdb=" C17 VX8 A1501 " pdb=" C20 VX8 A1501 " pdb=" O4 VX8 A1501 " pdb=" F2 VX8 A1501 " ideal model delta sinusoidal sigma weight residual 122.94 -101.99 -135.07 1 3.00e+01 1.11e-03 1.82e+01 ... (remaining 4670 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.122: 1326 0.122 - 0.244: 6 0.244 - 0.366: 0 0.366 - 0.488: 0 0.488 - 0.610: 1 Chirality restraints: 1333 Sorted by residual: chirality pdb=" C13 VX8 A1501 " pdb=" C12 VX8 A1501 " pdb=" C14 VX8 A1501 " pdb=" C22 VX8 A1501 " both_signs ideal model delta sigma weight residual True 1.48 0.87 0.61 2.00e-01 2.50e+01 9.30e+00 chirality pdb=" CA HIS A 139 " pdb=" N HIS A 139 " pdb=" C HIS A 139 " pdb=" CB HIS A 139 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.03e-01 chirality pdb=" CA ILE A1289 " pdb=" N ILE A1289 " pdb=" C ILE A1289 " pdb=" CB ILE A1289 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.97e-01 ... (remaining 1330 not shown) Planarity restraints: 1386 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 286 " -0.009 2.00e-02 2.50e+03 1.72e-02 2.97e+00 pdb=" C GLU A 286 " 0.030 2.00e-02 2.50e+03 pdb=" O GLU A 286 " -0.011 2.00e-02 2.50e+03 pdb=" N ASN A 287 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 350 " -0.008 2.00e-02 2.50e+03 1.64e-02 2.68e+00 pdb=" C VAL A 350 " 0.028 2.00e-02 2.50e+03 pdb=" O VAL A 350 " -0.010 2.00e-02 2.50e+03 pdb=" N THR A 351 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 959 " -0.022 5.00e-02 4.00e+02 3.40e-02 1.85e+00 pdb=" N PRO A 960 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 960 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 960 " -0.019 5.00e-02 4.00e+02 ... (remaining 1383 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1120 2.75 - 3.29: 8191 3.29 - 3.83: 12599 3.83 - 4.36: 13179 4.36 - 4.90: 22859 Nonbonded interactions: 57948 Sorted by model distance: nonbonded pdb=" O ASP A1377 " pdb=" N TYR A1381 " model vdw 2.213 2.520 nonbonded pdb=" O ILE A1015 " pdb=" OG1 THR A1019 " model vdw 2.223 2.440 nonbonded pdb=" NH2 ARG A 153 " pdb=" OD2 ASP A 192 " model vdw 2.243 2.520 nonbonded pdb=" O LEU A 850 " pdb=" OG1 THR A 854 " model vdw 2.312 2.440 nonbonded pdb=" OG SER A 313 " pdb=" NH1 ARG A 347 " model vdw 2.314 2.520 ... (remaining 57943 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: 1.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.530 Check model and map are aligned: 0.120 Set scattering table: 0.060 Process input model: 23.900 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 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 : 0.004 0.109 7968 Z= 0.290 Angle : 0.799 22.113 10877 Z= 0.456 Chirality : 0.045 0.610 1333 Planarity : 0.003 0.034 1386 Dihedral : 14.309 151.349 2505 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -2.10 (0.24), residues: 1120 helix: -0.49 (0.19), residues: 680 sheet: -4.59 (0.46), residues: 49 loop : -2.48 (0.29), residues: 391 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 111 average time/residue: 0.1727 time to fit residues: 27.6136 Evaluate side-chains 78 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 0.952 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 20.0000 chunk 86 optimal weight: 0.8980 chunk 47 optimal weight: 6.9990 chunk 29 optimal weight: 7.9990 chunk 58 optimal weight: 20.0000 chunk 46 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 54 optimal weight: 8.9990 chunk 66 optimal weight: 0.8980 chunk 103 optimal weight: 20.0000 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 270 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.1273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 7968 Z= 0.159 Angle : 0.543 6.413 10877 Z= 0.283 Chirality : 0.040 0.144 1333 Planarity : 0.003 0.066 1386 Dihedral : 10.897 147.536 1231 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer Outliers : 1.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.75 (0.26), residues: 1120 helix: 0.57 (0.20), residues: 697 sheet: -4.44 (0.46), residues: 49 loop : -1.90 (0.31), residues: 374 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 90 time to evaluate : 0.938 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 6 residues processed: 97 average time/residue: 0.1571 time to fit residues: 22.8404 Evaluate side-chains 83 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 77 time to evaluate : 0.920 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0731 time to fit residues: 2.0590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 20.0000 chunk 32 optimal weight: 0.8980 chunk 86 optimal weight: 0.5980 chunk 70 optimal weight: 7.9990 chunk 28 optimal weight: 4.9990 chunk 103 optimal weight: 0.7980 chunk 112 optimal weight: 20.0000 chunk 92 optimal weight: 30.0000 chunk 102 optimal weight: 20.0000 chunk 35 optimal weight: 5.9990 chunk 83 optimal weight: 5.9990 overall best weight: 2.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 7968 Z= 0.275 Angle : 0.590 6.597 10877 Z= 0.306 Chirality : 0.041 0.134 1333 Planarity : 0.003 0.056 1386 Dihedral : 11.078 147.518 1231 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer Outliers : 2.