Starting phenix.real_space_refine on Thu Mar 14 13:25:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y1m_33566/03_2024/7y1m_33566_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y1m_33566/03_2024/7y1m_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_33566/03_2024/7y1m_33566.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y1m_33566/03_2024/7y1m_33566.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y1m_33566/03_2024/7y1m_33566_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y1m_33566/03_2024/7y1m_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: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 5.23, per 1000 atoms: 0.58 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: 3.68 Conformation dependent library (CDL) restraints added in 1.7 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: 2.62 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: 3.18 Time building geometry restraints manager: 3.96 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: 5313 31.81 - 63.61: 81 63.61 - 95.42: 11 95.42 - 127.23: 3 127.23 - 159.03: 3 Dihedral angle restraints: 5411 sinusoidal: 2017 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 5408 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: 1.340 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: 7.150 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 28.210 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.910 ------------------------------------------------------------------------------- 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 : 12.727 159.034 3211 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1214 HIS 0.004 0.001 HIS A1065 PHE 0.011 0.001 PHE A1149 TYR 0.011 0.001 TYR A 505 ARG 0.002 0.000 ARG A1461 *********************** 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 : 0.985 Fit side-chains revert: symmetry clash REVERT: A 225 LYS cc_start: 0.8145 (mtmt) cc_final: 0.7415 (tptt) REVERT: A 284 SER cc_start: 0.8518 (t) cc_final: 0.8230 (m) REVERT: A 351 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.7900 (mp) REVERT: A 405 MET cc_start: 0.7217 (mmm) cc_final: 0.6848 (mmt) REVERT: A 687 ILE cc_start: 0.7741 (mt) cc_final: 0.7534 (mt) REVERT: A 698 MET cc_start: 0.8240 (mtm) cc_final: 0.8028 (mtp) REVERT: A 993 MET cc_start: 0.7777 (ttm) cc_final: 0.7556 (ttm) REVERT: A 1083 THR cc_start: 0.9035 (m) cc_final: 0.8528 (p) REVERT: A 1333 LYS cc_start: 0.8364 (mtmm) cc_final: 0.7955 (tmtt) REVERT: A 1445 PHE cc_start: 0.8392 (m-80) cc_final: 0.8149 (m-80) outliers start: 3 outliers final: 0 residues processed: 146 average time/residue: 0.2094 time to fit residues: 42.7841 Evaluate side-chains 105 residues out of total 1007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 104 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 351 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 49 optimal weight: 4.9990 chunk 30 optimal weight: 0.5980 chunk 59 optimal weight: 5.9990 chunk 47 optimal weight: 0.9980 chunk 91 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 55 optimal weight: 9.9990 chunk 68 optimal weight: 2.9990 chunk 106 optimal weight: 9.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- 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: 0.8324 moved from start: 0.1215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 9142 Z= 0.325 Angle : 0.632 9.463 12450 Z= 0.311 Chirality : 0.042 0.145 1504 Planarity : 0.005 0.051 1513 Dihedral : 10.755 151.047 1302 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 1.64 % Allowed : 8.33 % Favored : 90.02 % 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: 2.04 (0.25), residues: 1150 helix: 1.82 (0.18), residues: 792 sheet: 0.86 (0.60), residues: 65 loop : 0.30 (0.36), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1214 HIS 0.006 0.001 HIS A1065 PHE 0.019 0.001 PHE A 552 TYR 0.013 0.001 TYR A 228 ARG 0.005 0.001 ARG A1357 *********************** 