Starting phenix.real_space_refine (version: 1.21rc1) on Wed Oct 4 11:34:08 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y1m_33566/10_2023/7y1m_33566_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y1m_33566/10_2023/7y1m_33566.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y1m_33566/10_2023/7y1m_33566.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y1m_33566/10_2023/7y1m_33566.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y1m_33566/10_2023/7y1m_33566_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y1m_33566/10_2023/7y1m_33566_updated.pdb" } resolution = 3.57 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= 0.006 sd= 0.085 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 5 5.49 5 Mg 2 5.21 5 S 45 5.16 5 C 5836 2.51 5 N 1494 2.21 5 O 1575 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 8957 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 8957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1171, 8957 Unusual residues: {' MG': 2, 'ADP': 1, 'ATP': 1, 'BJX': 1} Classifications: {'peptide': 1166, 'undetermined': 5} Incomplete info: {'truncation_to_alanine': 94} Link IDs: {'PTRANS': 35, 'TRANS': 1130, None: 5} Not linked: pdbres="VAL A1541 " 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="BJX A1604 " Not linked: pdbres="BJX A1604 " pdbres="ADP A1605 " Chain breaks: 7 Unresolved non-hydrogen bonds: 331 Unresolved non-hydrogen angles: 411 Unresolved non-hydrogen dihedrals: 258 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 21, 'PHE:plan': 2, 'GLU:plan': 19, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 227 Time building chain proxies: 5.25, per 1000 atoms: 0.59 Number of scatterers: 8957 At special positions: 0 Unit cell: (70.89, 105.918, 130.104, 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 45 16.00 P 5 15.00 Mg 2 11.99 O 1575 8.00 N 1494 7.00 C 5836 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: 3.88 Conformation dependent library (CDL) restraints added in 1.5 seconds 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2200 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 46 helices and 4 sheets defined 66.1% alpha, 4.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.13 Creating SS restraints... Processing helix chain 'A' and resid 217 through 226 Processing helix chain 'A' and resid 229 through 238 removed outlier: 4.672A pdb=" N THR A 233 " --> 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 272 Processing helix chain 'A' and resid 285 through 323 removed outlier: 6.440A pdb=" N ARG A 295 " --> pdb=" O ARG A 291 " (cutoff:3.500A) Proline residue: A 296 - end of helix removed outlier: 3.810A pdb=" N ALA A 313 " --> pdb=" O LEU A 309 " (cutoff:3.500A) removed outlier: 4.274A 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 346 No H-bonds generated for 'chain 'A' and resid 344 through 346' Processing helix chain 'A' and resid 350 through 393 Processing helix chain 'A' and resid 406 through 415 Processing helix chain 'A' and resid 417 through 448 Proline residue: A 429 - end of helix removed outlier: 4.303A pdb=" N TRP A 432 " --> pdb=" O CYS A 428 " (cutoff:3.500A) Proline residue: A 435 - end of helix Processing helix chain 'A' and resid 450 through 496 removed outlier: 3.699A pdb=" N VAL A 455 " --> pdb=" O SER A 452 " (cutoff:3.500A) Proline residue: A 465 - end of helix Processing helix chain 'A' and resid 499 through 504 Processing helix chain 'A' and resid 508 through 558 removed outlier: 3.510A pdb=" N THR A 518 " --> pdb=" O SER A 514 " (cutoff:3.500A) removed outlier: 3.586A 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: 4.330A pdb=" N THR A 580 " --> pdb=" O HIS A 576 " (cutoff:3.500A) Proline residue: A 581 - end of helix removed outlier: 4.422A pdb=" N SER A 586 " --> pdb=" O LEU A 582 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N THR A 587 " --> pdb=" O PHE A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 715 Processing helix chain 'A' and resid 762 through 767 Processing helix chain 'A' and resid 774 through 784 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 854 through 857 No H-bonds generated for 'chain 'A' and resid 854 through 857' Processing helix chain 'A' and resid 872 through 874 No H-bonds generated for 'chain 'A' and resid 872 through 874' Processing helix chain 'A' and resid 892 through 898 Processing helix chain 'A' and resid 900 through 911 removed