Starting phenix.real_space_refine on Thu Mar 14 13:23:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y1l_33565/03_2024/7y1l_33565_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y1l_33565/03_2024/7y1l_33565.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y1l_33565/03_2024/7y1l_33565.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y1l_33565/03_2024/7y1l_33565.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y1l_33565/03_2024/7y1l_33565_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y1l_33565/03_2024/7y1l_33565_updated.pdb" } resolution = 3.73 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.063 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 36 5.16 5 C 5816 2.51 5 N 1516 2.21 5 O 1579 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 764": "OE1" <-> "OE2" Residue "A PHE 1092": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8955 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 8955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1194, 8955 Unusual residues: {' MG': 2, 'ATP': 2, 'BJX': 1} Classifications: {'peptide': 1189, 'undetermined': 5} Incomplete info: {'truncation_to_alanine': 152} Link IDs: {'PTRANS': 35, 'TRANS': 1153, None: 5} Not linked: pdbres="ALA A1543 " pdbres=" MG A1601 " Not linked: pdbres=" MG A1601 " pdbres=" MG A1602 " Not linked: pdbres=" MG A1602 " pdbres="ATP A1603 " Not linked: pdbres="ATP A1603 " pdbres="ATP A1604 " Not linked: pdbres="ATP A1604 " pdbres="BJX A1605 " Chain breaks: 7 Unresolved non-hydrogen bonds: 541 Unresolved non-hydrogen angles: 669 Unresolved non-hydrogen dihedrals: 429 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 8, 'ASP:plan': 28, 'PHE:plan': 2, 'GLU:plan': 29, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 341 Time building chain proxies: 5.32, per 1000 atoms: 0.59 Number of scatterers: 8955 At special positions: 0 Unit cell: (76.728, 100.914, 133.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 36 16.00 P 6 15.00 Mg 2 11.99 O 1579 8.00 N 1516 7.00 C 5816 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: 3.92 Conformation dependent library (CDL) restraints added in 1.7 seconds 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2246 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 45 helices and 5 sheets defined 65.7% alpha, 5.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.57 Creating SS restraints... Processing helix chain 'A' and resid 217 through 227 Processing helix chain 'A' and resid 229 through 238 removed outlier: 4.364A pdb=" N THR A 233 " --> pdb=" O TRP A 229 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LEU A 234 " --> pdb=" O TRP A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 255 No H-bonds generated for 'chain 'A' and resid 253 through 255' Processing helix chain 'A' and resid 257 through 273 Processing helix chain 'A' and resid 285 through 323 removed outlier: 6.526A pdb=" N ARG A 295 " --> pdb=" O ARG A 291 " (cutoff:3.500A) Proline residue: A 296 - end of helix removed outlier: 3.903A pdb=" N ALA A 313 " --> pdb=" O LEU A 309 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N GLY A 314 " --> pdb=" O LEU A 310 " (cutoff:3.500A) Proline residue: A 315 - end of helix Processing helix chain 'A' and resid 344 through 347 Processing helix chain 'A' and resid 350 through 394 Processing helix chain 'A' and resid 406 through 415 Processing helix chain 'A' and resid 417 through 496 Proline residue: A 429 - end of helix removed outlier: 3.942A pdb=" N TRP A 432 " --> pdb=" O CYS A 428 " (cutoff:3.500A) Proline residue: A 435 - end of helix removed outlier: 7.354A pdb=" N SER A 451 " --> pdb=" O ASN A 447 " (cutoff:3.500A) removed outlier: 8.677A pdb=" N SER A 452 " --> pdb=" O LEU A 448 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ALA A 453 " --> pdb=" O LEU A 449 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N LEU A 454 " --> pdb=" O GLY A 450 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N VAL A 455 " --> pdb=" O SER A 451 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N GLY A 456 " --> pdb=" O SER A 452 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU A 463 " --> pdb=" O VAL A 459 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ALA A 464 " --> pdb=" O ILE A 460 " (cutoff:3.500A) Proline residue: A 465 - end of helix Processing helix chain 'A' and resid 499 through 505 Processing helix chain 'A' and resid 508 through 558 removed outlier: 3.647A pdb=" N THR A 528 " --> pdb=" O SER A 524 " (cutoff:3.500A) Proline residue: A 544 - end of helix Processing helix chain 'A' and resid 565 through 606 removed outlier: 4.442A pdb=" N THR A 580 " --> pdb=" O HIS A 576 " (cutoff:3.500A) Proline residue: A 581 - end of helix removed outlier: 4.178A pdb=" N SER A 586 " --> pdb=" O LEU A 582 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N THR A 587 " --> pdb=" O PHE A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 714 Processing helix chain 'A' and resid 762 through 767 Processing helix chain 'A' and resid 774 through 783 Processing helix chain 'A' and resid 787 through 792 Processing helix chain 'A' and resid 810 through 823 Processing helix chain 'A' and resid 840 through 849 Processing helix chain 'A' and resid 853 through 858 removed