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 128 residues out of total 1007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 113 time to evaluate : 1.122 Fit side-chains revert: symmetry clash REVERT: A 225 LYS cc_start: 0.8151 (mtmt) cc_final: 0.7416 (tptt) REVERT: A 284 SER cc_start: 0.8631 (t) cc_final: 0.8344 (m) REVERT: A 405 MET cc_start: 0.7289 (mmm) cc_final: 0.6945 (mmt) REVERT: A 906 TRP cc_start: 0.8656 (m-10) cc_final: 0.8345 (m-10) REVERT: A 1083 THR cc_start: 0.9001 (m) cc_final: 0.8570 (p) REVERT: A 1123 MET cc_start: 0.8509 (tpp) cc_final: 0.7745 (tpp) REVERT: A 1333 LYS cc_start: 0.8407 (mtmm) cc_final: 0.7986 (tmtt) REVERT: A 1334 PRO cc_start: 0.7890 (Cg_endo) cc_final: 0.6875 (Cg_exo) outliers start: 15 outliers final: 11 residues processed: 123 average time/residue: 0.1962 time to fit residues: 34.6271 Evaluate side-chains 113 residues out of total 1007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 102 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 TRP Chi-restraints excluded: chain A residue 524 SER Chi-restraints excluded: chain A residue 725 VAL Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1093 SER Chi-restraints excluded: chain A residue 1162 SER Chi-restraints excluded: chain A residue 1378 LEU Chi-restraints excluded: chain A residue 1403 LEU Chi-restraints excluded: chain A residue 1437 THR Chi-restraints excluded: chain A residue 1466 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 59 optimal weight: 10.0000 chunk 32 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 72 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 106 optimal weight: 8.9990 chunk 114 optimal weight: 5.9990 chunk 94 optimal weight: 20.0000 chunk 105 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 85 optimal weight: 0.5980 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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: 0.8292 moved from start: 0.1501 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= 0.222 Angle : 0.555 7.471 12450 Z= 0.270 Chirality : 0.039 0.156 1504 Planarity : 0.004 0.046 1513 Dihedral : 10.364 146.134 1300 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.08 % Allowed : 10.20 % Favored : 87.72 % 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: 1.94 (0.25), residues: 1150 helix: 1.73 (0.19), residues: 797 sheet: 1.10 (0.62), residues: 60 loop : 0.24 (0.36), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1214 HIS 0.005 0.001 HIS A1065 PHE 0.015 0.001 PHE A1453 TYR 0.019 0.001 TYR A 903 ARG 0.003 0.000 ARG A1357 *********************** 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 133 residues out of total 1007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 114 time to evaluate : 0.929 Fit side-chains revert: symmetry clash REVERT: A 225 LYS cc_start: 0.8143 (mtmt) cc_final: 0.7410 (tptt) REVERT: A 239 HIS cc_start: 0.8364 (OUTLIER) cc_final: 0.7666 (m90) REVERT: A 284 SER cc_start: 0.8540 (t) cc_final: 0.8241 (m) REVERT: A 405 MET cc_start: 0.7227 (mmm) cc_final: 0.6904 (mmt) REVERT: A 906 TRP cc_start: 0.8713 (m-10) cc_final: 0.8505 (m-10) REVERT: A 910 MET cc_start: 0.7068 (OUTLIER) cc_final: 0.5825 (ttt) REVERT: A 1083 THR cc_start: 0.8898 (m) cc_final: 0.8544 (p) REVERT: A 1123 MET cc_start: 0.8457 (tpp) cc_final: 0.7738 (tpp) REVERT: A 1333 LYS cc_start: 0.8365 (mtmm) cc_final: 0.8060 (tmtt) REVERT: A 1334 PRO cc_start: 0.7846 (Cg_endo) cc_final: 0.6780 (Cg_exo) REVERT: A 1445 PHE cc_start: 0.8501 (m-80) cc_final: 0.8182 (m-80) outliers start: 19 outliers final: 11 residues processed: 123 average time/residue: 0.2020 time to fit residues: 35.3010 Evaluate side-chains 114 residues out of total 1007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 101 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 HIS Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 432 TRP Chi-restraints excluded: chain A residue 725 VAL Chi-restraints excluded: chain A residue 910 