outlier: 3.543A pdb=" N LEU A 909 " --> pdb=" O HIS A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 975 through 984 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 1127 removed outlier: 3.864A pdb=" N ASP A1095 " --> pdb=" O ARG A1091 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N THR A1096 " --> pdb=" O PHE A1092 " (cutoff:3.500A) removed outlier: 4.578A 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: 3.609A pdb=" N ALA A1136 " --> pdb=" O ILE A1133 " (cutoff:3.500A) Proline residue: A1137 - end of helix removed outlier: 3.535A pdb=" N SER A1153 " --> pdb=" O ARG A1150 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLN A1157 " --> pdb=" O LYS A1154 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU A1165 " --> pdb=" O SER A1162 " (cutoff:3.500A) Proline residue: A1166 - end of helix 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: 3.913A pdb=" N THR A1255 " --> pdb=" O ALA A1251 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASN A1256 " --> pdb=" O LEU A1252 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR A1257 " --> pdb=" O THR A1253 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ASN A1259 " --> pdb=" O THR A1255 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N TRP A1260 " --> pdb=" O ASN A1256 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL A1262 " --> pdb=" O LEU A1258 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA A1274 " --> pdb=" O VAL A1270 " (cutoff:3.500A) Processing helix chain 'A' and resid 1295 through 1297 No H-bonds generated for 'chain 'A' and resid 1295 through 1297' 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 1356 removed outlier: 3.855A pdb=" N SER A1352 " --> pdb=" O LYS A1348 " (cutoff:3.500A) 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 1421 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 1492 removed outlier: 3.656A pdb=" N PHE A1491 " --> pdb=" O VAL A1487 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ALA A1492 " --> pdb=" O MET A1488 " (cutoff:3.500A) Processing helix chain 'A' and resid 1503 through 1508 removed outlier: 4.325A pdb=" N THR A1508 " --> pdb=" O HIS A1504 " (cutoff:3.500A) Processing helix chain 'A' and resid 1526 through 1529 No H-bonds generated for 'chain 'A' and resid 1526 through 1529' Processing helix chain 'A' and resid 1536 through 1540 Processing sheet with id= A, first strand: chain 'A' and resid 668 through 671 removed outlier: 3.727A pdb=" N THR A 671 " --> pdb=" O LYS A 724 " (cutoff:3.500A) removed outlier: 3.740A 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: 6.619A pdb=" N ALA A 880 " --> pdb=" O LEU A 887 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLU A 889 " --> pdb=" O ILE A 878 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ILE A 878 " --> pdb=" O GLU A 889 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL A 862 " --> pdb=" O THR A 697 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N ILE A 699 " --> pdb=" O VAL A 862 " (cutoff:3.500A) removed outlier: 6.230A 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 removed outlier: 3.557A pdb=" N ALA A1330 " --> pdb=" O ILE A1310 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE A1308 " --> pdb=" O ILE A1332 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 1511 through 1514 removed outlier: 3.638A pdb=" N LEU A1511 " --> pdb=" O LYS A1337 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N CYS A1341 " --> pdb=" O ILE A1513 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N VAL A1496 " --> pdb=" O VAL A1338 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N ILE A1340 " --> pdb=" O VAL A1496 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N THR A1498 " --> pdb=" O ILE A1340 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N SER A1386 " --> pdb=" O ILE A1467 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N ASP A1469 " --> pdb=" O SER A1386 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE A1388 " --> pdb=" O ASP A1469 " (cutoff:3.500A) 565 hydrogen bonds defined for protein. 