outlier: 3.581A pdb=" N ASP A 858 " --> pdb=" O PHE A 854 " (cutoff:3.500A) Processing helix chain 'A' and resid 892 through 898 Processing helix chain 'A' and resid 900 through 911 removed outlier: 3.546A pdb=" N LYS A 907 " --> pdb=" O TYR A 903 " (cutoff:3.500A) Processing helix chain 'A' and resid 925 through 936 Processing helix chain 'A' and resid 975 through 985 removed outlier: 3.810A pdb=" N GLY A 985 " --> pdb=" O TYR A 981 " (cutoff:3.500A) Processing helix chain 'A' and resid 987 through 1016 Processing helix chain 'A' and resid 1029 through 1073 Processing helix chain 'A' and resid 1077 through 1082 Processing helix chain 'A' and resid 1085 through 1093 removed outlier: 3.869A pdb=" N PHE A1092 " --> pdb=" O ILE A1088 " (cutoff:3.500A) Processing helix chain 'A' and resid 1095 through 1127 removed outlier: 4.390A pdb=" N ILE A1103 " --> pdb=" O ILE A1099 " (cutoff:3.500A) Proline residue: A1104 - end of helix Processing helix chain 'A' and resid 1129 through 1175 removed outlier: 3.919A pdb=" N LEU A1132 " --> pdb=" O PRO A1129 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE A1133 " --> pdb=" O VAL A1130 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA A1136 " --> pdb=" O ILE A1133 " (cutoff:3.500A) Proline residue: A1137 - end of helix removed outlier: 3.924A pdb=" N LEU A1165 " --> pdb=" O SER A1162 " (cutoff:3.500A) Proline residue: A1166 - end of helix removed outlier: 3.514A pdb=" N THR A1174 " --> pdb=" O PHE A1171 " (cutoff:3.500A) Processing helix chain 'A' and resid 1178 through 1184 Processing helix chain 'A' and resid 1187 through 1236 Processing helix chain 'A' and resid 1241 through 1283 removed outlier: 4.062A pdb=" N THR A1255 " --> pdb=" O ALA A1251 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ASN A1256 " --> pdb=" O LEU A1252 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N TYR A1257 " --> pdb=" O THR A1253 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ASN A1259 " --> pdb=" O THR A1255 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N TRP A1260 " --> pdb=" O ASN A1256 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N VAL A1262 " --> pdb=" O LEU A1258 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA A1274 " --> pdb=" O VAL A1270 " (cutoff:3.500A) Processing helix chain 'A' and resid 1302 through 1304 No H-bonds generated for 'chain 'A' and resid 1302 through 1304' Processing helix chain 'A' and resid 1348 through 1355 Processing helix chain 'A' and resid 1378 through 1383 Processing helix chain 'A' and resid 1399 through 1403 Processing helix chain 'A' and resid 1411 through 1420 Processing helix chain 'A' and resid 1424 through 1429 Processing helix chain 'A' and resid 1433 through 1435 No H-bonds generated for 'chain 'A' and resid 1433 through 1435' Processing helix chain 'A' and resid 1440 through 1442 No H-bonds generated for 'chain 'A' and resid 1440 through 1442' Processing helix chain 'A' and resid 1447 through 1461 Processing helix chain 'A' and resid 1477 through 1489 Processing helix chain 'A' and resid 1503 through 1506 No H-bonds generated for 'chain 'A' and resid 1503 through 1506' Processing helix chain 'A' and resid 1526 through 1532 Processing helix chain 'A' and resid 1536 through 1542 Processing sheet with id= A, first strand: chain 'A' and resid 668 through 671 removed outlier: 3.503A pdb=" N LYS A 669 " --> pdb=" O TYR A 726 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS A 724 " --> pdb=" O THR A 671 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 886 through 890 removed outlier: 6.776A pdb=" N ALA A 880 " --> pdb=" O LEU A 887 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N GLU A 889 " --> pdb=" O ILE A 878 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ILE A 878 " --> pdb=" O GLU A 889 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N VAL A 862 " --> pdb=" O THR A 697 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N ILE A 699 " --> pdb=" O VAL A 862 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N LEU A 864 " --> pdb=" O ILE A 699 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 1330 through 1332 Processing sheet with id= D, first strand: chain 'A' and resid 1519 through 1524 removed outlier: 6.530A pdb=" N VAL A1514 " --> pdb=" O LEU A1521 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N TYR A1523 " --> pdb=" O VAL A1512 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VAL A1512 " --> pdb=" O TYR A1523 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N VAL A1496 " --> pdb=" O VAL A1338 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N ILE A1340 " --> pdb=" O VAL A1496 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N THR A1498 " --> pdb=" O ILE A1340 " (cutoff:3.500A) removed outlier: 8.513A pdb=" N GLY A1342 " --> pdb=" O THR A1498 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 1314 through 1316 removed outlier: 3.638A pdb=" N ASP A1363 " --> pdb=" O CYS A1314 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ARG A1316 " --> pdb=" O ILE A1361 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N ILE A1361 " --> pdb=" O ARG A1316 " (cutoff:3.500A) 579 hydrogen bonds defined for protein. 1614 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: 3.25 Time building geometry restraints manager: 4.