MET Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1162 SER Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1399 ILE Chi-restraints excluded: chain A residue 1403 LEU Chi-restraints excluded: chain A residue 1437 THR Chi-restraints excluded: chain A residue 1466 LEU Chi-restraints excluded: chain A residue 1483 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 105 optimal weight: 5.9990 chunk 80 optimal weight: 0.4980 chunk 55 optimal weight: 7.9990 chunk 11 optimal weight: 1.9990 chunk 50 optimal weight: 8.9990 chunk 71 optimal weight: 1.9990 chunk 106 optimal weight: 6.9990 chunk 113 optimal weight: 0.9980 chunk 101 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 94 optimal weight: 20.0000 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 686 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.1715 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= 0.247 Angle : 0.557 7.303 12450 Z= 0.270 Chirality : 0.039 0.148 1504 Planarity : 0.004 0.044 1513 Dihedral : 10.061 146.155 1300 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.19 % Allowed : 12.28 % Favored : 85.53 % 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: 1.83 (0.25), residues: 1150 helix: 1.64 (0.19), residues: 800 sheet: 1.08 (0.62), residues: 60 loop : 0.23 (0.36), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1214 HIS 0.005 0.001 HIS A1065 PHE 0.016 0.001 PHE A 552 TYR 0.017 0.001 TYR A 228 ARG 0.002 0.000 ARG A 774 *********************** 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 131 residues out of total 1007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 111 time to evaluate : 0.968 Fit side-chains revert: symmetry clash REVERT: A 225 LYS cc_start: 0.8206 (mtmt) cc_final: 0.7424 (tptt) REVERT: A 239 HIS cc_start: 0.8279 (OUTLIER) cc_final: 0.7428 (m90) REVERT: A 284 SER cc_start: 0.8591 (t) cc_final: 0.8292 (m) REVERT: A 405 MET cc_start: 0.7272 (mmm) cc_final: 0.6957 (mmt) REVERT: A 906 TRP cc_start: 0.8706 (m-10) cc_final: 0.8496 (m-10) REVERT: A 910 MET cc_start: 0.6639 (OUTLIER) cc_final: 0.5660 (ttt) REVERT: A 1083 THR cc_start: 0.8880 (m) cc_final: 0.8532 (p) REVERT: A 1123 MET cc_start: 0.8465 (tpp) cc_final: 0.7752 (tpp) REVERT: A 1322 LYS cc_start: 0.8677 (ttpt) cc_final: 0.7976 (tptt) REVERT: A 1333 LYS cc_start: 0.8360 (mtmm) cc_final: 0.8068 (tmtt) REVERT: A 1334 PRO cc_start: 0.7784 (Cg_endo) cc_final: 0.6709 (Cg_exo) REVERT: A 1445 PHE cc_start: 0.8547 (m-80) cc_final: 0.8129 (m-80) REVERT: A 1450 ARG cc_start: 0.8665 (mtt180) cc_final: 0.7997 (mtm180) outliers start: 20 outliers final: 15 residues processed: 125 average time/residue: 0.2085 time to fit residues: 36.5813 Evaluate side-chains 119 residues out of total 1007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 102 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 HIS Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 432 TRP Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 725 VAL Chi-restraints excluded: chain A residue 910 MET Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1093 SER Chi-restraints excluded: chain A residue 1162 SER Chi-restraints excluded: chain A residue 1219 THR Chi-restraints excluded: chain A residue 1355 PHE Chi-restraints excluded: chain A residue 1399 ILE Chi-restraints excluded: chain A residue 1403 LEU Chi-restraints excluded: chain A residue 1437 THR Chi-restraints excluded: chain A residue 1466 LEU 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: 0.5980 chunk 84 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 0 optimal weight: 0.9980 chunk 57 optimal weight: 0.0270 chunk 101 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 overall best weight: 0.6438 ------------------------------------------------------------------------------- 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: 0.8257 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9142 Z= 0.170 Angle : 0.529 8.087 12450 Z= 0.255 Chirality : 0.038 