1449 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: 3.06 Time building geometry restraints manager: 4.12 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: 1371 1.31 - 1.43: 2421 1.43 - 1.56: 5262 1.56 - 1.68: 16 1.68 - 1.81: 72 Bond restraints: 9142 Sorted by residual: bond pdb=" C16 BJX A1604 " pdb=" N1 BJX A1604 " ideal model delta sigma weight residual 1.344 1.449 -0.105 2.00e-02 2.50e+03 2.73e+01 bond pdb=" CA GLN A 323 " pdb=" C GLN A 323 " ideal model delta sigma weight residual 1.524 1.588 -0.064 1.27e-02 6.20e+03 2.58e+01 bond pdb=" CA ILE A 321 " pdb=" C ILE A 321 " ideal model delta sigma weight residual 1.524 1.575 -0.051 1.22e-02 6.72e+03 1.76e+01 bond pdb=" CA GLY A 320 " pdb=" C GLY A 320 " ideal model delta sigma weight residual 1.516 1.559 -0.043 1.09e-02 8.42e+03 1.54e+01 bond pdb=" CA VAL A 322 " pdb=" C VAL A 322 " ideal model delta sigma weight residual 1.523 1.573 -0.049 1.27e-02 6.20e+03 1.50e+01 ... (remaining 9137 not shown) Histogram of bond angle deviations from ideal: 99.81 - 107.78: 327 107.78 - 115.76: 5731 115.76 - 123.73: 6188 123.73 - 131.71: 178 131.71 - 139.68: 26 Bond angle restraints: 12450 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 111.97 105.44 6.53 1.28e+00 6.10e-01 2.60e+01 angle pdb=" C VAL A 322 " pdb=" CA VAL A 322 " pdb=" CB VAL A 322 " ideal model delta sigma weight residual 112.14 105.83 6.31 1.35e+00 5.49e-01 2.18e+01 angle pdb=" N VAL A 322 " pdb=" CA VAL A 322 " pdb=" CB VAL A 322 " ideal model delta sigma weight residual 110.54 115.92 -5.38 1.36e+00 5.41e-01 1.56e+01 angle pdb=" N GLN A 323 " pdb=" CA GLN A 323 " pdb=" CB GLN A 323 " ideal model delta sigma weight residual 110.01 115.58 -5.57 1.45e+00 4.76e-01 1.48e+01 angle pdb=" N ILE A 321 " pdb=" CA ILE A 321 " pdb=" CB ILE A 321 " ideal model delta sigma weight residual 110.55 114.76 -4.21 1.17e+00 7.31e-01 1.29e+01 ... (remaining 12445 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.81: 5295 31.81 - 63.61: 65 63.61 - 95.42: 4 95.42 - 127.23: 3 127.23 - 159.03: 3 Dihedral angle restraints: 5370 sinusoidal: 1976 harmonic: 3394 Sorted by residual: dihedral pdb=" O1B ADP A1605 " pdb=" O3A ADP A1605 " pdb=" PB ADP A1605 " pdb=" PA ADP A1605 " ideal model delta sinusoidal sigma weight residual 300.00 158.34 141.66 1 2.00e+01 2.50e-03 4.28e+01 dihedral pdb=" O2A ADP A1605 " pdb=" O3A ADP A1605 " pdb=" PA ADP A1605 " pdb=" PB ADP A1605 " ideal model delta sinusoidal sigma weight residual -60.00 49.28 -109.28 1 2.00e+01 2.50e-03 3.19e+01 dihedral pdb=" C5' ADP A1605 " pdb=" O5' ADP A1605 " pdb=" PA ADP A1605 " pdb=" O2A ADP A1605 " ideal model delta sinusoidal sigma weight residual -60.00 47.81 -107.80 1 2.00e+01 2.50e-03 3.13e+01 ... (remaining 5367 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1365 0.065 - 0.129: 128 0.129 - 0.194: 6 0.194 - 0.258: 2 0.258 - 0.323: 3 Chirality restraints: 1504 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 2.76 -0.32 2.00e-01 2.50e+01 2.60e+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 2.16e+00 chirality pdb=" C3' ATP A1603 " pdb=" C2' ATP A1603 " pdb=" C4' ATP A1603 " pdb=" O3' ATP A1603 " both_signs ideal model delta sigma weight residual False -2.63 -2.92 0.28 2.00e-01 2.50e+01 1.98e+00 ... (remaining 1501 not shown) Planarity restraints: 1513 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 580 " 0.035 5.00e-02 4.00e+02 5.29e-02 4.48e+00 pdb=" N PRO A 581 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO A 581 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 581 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 752 " -0.007 2.00e-02 2.50e+03 1.31e-02 1.72e+00 pdb=" C ALA A 752 " 0.023 2.00e-02 2.50e+03 pdb=" O ALA A 752 " -0.009 2.00e-02 2.50e+03 pdb=" N GLN A 753 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 505 " 0.006 2.00e-02 2.50e+03 1.30e-02 1.68e+00 pdb=" C TYR A 505 " -0.022 2.00e-02 2.50e+03 pdb=" O TYR A 505 " 0.008 2.00e-02 2.50e+03 pdb=" N ALA A 506 " 0.008 2.00e-02 2.50e+03 ... (remaining 1510 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1677 2.77 - 3.30: 9595 3.30 - 3.83: 14923 3.83 - 4.37: 16753 4.37 - 4.90: 29830 Nonbonded interactions: 72778 Sorted by model distance: nonbonded pdb="MG MG A1602 " pdb=" O1G ATP A1603 " model vdw 2.234 2.170 nonbonded pdb=" N GLU A 889 " pdb=" OE1 GLU A 889 " model vdw 2.239 2.520 nonbonded pdb=" O CYS A1314 " pdb=" N PHE A1362 " model vdw 2.257 2.520 nonbonded pdb=" OG SER A1349 " pdb=" O1A ADP A1605 " model vdw 2.269 2.440 nonbonded pdb=" OE1 GLN A 753 " pdb="MG MG A1602 " model vdw 2.284 2.170 ... (remaining 72773 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: 5.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 6.220 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 27.350 Find NCS groups from input model: 0.250 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:3.