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.68 (0.26), residues: 1120 helix: 0.67 (0.20), residues: 693 sheet: -4.04 (0.47), residues: 60 loop : -1.92 (0.32), residues: 367 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 85 time to evaluate : 1.041 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 7 residues processed: 91 average time/residue: 0.1615 time to fit residues: 22.1360 Evaluate side-chains 84 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 77 time to evaluate : 0.840 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0819 time to fit residues: 2.1134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 9.9990 chunk 77 optimal weight: 4.9990 chunk 53 optimal weight: 10.0000 chunk 11 optimal weight: 0.9980 chunk 49 optimal weight: 8.9990 chunk 69 optimal weight: 1.9990 chunk 104 optimal weight: 6.9990 chunk 110 optimal weight: 30.0000 chunk 54 optimal weight: 5.9990 chunk 98 optimal weight: 10.0000 chunk 29 optimal weight: 3.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.047 7968 Z= 0.359 Angle : 0.664 6.626 10877 Z= 0.343 Chirality : 0.044 0.178 1333 Planarity : 0.004 0.054 1386 Dihedral : 11.281 147.575 1231 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer Outliers : 3.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.87 (0.25), residues: 1120 helix: 0.56 (0.20), residues: 688 sheet: -4.09 (0.50), residues: 60 loop : -2.06 (0.31), residues: 372 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 81 time to evaluate : 0.851 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 10 residues processed: 93 average time/residue: 0.1701 time to fit residues: 23.4603 Evaluate side-chains 88 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 78 time to evaluate : 0.999 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0877 time to fit residues: 2.8451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 30.0000 chunk 62 optimal weight: 4.9990 chunk 1 optimal weight: 0.7980 chunk 82 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 94 optimal weight: 20.0000 chunk 76 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 56 optimal weight: 10.0000 chunk 98 optimal weight: 8.9990 chunk 27 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.026 7968 Z= 0.156 Angle : 0.521 7.135 10877 Z= 0.266 Chirality : 0.039 0.159 1333 Planarity : 0.003 0.041 1386 Dihedral : 10.764 146.682 1231 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer Outliers : 1.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.11 (0.26), residues: 1120 helix: 1.14 (0.21), residues: 694 sheet: -3.99 (0.51), residues: 59 loop : -1.72 (0.32), residues: 367 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 90 time to evaluate : 0.950 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 4 residues processed: 95 average time/residue: 0.1885 time to fit residues: 25.5494 Evaluate side-chains 84 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 80 time to evaluate : 0.857 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0709 time to fit residues: 1.7128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 20.0000 chunk 99 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 64 optimal weight: 8.9990 chunk 27 optimal weight: 1.9990 chunk 110 optimal weight: 30.0000 chunk 91 optimal weight: 30.0000 chunk 51 optimal weight: 3.9990 chunk 9 optimal weight: 6.9990 chunk 36 optimal weight: 6.9990 chunk 57 optimal weight: 0.7980 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 7968 Z= 0.267 Angle : 0.589 8.326 10877 Z= 0.299 Chirality : 0.042 0.306 1333 Planarity : 0.003 0.046 1386 Dihedral : 10.969 147.213 1231 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer Outliers : 1.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.14 (0.26), residues: 1120 helix: 1.14 (0.21), residues: 687 sheet: -3.99 (0.52), residues: 59 loop : -1.72 (0.32), residues: 374 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 81 time to evaluate : 0.925 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 5 residues processed: 89 average time/residue: 0.1694 time to fit residues: 22.4456 Evaluate side-chains 86 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 81 time to evaluate : 0.977 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0748 time to fit residues: 1.9999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 62 optimal weight: 5.9990 chunk 80 optimal weight: 0.5980 chunk 92 optimal weight: 30.0000 chunk 61 optimal weight: 4.9990 chunk 109 optimal weight: 20.0000 chunk 68 optimal weight: 1.9990 chunk 66 optimal weight: 8.9990 chunk 50 optimal weight: 30.0000 chunk 67 optimal weight: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 146 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 7968 Z= 0.161 Angle : 0.528 9.918 10877 Z= 0.264 Chirality : 0.039 0.254 1333 Planarity : 0.003 0.039 1386 Dihedral : 10.735 146.693 1231 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer Outliers : 1.