0.172 1504 Planarity : 0.004 0.041 1513 Dihedral : 9.807 137.202 1300 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.19 % Allowed : 12.61 % 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: 2.03 (0.25), residues: 1150 helix: 1.80 (0.19), residues: 798 sheet: 0.90 (0.54), residues: 75 loop : 0.28 (0.37), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 756 HIS 0.003 0.001 HIS A1065 PHE 0.017 0.001 PHE A1356 TYR 0.014 0.001 TYR A 228 ARG 0.002 0.000 ARG A1461 *********************** 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 135 residues out of total 1007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 115 time to evaluate : 0.980 Fit side-chains revert: symmetry clash REVERT: A 225 LYS cc_start: 0.8202 (mtmt) cc_final: 0.7474 (tptt) REVERT: A 231 MET cc_start: 0.8286 (tpt) cc_final: 0.8024 (tpt) REVERT: A 284 SER cc_start: 0.8591 (t) cc_final: 0.8283 (m) REVERT: A 405 MET cc_start: 0.7310 (mmm) cc_final: 0.6966 (mmt) REVERT: A 906 TRP cc_start: 0.8702 (m-10) cc_final: 0.8449 (m-10) REVERT: A 910 MET cc_start: 0.6000 (OUTLIER) cc_final: 0.5576 (ttt) REVERT: A 1123 MET cc_start: 0.8334 (tpp) cc_final: 0.7706 (tpp) REVERT: A 1322 LYS cc_start: 0.8684 (ttpt) cc_final: 0.7977 (tptt) REVERT: A 1333 LYS cc_start: 0.8329 (mtmm) cc_final: 0.8066 (tmtt) REVERT: A 1334 PRO cc_start: 0.7724 (Cg_endo) cc_final: 0.6529 (Cg_exo) REVERT: A 1445 PHE cc_start: 0.8515 (m-80) cc_final: 0.8127 (m-80) REVERT: A 1450 ARG cc_start: 0.8629 (mtt180) cc_final: 0.7985 (mtm180) outliers start: 20 outliers final: 16 residues processed: 129 average time/residue: 0.2026 time to fit residues: 37.4618 Evaluate side-chains 120 residues out of total 1007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 103 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 432 TRP Chi-restraints excluded: chain A residue 725 VAL Chi-restraints excluded: chain A residue 910 MET Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1093 SER Chi-restraints excluded: chain A residue 1111 THR Chi-restraints excluded: chain A residue 1162 SER Chi-restraints excluded: chain A residue 1219 THR Chi-restraints excluded: chain A residue 1355 PHE Chi-restraints excluded: chain A residue 1399 ILE Chi-restraints excluded: chain A residue 1403 LEU Chi-restraints excluded: chain A residue 1437 THR Chi-restraints excluded: chain A residue 1464 SER Chi-restraints excluded: chain A residue 1483 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 101 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 66 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 113 optimal weight: 10.0000 chunk 93 optimal weight: 7.9990 chunk 52 optimal weight: 5.9990 chunk 9 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 59 optimal weight: 9.9990 chunk 109 optimal weight: 3.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- 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: 0.8325 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 9142 Z= 0.299 Angle : 0.589 7.945 12450 Z= 0.282 Chirality : 0.040 0.137 1504 Planarity : 0.004 0.041 1513 Dihedral : 9.765 144.781 1300 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.96 % Allowed : 12.28 % Favored : 84.76 % 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: 1.81 (0.25), residues: 1150 helix: 1.59 (0.19), residues: 798 sheet: 0.90 (0.59), residues: 65 loop : 0.36 (0.36), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1214 HIS 0.006 0.001 HIS A1065 PHE 0.018 0.001 PHE A 552 TYR 0.015 0.001 TYR A 228 ARG 0.003 0.000 ARG A 590 *********************** 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 134 residues out of total 1007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 107 time to evaluate : 1.000 Fit side-chains revert: symmetry clash REVERT: A 225 LYS cc_start: 0.8211 (mtmt) cc_final: 0.7450 (tptt) REVERT: A 239 HIS cc_start: 0.8234 (OUTLIER) cc_final: 0.7342 (m90) REVERT: A 284 SER cc_start: 0.8636 (t) cc_final: 0.8329 (m) REVERT: A 405 MET cc_start: 0.7375 (mmm) cc_final: 0.7032 (mmt) REVERT: A 906 TRP cc_start: 0.8692 (m-10) cc_final: 0.8435 (m-10) REVERT: A 910 MET cc_start: 0.6254 (OUTLIER) cc_final: 0.5721 (ttt) REVERT: A 1123 MET cc_start: 0.8510 (tpp) cc_final: 0.7743 (tpp) REVERT: A 1128 THR cc_start: 0.8640 (OUTLIER) cc_final: 0.8043 (p) REVERT: A 1322 LYS cc_start: 0.8691 (ttpt) cc_final: 0.7991 (tptt) REVERT: A 1333 LYS cc_start: 0.8338 (mtmm) cc_final: 0.8069 (tmtt) REVERT: A 1334 PRO cc_start: 0.7742 (Cg_endo) cc_final: 0.6579 (Cg_exo) REVERT: A 1445 PHE cc_start: 0.8586 (m-80) cc_final: 0.8145 (m-80) REVERT: A 1450 ARG cc_start: 0.8666 (mtt180) cc_final: 0.7980 (mtm180) outliers start: 27 outliers final: 19 residues processed: 129 average time/residue: 0.2029 time to fit residues: 37.2397 Evaluate side-chains 124 residues out of total 1007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 102 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 HIS Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 432 TRP Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 725 VAL Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 910 MET Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1093 SER Chi-restraints excluded: chain A residue 1111 THR Chi-restraints excluded: chain A residue 1128 THR Chi-restraints excluded: chain A residue 1162 SER Chi-restraints excluded: chain A residue 1219 THR Chi-restraints excluded: chain A residue 1355 PHE Chi-restraints excluded: chain A residue 1399 ILE Chi-restraints excluded: chain A residue 1403 LEU Chi-restraints excluded: chain A residue 1437 THR Chi-restraints excluded: chain A residue 1464 SER Chi-restraints excluded: chain A residue 1489 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 12 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 chunk 95 optimal weight: 7.9990 chunk 63 optimal weight: 1.9990 chunk 112 optimal weight: 10.0000 chunk 70 optimal weight: 0.6980 chunk 68 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- 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: 0.8296 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9142 Z= 0.220 Angle : 0.558 8.207 12450 Z= 0.266 Chirality : 0.039 0.153 1504 Planarity : 0.004 0.040 1513 Dihedral : 9.600 139.930 1300 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.85 % Allowed : 12.72 % Favored : 84.43 % 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: 1.67 (0.19), residues: 799 sheet: 0.97 (0.59), residues: 65 loop : 0.32 (0.37), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1214 HIS 0.005 0.001 HIS A1065 PHE 0.016 0.001 PHE A 552 TYR 0.015 0.001 TYR A 228 ARG 0.002 0.000 ARG A 774 *********************** 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 131 residues out of total 1007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 105 time to evaluate : 1.068 Fit side-chains revert: symmetry clash REVERT: A 225 LYS cc_start: 0.8206 (mtmt) cc_final: 0.7462 (tptt) REVERT: A 231 MET cc_start: 0.8436 (tpt) cc_final: 0.8182 (tpt) REVERT: A 239 HIS cc_start: 0.8203 (OUTLIER) cc_final: 0.7278 (m90) REVERT: A 284 SER cc_start: 0.8649 (t) cc_final: 0.8322 (m) REVERT: A 405 MET cc_start: 0.7308 (mmm) cc_final: 0.6982 (mmt) REVERT: A 520 MET cc_start: 0.7478 (OUTLIER) cc_final: 0.7070 (mtp) REVERT: A 906 TRP cc_start: 0.8688 (m-10) cc_final: 0.8433 (m-10) REVERT: A 910 MET cc_start: 0.6155 (OUTLIER) cc_final: 0.5714 (ttt) REVERT: A 1123 MET cc_start: 0.8470 (tpp) cc_final: 0.7778 (tpp) REVERT: A 1322 LYS cc_start: 0.8683 (ttpt) cc_final: 0.7991 (tptt) REVERT: A 1333 LYS cc_start: 0.8366 (mtmm) cc_final: 0.8098 (tmtt) REVERT: A 1334 PRO cc_start: 0.7714 (Cg_endo) cc_final: 0.6506 (Cg_exo) REVERT: A 1445 PHE cc_start: 0.8598 (m-80) cc_final: 0.8169 (m-80) REVERT: A 1450 ARG cc_start: 0.8641 (mtt180) cc_final: 0.7969 (mtm180) outliers start: 26 outliers final: 21 residues processed: 125 average time/residue: 0.1902 time to fit residues: 34.1390 Evaluate