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 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 0.105 9142 Z= 0.244 Angle : 0.526 7.805 12450 Z= 0.279 Chirality : 0.040 0.323 1504 Planarity : 0.003 0.053 1513 Dihedral : 11.808 159.034 3170 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.33 % Allowed : 2.74 % Favored : 96.93 % 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: 2.52 (0.25), residues: 1150 helix: 2.26 (0.19), residues: 790 sheet: 0.77 (0.62), residues: 73 loop : 0.32 (0.36), residues: 287 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 143 time to evaluate : 1.006 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 146 average time/residue: 0.2073 time to fit residues: 42.5266 Evaluate side-chains 101 residues out of total 1007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 0.885 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 chunk 49 optimal weight: 0.0980 chunk 30 optimal weight: 0.5980 chunk 59 optimal weight: 5.9990 chunk 47 optimal weight: 8.9990 chunk 91 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 55 optimal weight: 9.9990 chunk 68 optimal weight: 3.9990 chunk 106 optimal weight: 9.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 814 GLN A1028 GLN A1186 HIS A1504 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.1234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 9142 Z= 0.330 Angle : 0.635 9.891 12450 Z= 0.312 Chirality : 0.042 0.146 1504 Planarity : 0.005 0.050 1513 Dihedral : 8.898 155.465 1259 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.54 % Allowed : 8.88 % Favored : 89.58 % 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: 2.01 (0.25), residues: 1150 helix: 1.83 (0.19), residues: 791 sheet: 0.78 (0.60), residues: 65 loop : 0.25 (0.36), residues: 294 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 109 time to evaluate : 1.002 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 11 residues processed: 118 average time/residue: 0.2051 time to fit residues: 35.3948 Evaluate side-chains 108 residues out of total 1007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 97 time to evaluate : 1.012 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0859 time to fit residues: 2.9952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 59 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 88 optimal weight: 0.5980 chunk 72 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 106 optimal weight: 10.0000 chunk 114 optimal weight: 3.9990 chunk 94 optimal weight: 20.0000 chunk 105 optimal weight: 8.9990 chunk 36 optimal weight: 0.9980 chunk 85 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9142 Z= 0.230 Angle : 0.565 7.587 12450 Z= 0.276 Chirality : 0.039 0.144 1504 Planarity : 0.004 0.046 1513 Dihedral : 8.508 153.300 1259 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.99 % Allowed : 10.96 % Favored : 88.05 % 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: 1.90 (0.25), residues: 1150 helix: 1.72 (0.19), residues: 796 sheet: 0.94 (0.62), residues: 60 loop : 0.21 (0.36), residues: 294 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 109 time to evaluate : 1.002 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 4 residues processed: 114 average time/residue: 0.2041 time to fit residues: 33.4407 Evaluate side-chains 99 residues out of total 1007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 95 time to evaluate : 0.984 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0885 time to fit residues: 1.9661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 105 optimal weight: 3.9990 chunk 80 optimal weight: 0.6980 chunk 55 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 50 optimal weight: 7.9990 chunk 71 optimal weight: 0.0980 chunk 106 optimal weight: 2.9990 chunk 113 optimal weight: 20.0000 chunk 101 optimal weight: 0.9980 chunk 30 optimal weight: 0.3980 chunk 94 optimal weight: 20.0000 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9142 Z= 0.200 Angle : 0.544 7.860 12450 Z= 0.264 Chirality : 0.039 0.139 1504 Planarity : 0.004 0.043 1513 Dihedral : 8.190 151.948 1259 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.32 % Allowed : 12.06 % Favored : 86.62 % 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: 1.91 (0.25), residues: 1150 helix: 1.71 (0.19), residues: 