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1360 1.31 - 1.43: 2411 1.43 - 1.56: 5277 1.56 - 1.68: 31 1.68 - 1.81: 58 Bond restraints: 9137 Sorted by residual: bond pdb=" C16 BJX A1605 " pdb=" N1 BJX A1605 " ideal model delta sigma weight residual 1.344 1.453 -0.109 2.00e-02 2.50e+03 2.99e+01 bond pdb=" CA MET A 231 " pdb=" C MET A 231 " ideal model delta sigma weight residual 1.522 1.588 -0.065 1.36e-02 5.41e+03 2.30e+01 bond pdb=" CA ARG A1542 " pdb=" C ARG A1542 " ideal model delta sigma weight residual 1.523 1.584 -0.061 1.30e-02 5.92e+03 2.20e+01 bond pdb=" CA ASN A 232 " pdb=" CB ASN A 232 " ideal model delta sigma weight residual 1.528 1.599 -0.070 1.56e-02 4.11e+03 2.02e+01 bond pdb=" CA VAL A1541 " pdb=" C VAL A1541 " ideal model delta sigma weight residual 1.524 1.579 -0.055 1.22e-02 6.72e+03 2.00e+01 ... (remaining 9132 not shown) Histogram of bond angle deviations from ideal: 99.76 - 107.78: 336 107.78 - 115.80: 5737 115.80 - 123.81: 6184 123.81 - 131.83: 182 131.83 - 139.84: 27 Bond angle restraints: 12466 Sorted by residual: angle pdb=" C ILE A 321 " pdb=" CA ILE A 321 " pdb=" CB ILE A 321 " ideal model delta sigma weight residual 111.97 104.22 7.75 1.28e+00 6.10e-01 3.66e+01 angle pdb=" C VAL A 322 " pdb=" CA VAL A 322 " pdb=" CB VAL A 322 " ideal model delta sigma weight residual 112.14 105.00 7.14 1.35e+00 5.49e-01 2.79e+01 angle pdb=" N TRP A 229 " pdb=" CA TRP A 229 " pdb=" CB TRP A 229 " ideal model delta sigma weight residual 110.12 117.70 -7.58 1.47e+00 4.63e-01 2.66e+01 angle pdb=" O ILE A 318 " pdb=" C ILE A 318 " pdb=" N SER A 319 " ideal model delta sigma weight residual 121.87 126.38 -4.51 9.70e-01 1.06e+00 2.16e+01 angle pdb=" N ILE A 321 " pdb=" CA ILE A 321 " pdb=" CB ILE A 321 " ideal model delta sigma weight residual 110.55 115.94 -5.39 1.17e+00 7.31e-01 2.12e+01 ... (remaining 12461 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.03: 5302 31.03 - 62.06: 101 62.06 - 93.10: 9 93.10 - 124.13: 0 124.13 - 155.16: 1 Dihedral angle restraints: 5413 sinusoidal: 1950 harmonic: 3463 Sorted by residual: dihedral pdb=" O BJX A1605 " pdb=" C16 BJX A1605 " pdb=" C17 BJX A1605 " pdb=" C18 BJX A1605 " ideal model delta sinusoidal sigma weight residual 10.31 -144.85 155.16 1 3.00e+01 1.11e-03 2.03e+01 dihedral pdb=" CA GLN A 323 " pdb=" C GLN A 323 " pdb=" N ARG A 324 " pdb=" CA ARG A 324 " ideal model delta harmonic sigma weight residual 180.00 158.87 21.13 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" CA ASP A1100 " pdb=" C ASP A1100 " pdb=" N GLN A1101 " pdb=" CA GLN A1101 " ideal model delta harmonic sigma weight residual 180.00 -163.50 -16.50 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 5410 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1371 0.064 - 0.129: 129 0.129 - 0.193: 10 0.193 - 0.257: 1 0.257 - 0.322: 8 Chirality restraints: 1519 Sorted by residual: chirality pdb=" CA ILE A 321 " pdb=" N ILE A 321 " pdb=" C ILE A 321 " pdb=" CB ILE A 321 " both_signs ideal model delta sigma weight residual False 2.43 2.75 -0.32 2.00e-01 2.50e+01 2.59e+00 chirality pdb=" CA VAL A1541 " pdb=" N VAL A1541 " pdb=" C VAL A1541 " pdb=" CB VAL A1541 " both_signs ideal model delta sigma weight residual False 2.44 2.74 -0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" C2' ATP A1603 " pdb=" C1' ATP A1603 " pdb=" C3' ATP A1603 " pdb=" O2' ATP A1603 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.14e+00 ... (remaining 1516 not shown) Planarity restraints: 1519 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 227 " 0.020 2.00e-02 2.50e+03 4.11e-02 1.69e+01 pdb=" C THR A 227 " -0.071 2.00e-02 2.50e+03 pdb=" O THR A 227 " 0.027 2.00e-02 2.50e+03 pdb=" N TYR A 228 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 229 " 0.032 2.00e-02 2.50e+03 2.00e-02 1.00e+01 pdb=" CG TRP A 229 " -0.053 2.00e-02 2.50e+03 pdb=" CD1 TRP A 229 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 TRP A 229 " 0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP A 229 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP A 229 " 0.007 2.00e-02 2.50e+03 pdb=" CE3 TRP A 229 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 229 " 0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 229 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP A 229 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 580 " -0.035 5.00e-02 4.00e+02 5.36e-02 4.59e+00 pdb=" N PRO A 581 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 581 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 581 " -0.030 5.00e-02 4.00e+02 ... (remaining 1516 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1143 2.74 - 3.28: 10141 3.28 - 3.82: 15444 3.82 - 4.36: 16818 4.36 - 4.90: 29374 Nonbonded interactions: 72920 Sorted by model distance: nonbonded pdb=" OE1 GLN A 753 " pdb="MG MG A1602 " model vdw 2.202 2.170 nonbonded pdb=" OD2 ASP A1008 " pdb=" OH TYR A1250 " model vdw 2.207 2.440 nonbonded pdb=" ND2 ASN A 430 " pdb=" O BJX A1605 " model vdw 2.212 2.520 nonbonded pdb=" OD1 ASN A 232 " pdb=" NE1 TRP A1214 " model vdw 2.216 2.520 nonbonded pdb="MG MG A1601 " pdb=" O3B ATP A1604 " model vdw 2.220 2.170 ... (remaining 72915 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: 1.420 