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.20 (0.27), residues: 1120 helix: 1.32 (0.21), residues: 700 sheet: -3.73 (0.56), residues: 58 loop : -1.54 (0.33), residues: 362 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 89 time to evaluate : 0.843 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 95 average time/residue: 0.1668 time to fit residues: 23.4975 Evaluate side-chains 85 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 81 time to evaluate : 0.862 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0736 time to fit residues: 1.6545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 20.0000 chunk 65 optimal weight: 0.0370 chunk 33 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 74 optimal weight: 0.9990 chunk 54 optimal weight: 0.4980 chunk 10 optimal weight: 0.0770 chunk 86 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 105 optimal weight: 7.9990 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 146 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 7968 Z= 0.135 Angle : 0.509 10.516 10877 Z= 0.254 Chirality : 0.039 0.220 1333 Planarity : 0.003 0.037 1386 Dihedral : 10.621 146.517 1231 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer Outliers : 0.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.61 (0.27), residues: 1120 helix: 1.57 (0.21), residues: 709 sheet: -4.05 (0.64), residues: 48 loop : -1.29 (0.34), residues: 363 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 95 time to evaluate : 0.961 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 98 average time/residue: 0.1869 time to fit residues: 26.4334 Evaluate side-chains 92 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 89 time to evaluate : 0.925 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0830 time to fit residues: 1.6309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 6.9990 chunk 102 optimal weight: 9.9990 chunk 105 optimal weight: 10.0000 chunk 61 optimal weight: 3.9990 chunk 44 optimal weight: 10.0000 chunk 80 optimal weight: 0.9990 chunk 31 optimal weight: 0.0670 chunk 92 optimal weight: 30.0000 chunk 67 optimal weight: 2.9990 chunk 108 optimal weight: 9.9990 chunk 66 optimal weight: 7.9990 overall best weight: 3.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.036 7968 Z= 0.300 Angle : 0.657 10.404 10877 Z= 0.323 Chirality : 0.042 0.236 1333 Planarity : 0.004 0.045 1386 Dihedral : 10.858 146.198 1231 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer Outliers : 1.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.21 (0.26), residues: 1120 helix: 1.28 (0.20), residues: 700 sheet: -3.58 (0.60), residues: 58 loop : -1.46 (0.33), residues: 362 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 79 time to evaluate : 0.949 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 85 average time/residue: 0.1539 time to fit residues: 20.2237 Evaluate side-chains 82 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 77 time to evaluate : 0.971 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0824 time to fit residues: 2.0084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 6.9990 chunk 75 optimal weight: 0.6980 chunk 113 optimal weight: 20.0000 chunk 104 optimal weight: 0.0170 chunk 90 optimal weight: 20.0000 chunk 9 optimal weight: 3.9990 chunk 69 optimal weight: 0.8980 chunk 55 optimal weight: 20.0000 chunk 71 optimal weight: 0.8980 chunk 96 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 overall best weight: 1.3020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 7968 Z= 0.182 Angle : 0.568 10.795 10877 Z= 0.277 Chirality : 0.040 0.249 1333 Planarity : 0.003 0.040 1386 Dihedral : 10.701 145.969 1231 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer Outliers : 0.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.53 (0.27), residues: 1120 helix: 1.50 (0.21), residues: 706 sheet: -3.36 (0.64), residues: 58 loop : -1.32 (0.34), residues: 356 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 77 time to evaluate : 0.932 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 78 average time/residue: 0.1553 time to fit residues: 18.6021 Evaluate side-chains 79 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 78 time to evaluate : 0.948 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0774 time to fit residues: 1.4317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 chunk 90 optimal weight: 1.9990 chunk 37 optimal weight: 40.0000 chunk 93 optimal weight: 10.0000 chunk 11 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 65 optimal weight: 10.0000 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN A 199 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.115612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.104484 restraints weight = 21895.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.106460 restraints weight = 11902.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.107689 restraints weight = 7597.215| |-----------------------------------------------------------------------------| r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 7968 Z= 0.271 Angle : 0.623 10.799 10877 Z= 0.307 Chirality : 0.042 0.258 1333 Planarity : 0.003 0.044 1386 Dihedral : 10.795 145.647 1231 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer Outliers : 0.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.26 (0.26), residues: 1120 helix: 1.33 (0.20), residues: 700 sheet: -3.53 (0.62), residues: 58 loop : -1.46 (0.33), residues: 362 =============================================================================== Job complete usr+sys time: 1404.09 seconds wall clock time: 26 minutes 19.65 seconds (1579.65 seconds total)