797 sheet: 1.17 (0.61), residues: 60 loop : 0.21 (0.36), residues: 293 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 109 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 8 residues processed: 115 average time/residue: 0.2107 time to fit residues: 34.7249 Evaluate side-chains 107 residues out of total 1007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 99 time to evaluate : 1.090 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0941 time to fit residues: 2.7678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 64 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 84 optimal weight: 0.9990 chunk 46 optimal weight: 0.6980 chunk 96 optimal weight: 10.0000 chunk 78 optimal weight: 1.9990 chunk 0 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 38 optimal weight: 7.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9142 Z= 0.202 Angle : 0.546 8.668 12450 Z= 0.262 Chirality : 0.038 0.175 1504 Planarity : 0.004 0.041 1513 Dihedral : 7.984 151.195 1259 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.66 % Allowed : 13.27 % Favored : 86.07 % 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: 1.98 (0.25), residues: 1150 helix: 1.75 (0.19), residues: 798 sheet: 1.08 (0.59), residues: 65 loop : 0.25 (0.36), residues: 287 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 106 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 112 average time/residue: 0.2110 time to fit residues: 33.5142 Evaluate side-chains 101 residues out of total 1007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 97 time to evaluate : 1.022 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0906 time to fit residues: 2.0639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 101 optimal weight: 6.9990 chunk 22 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 113 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 9 optimal weight: 0.3980 chunk 37 optimal weight: 3.9990 chunk 59 optimal weight: 8.9990 chunk 109 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9142 Z= 0.192 Angle : 0.532 7.904 12450 Z= 0.257 Chirality : 0.038 0.141 1504 Planarity : 0.004 0.039 1513 Dihedral : 7.771 148.813 1259 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.21 % Allowed : 13.60 % Favored : 85.20 % 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: 2.00 (0.25), residues: 1150 helix: 1.77 (0.19), residues: 799 sheet: 1.13 (0.60), residues: 65 loop : 0.24 (0.36), residues: 286 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 104 time to evaluate : 1.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 6 residues processed: 109 average time/residue: 0.2190 time to fit residues: 34.0400 Evaluate side-chains 103 residues out of total 1007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 97 time to evaluate : 1.013 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0969 time to fit residues: 2.4386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 12 optimal weight: 0.9980 chunk 64 optimal weight: 0.5980 chunk 82 optimal weight: 1.9990 chunk 95 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 112 optimal weight: 7.9990 chunk 70 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 52 optimal weight: 0.0010 chunk 69 optimal weight: 0.9990 chunk 45 optimal weight: 5.9990 overall best weight: 0.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9142 Z= 0.181 Angle : 0.540 8.071 12450 Z= 0.258 Chirality : 0.038 0.141 1504 Planarity : 0.004 0.040 1513 Dihedral : 7.580 145.242 1259 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.77 % Allowed : 12.94 % Favored : 86.29 % 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: 2.01 (0.25), residues: 1150 helix: 1.78 (0.19), residues: 799 sheet: 1.20 (0.61), residues: 65 loop : 0.21 (0.36), residues: 286 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 103 time to evaluate : 0.