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: 7.140 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 28.980 Find NCS groups from input model: 0.260 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: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 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 0.109 9137 Z= 0.317 Angle : 0.587 7.748 12466 Z= 0.344 Chirality : 0.043 0.322 1519 Planarity : 0.004 0.068 1519 Dihedral : 12.439 155.161 3167 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.03 % Allowed : 4.45 % Favored : 94.52 % 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: 2.57 (0.25), residues: 1173 helix: 2.33 (0.18), residues: 794 sheet: 1.23 (0.67), residues: 68 loop : 0.20 (0.37), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.001 TRP A 229 HIS 0.005 0.001 HIS A1504 PHE 0.014 0.001 PHE A1149 TYR 0.026 0.001 TYR A 228 ARG 0.003 0.000 ARG A1218 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 169 time to evaluate : 1.021 Fit side-chains revert: symmetry clash REVERT: A 228 TYR cc_start: 0.9049 (m-80) cc_final: 0.8114 (m-80) REVERT: A 434 MET cc_start: 0.8460 (tpp) cc_final: 0.7850 (mmm) REVERT: A 523 LEU cc_start: 0.9038 (mm) cc_final: 0.8570 (pp) REVERT: A 786 LEU cc_start: 0.9339 (tp) cc_final: 0.9098 (tp) REVERT: A 814 GLN cc_start: 0.8797 (pt0) cc_final: 0.8183 (tt0) REVERT: A 1044 PHE cc_start: 0.8345 (t80) cc_final: 0.8078 (t80) REVERT: A 1091 ARG cc_start: 0.8267 (mmt-90) cc_final: 0.8035 (mmt180) REVERT: A 1367 VAL cc_start: 0.6280 (t) cc_final: 0.6011 (t) REVERT: A 1426 MET cc_start: 0.9063 (mmm) cc_final: 0.8846 (tpp) outliers start: 9 outliers final: 3 residues processed: 176 average time/residue: 0.1556 time to fit residues: 41.3162 Evaluate side-chains 128 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 125 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 1160 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 100 optimal weight: 5.9990 chunk 90 optimal weight: 0.9980 chunk 50 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 60 optimal weight: 0.0470 chunk 48 optimal weight: 0.9980 chunk 93 optimal weight: 0.0370 chunk 36 optimal weight: 2.9990 chunk 56 optimal weight: 8.9990 chunk 69 optimal weight: 0.9980 chunk 108 optimal weight: 7.9990 overall best weight: 0.5556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 576 HIS ** A 759 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 867 HIS A1186 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.1243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9137 Z= 0.168 Angle : 0.554 8.352 12466 Z= 0.275 Chirality : 0.039 0.163 1519 Planarity : 0.004 0.042 1519 Dihedral : 9.704 143.568 1359 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 0.91 % Allowed : 11.19 % Favored : 87.90 % 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: 2.79 (0.25), residues: 1173 helix: 2.51 (0.18), residues: 793 sheet: 1.28 (0.63), residues: 72 loop : 0.25 (0.37), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 230 HIS 0.006 0.001 HIS A1504 PHE 0.016 0.001 PHE A 569 TYR 0.014 0.001 TYR A 750 ARG 0.002 0.000 ARG A1218 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 154 time to evaluate : 1.055 Fit side-chains revert: symmetry clash REVERT: A 228 TYR cc_start: 0.9004 (m-80) cc_final: 0.8174 (m-80) REVERT: A 243 ILE cc_start: 0.9282 (mm) cc_final: 0.9077 (mm) REVERT: A 434 MET cc_start: 0.8514 (tpp) cc_final: 0.7882 (mmm) REVERT: A 814 GLN cc_start: 0.8853 (pt0) cc_final: 0.8382 (tt0) REVERT: A 975 TRP cc_start: 0.8636 (m100) cc_final: 0.8120 (m100) REVERT: A 1044 PHE cc_start: 0.8343 (t80) cc_final: 0.8020 (t80) REVERT: A 1091 ARG cc_start: 0.8235 (mmt-90) cc_final: 0.7960 (mmt180) outliers start: 8 outliers final: 4 residues processed: 159 average time/residue: 0.1580 time to fit residues: 37.9182 Evaluate side-chains 128 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 124 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 725 VAL Chi-restraints excluded: chain A residue 1128 THR Chi-restraints excluded: chain A residue 1135 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 60 optimal weight: 9.9990 chunk 33 optimal weight: 0.4980 chunk 89 optimal weight: 0.8980 chunk 73 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 108 optimal weight: 20.0000 chunk 116 optimal weight: 20.0000 chunk 96 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 86 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 759 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1379 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9137 Z= 0.187 Angle : 0.532 6.761 12466 Z= 0.264 Chirality : 0.039 0.176 1519 Planarity : 0.004 0.037 1519 Dihedral : 9.290 149.971 1355 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 1.71 % Allowed : 13.24 % Favored : 85.05 % 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: 2.70 (0.25), residues: 1173 helix: 2.43 (0.18), residues: 792 sheet: 1.32 (0.62), residues: 72 loop : 0.24 (0.36), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1302 HIS 0.007 0.001 HIS A1504 PHE 0.019 0.001 PHE A1362 TYR 0.014 0.001 TYR A1205 ARG 0.005 0.000 ARG A 363 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 141 time to evaluate : 1.146 Fit side-chains revert: symmetry clash REVERT: A 228 TYR cc_start: 