side-chains 126 residues out of total 1007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 102 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 HIS Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 432 TRP Chi-restraints excluded: chain A residue 520 MET Chi-restraints excluded: chain A residue 524 SER Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 725 VAL Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 910 MET Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1093 SER Chi-restraints excluded: chain A residue 1111 THR Chi-restraints excluded: chain A residue 1146 GLN Chi-restraints excluded: chain A residue 1162 SER Chi-restraints excluded: chain A residue 1219 THR Chi-restraints excluded: chain A residue 1355 PHE Chi-restraints excluded: chain A residue 1399 ILE Chi-restraints excluded: chain A residue 1403 LEU Chi-restraints excluded: chain A residue 1437 THR Chi-restraints excluded: chain A residue 1464 SER Chi-restraints excluded: chain A residue 1489 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 67 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 22 optimal weight: 0.0970 chunk 21 optimal weight: 0.9980 chunk 71 optimal weight: 7.9990 chunk 76 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 chunk 102 optimal weight: 0.5980 chunk 108 optimal weight: 1.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 399 ASN ** A 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.2196 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= 0.177 Angle : 0.543 8.310 12450 Z= 0.257 Chirality : 0.038 0.170 1504 Planarity : 0.004 0.047 1513 Dihedral : 9.470 135.270 1300 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.18 % Allowed : 12.28 % Favored : 84.54 % 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: 2.04 (0.25), residues: 1150 helix: 1.77 (0.19), residues: 798 sheet: 1.27 (0.62), residues: 60 loop : 0.37 (0.37), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 230 HIS 0.004 0.001 HIS A1001 PHE 0.013 0.001 PHE A 552 TYR 0.012 0.001 TYR A 228 ARG 0.002 0.000 ARG A1461 *********************** 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 139 residues out of total 1007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 110 time to evaluate : 1.021 Fit side-chains revert: symmetry clash REVERT: A 225 LYS cc_start: 0.8210 (mtmt) cc_final: 0.7480 (tptt) REVERT: A 231 MET cc_start: 0.8353 (tpt) cc_final: 0.8082 (tpt) REVERT: A 239 HIS cc_start: 0.8173 (OUTLIER) cc_final: 0.7262 (m90) REVERT: A 284 SER cc_start: 0.8659 (t) cc_final: 0.8339 (m) REVERT: A 405 MET cc_start: 0.7266 (mmm) cc_final: 0.6945 (mmt) REVERT: A 520 MET cc_start: 0.7470 (OUTLIER) cc_final: 0.7091 (mtp) REVERT: A 906 TRP cc_start: 0.8682 (m-10) cc_final: 0.8430 (m-10) REVERT: A 910 MET cc_start: 0.6126 (OUTLIER) cc_final: 0.5690 (ttt) REVERT: A 1123 MET cc_start: 0.8360 (tpp) cc_final: 0.7712 (tpp) REVERT: A 1128 THR cc_start: 0.8612 (OUTLIER) cc_final: 0.8123 (p) REVERT: A 1322 LYS cc_start: 0.8686 (ttpt) cc_final: 0.7986 (tptt) REVERT: A 1333 LYS cc_start: 0.8358 (mtmm) cc_final: 0.8093 (tmtt) REVERT: A 1334 PRO cc_start: 0.7713 (Cg_endo) cc_final: 0.6411 (Cg_exo) REVERT: A 1378 LEU cc_start: 0.7982 (pt) cc_final: 0.7732 (pt) REVERT: A 1445 PHE cc_start: 0.8592 (m-80) cc_final: 0.8151 (m-80) REVERT: A 1450 ARG cc_start: 0.8600 (mtt180) cc_final: 0.7928 (mtm180) outliers start: 29 outliers final: 23 residues processed: 131 average time/residue: 0.2035 time to fit residues: 38.1085 Evaluate side-chains 131 residues out of total 1007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 104 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 HIS Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 432 TRP Chi-restraints excluded: chain A residue 520 MET Chi-restraints excluded: chain A residue 524 SER Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 725 VAL Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 910 