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 109 average time/residue: 0.2113 time to fit residues: 32.7870 Evaluate side-chains 100 residues out of total 1007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 97 time to evaluate : 1.017 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0923 time to fit residues: 1.9111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 67 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 71 optimal weight: 0.6980 chunk 76 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 chunk 10 optimal weight: 4.9990 chunk 88 optimal weight: 0.9980 chunk 102 optimal weight: 0.5980 chunk 108 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9142 Z= 0.184 Angle : 0.539 8.207 12450 Z= 0.257 Chirality : 0.038 0.147 1504 Planarity : 0.004 0.043 1513 Dihedral : 7.411 141.686 1259 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.22 % Allowed : 14.14 % Favored : 85.64 % 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: 2.06 (0.25), residues: 1150 helix: 1.82 (0.19), residues: 798 sheet: 1.51 (0.64), residues: 60 loop : 0.18 (0.36), residues: 292 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 104 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 104 average time/residue: 0.2106 time to fit residues: 31.2141 Evaluate side-chains 95 residues out of total 1007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 94 time to evaluate : 0.909 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0797 time to fit residues: 1.4051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 0.0980 chunk 105 optimal weight: 0.5980 chunk 108 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 94 optimal weight: 9.9990 chunk 99 optimal weight: 8.9990 chunk 104 optimal weight: 3.9990 chunk 69 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9142 Z= 0.192 Angle : 0.544 10.221 12450 Z= 0.257 Chirality : 0.038 0.149 1504 Planarity : 0.004 0.044 1513 Dihedral : 7.247 139.293 1259 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.33 % Allowed : 14.47 % Favored : 85.20 % 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: 2.09 (0.25), residues: 1150 helix: 1.84 (0.19), residues: 798 sheet: 1.61 (0.65), residues: 60 loop : 0.20 (0.36), residues: 292 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 99 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 101 average time/residue: 0.2224 time to fit residues: 32.4035 Evaluate side-chains 99 residues out of total 1007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 97 time to evaluate : 0.987 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0956 time to fit residues: 1.7133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 111 optimal weight: 0.6980 chunk 67 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 116 optimal weight: 0.3980 chunk 107 optimal weight: 6.9990 chunk 92 optimal weight: 0.8980 chunk 9 optimal weight: 0.3980 chunk 71 optimal weight: 0.9990 chunk 56 optimal weight: 8.9990 chunk 73 optimal weight: 0.0670 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9142 Z= 0.157 Angle : 0.525 8.325 12450 Z= 0.249 Chirality : 0.037 0.166 1504 Planarity : 0.004 0.044 1513 Dihedral : 7.049 133.210 1259 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.22 % Allowed : 14.58 % Favored : 85.20 % 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: 2.20 (0.25), residues: 1150 helix: 1.93 (0.19), residues: 797 sheet: 1.68 (0.65), residues: 60 loop : 0.22 (0.36), residues: 293 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 107 time to evaluate : 1.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 108 average time/residue: 0.2058 time to fit residues: 32.0613 Evaluate side-chains 101 residues out of total 1007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 99 time to evaluate : 0.993 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0880 time to fit residues: 1.7100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 92 optimal weight: 0.3980 chunk 38 optimal weight: 0.1980 chunk 95 optimal weight: 9.9990 chunk 11 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.151212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.117926 restraints weight = 12841.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.117913 restraints weight = 8423.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.118806 restraints weight = 6089.114| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9142 Z= 0.199 Angle : 0.551 8.212 12450 Z= 0.259 Chirality : 0.038 0.150 1504 Planarity : 0.004 0.045 1513 Dihedral : 7.004 136.902 1259 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.11 % Allowed : 14.80 % Favored : 85.09 % 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: 2.13 (0.25), residues: 1150 helix: 1.85 (0.19), residues: 799 sheet: 1.68 (0.65), residues: 60 loop : 0.22 (0.36), residues: 291 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1759.10 seconds wall clock time: 33 minutes 35.83 seconds (2015.83 seconds total)