0.9042 (m-80) cc_final: 0.8177 (m-80) REVERT: A 517 GLU cc_start: 0.8692 (tp30) cc_final: 0.8131 (tp30) REVERT: A 814 GLN cc_start: 0.8861 (pt0) cc_final: 0.8374 (tt0) REVERT: A 1044 PHE cc_start: 0.8349 (t80) cc_final: 0.7998 (t80) REVERT: A 1302 TRP cc_start: 0.8262 (t60) cc_final: 0.8032 (t60) outliers start: 15 outliers final: 9 residues processed: 149 average time/residue: 0.1600 time to fit residues: 36.2410 Evaluate side-chains 133 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 124 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 509 HIS Chi-restraints excluded: chain A residue 725 VAL Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 1128 THR Chi-restraints excluded: chain A residue 1258 LEU Chi-restraints excluded: chain A residue 1259 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 106 optimal weight: 8.9990 chunk 81 optimal weight: 2.9990 chunk 56 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 chunk 51 optimal weight: 0.3980 chunk 72 optimal weight: 2.9990 chunk 108 optimal weight: 20.0000 chunk 115 optimal weight: 20.0000 chunk 102 optimal weight: 0.0980 chunk 30 optimal weight: 1.9990 chunk 95 optimal weight: 20.0000 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 HIS A 576 HIS ** A 759 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1444 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9137 Z= 0.257 Angle : 0.552 6.936 12466 Z= 0.277 Chirality : 0.040 0.189 1519 Planarity : 0.004 0.035 1519 Dihedral : 9.080 152.024 1355 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 2.63 % Allowed : 14.04 % Favored : 83.33 % 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: 2.57 (0.25), residues: 1173 helix: 2.38 (0.19), residues: 790 sheet: 0.86 (0.60), residues: 72 loop : 0.20 (0.36), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1302 HIS 0.007 0.001 HIS A1504 PHE 0.013 0.001 PHE A1356 TYR 0.014 0.001 TYR A1523 ARG 0.003 0.000 ARG A1382 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 131 time to evaluate : 0.969 Fit side-chains revert: symmetry clash REVERT: A 228 TYR cc_start: 0.9084 (m-80) cc_final: 0.8240 (m-80) REVERT: A 363 ARG cc_start: 0.8080 (mmt90) cc_final: 0.7419 (mtt90) REVERT: A 517 GLU cc_start: 0.8714 (tp30) cc_final: 0.8171 (tp30) REVERT: A 523 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8573 (pp) REVERT: A 814 GLN cc_start: 0.8851 (pt0) cc_final: 0.8380 (tt0) REVERT: A 1044 PHE cc_start: 0.8405 (t80) cc_final: 0.8006 (t80) REVERT: A 1356 PHE cc_start: 0.9077 (m-80) cc_final: 0.8805 (m-80) outliers start: 23 outliers final: 16 residues processed: 145 average time/residue: 0.1576 time to fit residues: 35.1562 Evaluate side-chains 137 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 120 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 317 CYS Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 509 HIS Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 718 MET Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 1115 LEU Chi-restraints excluded: chain A residue 1128 THR Chi-restraints excluded: chain A residue 1135 LEU Chi-restraints excluded: chain A residue 1159 LEU Chi-restraints excluded: chain A residue 1258 LEU Chi-restraints excluded: chain A residue 1259 ASN Chi-restraints excluded: chain A residue 1282 LEU Chi-restraints excluded: chain A residue 1361 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 65 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 85 optimal weight: 0.7980 chunk 47 optimal weight: 0.8980 chunk 98 optimal weight: 6.9990 chunk 79 optimal weight: 0.7980 chunk 0 optimal weight: 0.9980 chunk 58 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 38 optimal weight: 9.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 HIS ** A 759 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1444 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9137 Z= 0.175 Angle : 0.514 6.815 12466 Z= 0.257 Chirality : 0.038 0.170 1519 Planarity : 0.004 0.034 1519 Dihedral : 8.775 151.296 1355 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 2.51 % Allowed : 15.98 % Favored : 81.51 % 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: 2.57 (0.25), residues: 1173 helix: 2.41 (0.19), residues: 789 sheet: 0.79 (0.60), residues: 72 loop : 0.11 (0.34), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1302 HIS 0.008 0.001 HIS A1504 PHE 0.016 0.001 PHE A1453 TYR 0.014 0.001 TYR A1523 ARG 0.002 0.000 ARG A1382 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 141 time to evaluate : 1.061 Fit side-chains revert: symmetry clash REVERT: A 228 TYR cc_start: 0.9025 (m-80) cc_final: 0.8197 (m-80) REVERT: A 229 TRP cc_start: 0.7489 (OUTLIER) cc_final: 0.7151 (t-100) REVERT: A 363 ARG cc_start: 0.8069 (mmt90) cc_final: 0.7613 (mtt90) REVERT: A 507 TRP cc_start: 0.8602 (m-10) cc_final: 0.8370 (m-10) REVERT: A 517 GLU cc_start: 0.8703 (tp30) cc_final: 0.8081 (tp30) REVERT: A 523 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8553 (pp) REVERT: A 814 GLN cc_start: 0.8855 (pt0) cc_final: 0.8371 (tt0) REVERT: A 1044 PHE cc_start: 0.8370 (t80) cc_final: 0.7979 (t80) REVERT: A 1302 TRP cc_start: 0.8365 (t60) cc_final: 0.7965 (t60) REVERT: A 1356 PHE cc_start: 0.9062 (m-80) cc_final: 0.8850 (m-80) outliers start: 22 outliers final: 17 residues processed: 153 average time/residue: 0.1539 time to fit residues: 36.2306 Evaluate side-chains 146 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 127 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 229 TRP Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 509 HIS Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 718 MET Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 1096 THR Chi-restraints excluded: chain A residue 1115 LEU Chi-restraints excluded: chain A residue 1128 THR Chi-restraints excluded: chain A residue 1135 LEU Chi-restraints excluded: chain A residue 1159 LEU Chi-restraints excluded: chain A residue 1246 LEU Chi-restraints excluded: chain A residue 1258 LEU Chi-restraints excluded: chain A residue 1259 ASN Chi-restraints excluded: chain A residue 1282 LEU Chi-restraints excluded: chain A residue 1361 ILE Chi-restraints excluded: chain A residue 1444 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 103 optimal weight: 0.0470 chunk 22 optimal weight: 1.9990 chunk 67 optimal weight: 8.9990 chunk 28 optimal weight: 5.9990 chunk 115 optimal weight: 4.9990 chunk 95 optimal weight: 9.9990 chunk 53 optimal weight: 10.0000 chunk 9 optimal weight: 0.8980 chunk 38 optimal weight: 10.0000 chunk 60 optimal weight: 8.9990 chunk 111 optimal weight: 7.9990 overall best weight: 2.7884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 576 HIS ** A 759 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 9137 Z= 0.376 Angle : 0.623 8.631 12466 Z= 0.317 Chirality : 0.041 0.213 1519 Planarity : 0.004 0.036 1519 Dihedral : 8.923 153.788 1355 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.97 % Allowed : 18.26 % Favored : 78.77 % 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: 2.31 (0.25), residues: 1173 helix: 2.21 (0.19), residues: 791 sheet: 0.64 (0.61), residues: 72 loop : 0.04 (0.35), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1214 HIS 0.007 0.002 HIS A1504 PHE 0.016 0.002 PHE A 988 TYR 0.014 0.001 TYR A1523 ARG 0.003 0.000 ARG A1218 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 123 time to evaluate : 1.091 Fit side-chains REVERT: A 228 TYR cc_start: 0.9147 (m-80) cc_final: 0.8279 (m-80) REVERT: A 229 TRP cc_start: 0.7604 (OUTLIER) cc_final: 0.7027 (t60) REVERT: A 517 GLU cc_start: 0.8776 (tp30) cc_final: 0.8114 (tp30) REVERT: A 814 GLN cc_start: 0.8810 (pt0) cc_final: 0.8390 (tt0) REVERT: A 970 ARG cc_start: 0.7449 (ptt90) cc_final: 0.7233 (ptt90) REVERT: A 1044 PHE cc_start: 0.8465 (t80) cc_final: 0.8156 (t80) REVERT: A 1356 PHE cc_start: 0.9150 (m-80) cc_final: 0.8948 (m-80) outliers start: 26 outliers final: 19 residues processed: 140 average time/residue: 0.1601 time to fit residues: 33.8402 Evaluate side-chains 136 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 116 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 229 TRP Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain A residue 509 HIS Chi-restraints excluded: chain A residue 718 MET Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 971 THR Chi-restraints excluded: chain A residue 1096 THR Chi-restraints excluded: chain A residue 1106 THR Chi-restraints excluded: chain A residue 1128 THR Chi-restraints excluded: chain A residue 1135 LEU Chi-restraints excluded: chain A residue 1159 LEU Chi-restraints excluded: chain A residue 1226 ILE Chi-restraints excluded: chain A residue 1258 LEU Chi-restraints excluded: chain A residue 1259 ASN Chi-restraints excluded: chain A residue 1282 LEU Chi-restraints excluded: chain A residue 1361 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 12 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 96 optimal weight: 5.9990 chunk 64 optimal weight: 0.8980 chunk 114 optimal weight: 5.9990 chunk 71 optimal weight: 6.9990 chunk 69 optimal weight: 0.9980 chunk 52 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 45 optimal weight: 8.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 576 HIS ** A 759 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9137 Z= 0.184 Angle : 0.543 8.210 12466 Z= 0.269 Chirality : 0.039 0.179 1519 Planarity : 0.004 0.048 1519 Dihedral : 8.676 152.264 1355 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.63 % Allowed : 18.26 % Favored : 79.11 % 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: 2.44 (0.25), residues: 1173 helix: 2.32 (0.19), residues: 790 sheet: 0.69 (0.60), residues: 72 loop : 0.03 (0.34), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A1302 HIS 0.008 0.001 HIS A1504 PHE 0.015 0.001 PHE A1453 TYR 0.015 0.001 TYR A1205 ARG 0.002 0.000 ARG A 970 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 132 time to evaluate : 1.004 Fit side-chains revert: symmetry clash REVERT: A 228 TYR cc_start: 0.9001 (m-80) cc_final: 0.8192 (m-80) REVERT: A 229 TRP cc_start: 0.7538 (OUTLIER) cc_final: 0.6981 (t-100) REVERT: A 507 TRP cc_start: 0.8654 (m-10) cc_final: 0.8398 (m-10) REVERT: A 517 GLU cc_start: 0.8728 (tp30) cc_final: 0.8125 (tp30) REVERT: A 523 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8563 (pp) REVERT: A 814 GLN cc_start: 0.8829 (pt0) cc_final: 0.8411 (tt0) REVERT: A 970 ARG cc_start: 0.7441 (ptt90) cc_final: 0.7201 (ptt90) REVERT: A 1044 PHE cc_start: 0.8391 (t80) cc_final: 0.8002 (t80) REVERT: A 1302 TRP cc_start: 0.8387 (t60) cc_final: 0.8057 (t60) outliers start: 23 outliers final: 16 residues processed: 144 average time/residue: 0.1481 time to fit residues: 33.3744 Evaluate side-chains 141 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 123 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 229 TRP Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 509 HIS Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 604 GLU Chi-restraints excluded: chain A residue 718 MET Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 1135 LEU Chi-restraints excluded: chain A residue 1159 LEU Chi-restraints excluded: chain A residue 1226 ILE Chi-restraints excluded: chain A residue 1246 LEU Chi-restraints excluded: chain A residue 1258 LEU Chi-restraints excluded: chain A residue 1259 ASN Chi-restraints excluded: chain A residue 1282 LEU Chi-restraints excluded: chain A residue 1361 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 68 optimal weight: 4.9990 chunk 34 optimal weight: 0.2980 chunk 22 optimal weight: 0.9980 chunk 72 optimal weight: 0.3980 chunk 78 optimal weight: 0.9990 chunk 56 optimal weight: 5.9990 chunk 10 optimal weight: 0.0060 chunk 90 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 chunk 109 optimal weight: 7.9990 chunk 100 optimal weight: 1.9990 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 759 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 9137 Z= 0.160 Angle : 0.536 7.560 12466 Z= 0.264 Chirality : 0.039 0.195 1519 Planarity : 0.004 0.035 1519 Dihedral : 8.465 153.594 1355 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 2.28 % Allowed : 19.41 % Favored : 78.31 % 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: 2.43 (0.25), residues: 1173 helix: 2.30 (0.19), residues: 790 sheet: 0.80 (0.60), residues: 72 loop : 0.02 (0.34), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1302 HIS 0.008 0.001 HIS A1504 PHE 0.020 0.001 PHE A 988 TYR 0.014 0.001 TYR A1205 ARG 0.002 0.000 ARG A 970 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 143 time to evaluate : 0.973 Fit side-chains revert: symmetry clash REVERT: A 228 TYR cc_start: 0.8982 (m-80) cc_final: 0.8190 (m-80) REVERT: A 507 TRP cc_start: 0.8637 (m-10) cc_final: 0.8421 (m-10) REVERT: A 517 GLU cc_start: 0.8689 (tp30) cc_final: 0.8096 (tp30) REVERT: A 523 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8552 (pp) REVERT: A 814 GLN cc_start: 0.8814 (pt0) cc_final: 0.8390 (tt0) REVERT: A 1044 PHE cc_start: 0.8377 (t80) cc_final: 0.8002 (t80) REVERT: A 1302 TRP cc_start: 0.8381 (t60) cc_final: 0.8094 (t60) REVERT: A 1453 PHE cc_start: 0.8689 (m-80) cc_final: 0.8349 (m-80) outliers start: 20 outliers final: 17 residues processed: 157 average time/residue: 0.1417 time to fit residues: 34.7206 Evaluate side-chains 146 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 128 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 509 HIS Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 971 THR Chi-restraints excluded: chain A residue 1106 THR Chi-restraints excluded: chain A residue 1115 LEU Chi-restraints excluded: chain A residue 1135 LEU Chi-restraints excluded: chain A residue 1159 LEU Chi-restraints excluded: chain A residue 1179 THR Chi-restraints excluded: chain A residue 1226 ILE Chi-restraints excluded: chain A residue 1246 LEU Chi-restraints excluded: chain A residue 1258 LEU Chi-restraints excluded: chain A residue 1259 ASN Chi-restraints excluded: chain A residue 1361 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 106 optimal weight: 10.0000 chunk 109 optimal weight: 10.0000 chunk 64 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 83 optimal weight: 0.6980 chunk 32 optimal weight: 0.7980 chunk 96 optimal weight: 6.9990 chunk 101 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 113 optimal weight: 0.3980 chunk 68 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 576 HIS ** A 759 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9137 Z= 0.195 Angle : 0.569 10.761 12466 Z= 0.276 Chirality : 0.040 0.202 1519 Planarity : 0.004 0.034 1519 Dihedral : 8.418 154.567 1355 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 2.74 % Allowed : 19.63 % Favored : 77.63 % 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: 2.44 (0.25), residues: 1173 helix: 2.32 (0.19), residues: 789 sheet: 0.81 (0.59), residues: 72 loop : 0.02 (0.34), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1302 HIS 0.008 0.001 HIS A1504 PHE 0.017 0.001 PHE A 988 TYR 0.013 0.001 TYR A1205 ARG 0.003 0.000 ARG A1382 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 132 time to evaluate : 0.985 Fit side-chains revert: symmetry clash REVERT: A 228 TYR cc_start: 0.9023 (m-80) cc_final: 0.8194 (m-80) REVERT: A 229 TRP cc_start: 0.7408 (OUTLIER) cc_final: 0.6886 (t-100) REVERT: A 235 ILE cc_start: 0.9372 (mm) cc_final: 0.8781 (mt) REVERT: A 402 MET cc_start: 0.8004 (ttp) cc_final: 0.7760 (ptm) REVERT: A 507 TRP cc_start: 0.8643 (m-10) cc_final: 0.8442 (m-10) REVERT: A 517 GLU cc_start: 0.8691 (tp30) cc_final: 0.8090 (tp30) REVERT: A 523 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8586 (pp) REVERT: A 814 GLN cc_start: 0.8806 (pt0) cc_final: 0.8390 (tt0) REVERT: A 1044 PHE cc_start: 0.8393 (t80) cc_final: 0.8017 (t80) REVERT: A 1302 TRP cc_start: 0.8364 (t60) cc_final: 0.8106 (t60) outliers start: 24 outliers final: 19 residues processed: 146 average time/residue: 0.1458 time to fit residues: 33.2703 Evaluate side-chains 149 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 128 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 229 TRP Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 509 HIS Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 718 MET Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 1096 THR Chi-restraints excluded: chain A residue 1106 THR Chi-restraints excluded: chain A residue 1115 LEU Chi-restraints excluded: chain A residue 1135 LEU Chi-restraints excluded: chain A residue 1140 VAL Chi-restraints excluded: chain A residue 1159 LEU Chi-restraints excluded: chain A residue 1179 THR Chi-restraints excluded: chain A residue 1246 LEU Chi-restraints excluded: chain A residue 1258 LEU Chi-restraints excluded: chain A residue 1259 ASN Chi-restraints excluded: chain A residue 1282 LEU Chi-restraints excluded: chain A residue 1361 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 53 optimal weight: 10.0000 chunk 78 optimal weight: 0.8980 chunk 118 optimal weight: 9.9990 chunk 109 optimal weight: 10.0000 chunk 94 optimal weight: 0.8980 chunk 9 optimal weight: 0.0870 chunk 72 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 chunk 100 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.7760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 759 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9137 Z= 0.176 Angle : 0.557 8.492 12466 Z= 0.269 Chirality : 0.039 0.202 1519 Planarity : 0.004 0.035 1519 Dihedral : 8.310 151.627 1355 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.51 % Allowed : 19.98 % Favored : 77.51 % 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: 2.44 (0.25), residues: 1173 helix: 2.32 (0.19), residues: 788 sheet: 0.85 (0.58), residues: 72 loop : 0.01 (0.34), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1302 HIS 0.008 0.001 HIS A1504 PHE 0.025 0.001 PHE A 988 TYR 0.014 0.001 TYR A1205 ARG 0.004 0.000 ARG A 970 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 137 time to evaluate : 1.086 Fit side-chains revert: symmetry clash REVERT: A 228 TYR cc_start: 0.8994 (m-80) cc_final: 0.8196 (m-80) REVERT: A 229 TRP cc_start: 0.7356 (OUTLIER) cc_final: 0.6838 (t-100) REVERT: A 235 ILE cc_start: 0.9346 (mm) cc_final: 0.8742 (mt) REVERT: A 402 MET cc_start: 0.8008 (ttp) cc_final: 0.7806 (ptm) REVERT: A 517 GLU cc_start: 0.8676 (tp30) cc_final: 0.8083 (tp30) REVERT: A 523 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8575 (pp) REVERT: A 814 GLN cc_start: 0.8797 (pt0) cc_final: 0.8379 (tt0) REVERT: A 973 MET cc_start: 0.8849 (ppp) cc_final: 0.8336 (ppp) REVERT: A 1044 PHE cc_start: 0.8366 (t80) cc_final: 0.8010 (t80) REVERT: A 1302 TRP cc_start: 0.8326 (t60) cc_final: 0.8079 (t60) REVERT: A 1453 PHE cc_start: 0.8680 (m-80) cc_final: 0.8409 (m-80) outliers start: 22 outliers final: 18 residues processed: 150 average time/residue: 0.1486 time to fit residues: 34.9563 Evaluate side-chains 151 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 131 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 229 TRP Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 509 HIS Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 971 THR Chi-restraints excluded: chain A residue 1069 LEU Chi-restraints excluded: chain A residue 1096 THR Chi-restraints excluded: chain A residue 1106 THR Chi-restraints excluded: chain A residue 1115 LEU Chi-restraints excluded: chain A residue 1159 LEU Chi-restraints excluded: chain A residue 1179 THR Chi-restraints excluded: chain A residue 1246 LEU Chi-restraints excluded: chain A residue 1258 LEU Chi-restraints excluded: chain A residue 1259 ASN Chi-restraints excluded: chain A residue 1282 LEU Chi-restraints excluded: chain A residue 1361 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 87 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 chunk 94 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 576 HIS ** A 759 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.116129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.088857 restraints weight = 21283.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.086856 restraints weight = 12525.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.087948 restraints weight = 9796.987| |-----------------------------------------------------------------------------| r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9137 Z= 0.244 Angle : 0.575 8.236 12466 Z= 0.284 Chirality : 0.040 0.199 1519 Planarity : 0.004 0.034 1519 Dihedral : 8.399 150.577 1355 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.40 % Allowed : 20.78 % Favored : 76.83 % 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: 2.45 (0.25), residues: 1173 helix: 2.32 (0.19), residues: 788 sheet: 0.82 (0.59), residues: 67 loop : 0.05 (0.34), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1302 HIS 0.007 0.001 HIS A1504 PHE 0.024 0.001 PHE A 988 TYR 0.015 0.001 TYR A1523 ARG 0.003 0.000 ARG A1382 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1763.56 seconds wall clock time: 32 minutes 33.26 seconds (1953.26 seconds total)