MET Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1093 SER Chi-restraints excluded: chain A residue 1111 THR Chi-restraints excluded: chain A residue 1128 THR Chi-restraints excluded: chain A residue 1146 GLN Chi-restraints excluded: chain A residue 1162 SER Chi-restraints excluded: chain A residue 1219 THR Chi-restraints excluded: chain A residue 1262 VAL Chi-restraints excluded: chain A residue 1355 PHE Chi-restraints excluded: chain A residue 1399 ILE Chi-restraints excluded: chain A residue 1403 LEU Chi-restraints excluded: chain A residue 1437 THR Chi-restraints excluded: chain A residue 1464 SER Chi-restraints excluded: chain A residue 1489 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 0.6980 chunk 105 optimal weight: 0.9980 chunk 108 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 32 optimal weight: 0.3980 chunk 94 optimal weight: 7.9990 chunk 99 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 69 optimal weight: 0.5980 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: 0.8260 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9142 Z= 0.180 Angle : 0.552 8.437 12450 Z= 0.263 Chirality : 0.038 0.244 1504 Planarity : 0.004 0.044 1513 Dihedral : 9.382 135.082 1300 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.74 % Allowed : 13.27 % Favored : 83.99 % 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: 2.07 (0.25), residues: 1150 helix: 1.81 (0.19), residues: 798 sheet: 1.23 (0.58), residues: 70 loop : 0.30 (0.38), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1214 HIS 0.004 0.001 HIS A1001 PHE 0.013 0.001 PHE A 552 TYR 0.010 0.001 TYR A 228 ARG 0.008 0.000 ARG A1091 *********************** 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 136 residues out of total 1007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 111 time to evaluate : 1.179 Fit side-chains revert: symmetry clash REVERT: A 225 LYS cc_start: 0.8187 (mtmt) cc_final: 0.7490 (tttp) REVERT: A 231 MET cc_start: 0.8349 (tpt) cc_final: 0.8073 (tpt) REVERT: A 239 HIS cc_start: 0.8183 (OUTLIER) cc_final: 0.7252 (m90) REVERT: A 284 SER cc_start: 0.8663 (t) cc_final: 0.8338 (m) REVERT: A 405 MET cc_start: 0.7265 (mmm) cc_final: 0.6909 (mmt) REVERT: A 520 MET cc_start: 0.7466 (OUTLIER) cc_final: 0.7086 (mtp) REVERT: A 906 TRP cc_start: 0.8686 (m-10) cc_final: 0.8438 (m-10) REVERT: A 910 MET cc_start: 0.6005 (OUTLIER) cc_final: 0.5726 (ttt) REVERT: A 1123 MET cc_start: 0.8356 (tpp) cc_final: 0.7717 (tpp) REVERT: A 1128 THR cc_start: 0.8615 (OUTLIER) cc_final: 0.8155 (p) REVERT: A 1322 LYS cc_start: 0.8687 (ttpt) cc_final: 0.7978 (tptt) REVERT: A 1333 LYS cc_start: 0.8341 (mtmm) cc_final: 0.8061 (tmtt) REVERT: A 1334 PRO cc_start: 0.7625 (Cg_endo) cc_final: 0.6296 (Cg_exo) REVERT: A 1378 LEU cc_start: 0.7998 (pt) cc_final: 0.7758 (pt) REVERT: A 1445 PHE cc_start: 0.8566 (m-80) cc_final: 0.8119 (m-80) REVERT: A 1450 ARG cc_start: 0.8575 (mtt180) cc_final: 0.7936 (mtm180) outliers start: 25 outliers final: 21 residues processed: 129 average time/residue: 0.1984 time to fit residues: 36.4999 Evaluate side-chains 126 residues out of total 1007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 101 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 HIS Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 432 TRP Chi-restraints excluded: chain A residue 520 MET Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 725 VAL Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 910 MET Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1111 THR Chi-restraints excluded: chain A residue 1128 THR Chi-restraints excluded: chain A residue 1146 GLN Chi-restraints excluded: chain A residue 1162 SER Chi-restraints excluded: chain A residue 1219 THR Chi-restraints excluded: chain A residue 1262 VAL Chi-restraints excluded: chain A residue 1355 PHE Chi-restraints excluded: chain A residue 1399 ILE Chi-restraints excluded: chain A residue 1403 LEU Chi-restraints excluded: chain A residue 1437 THR Chi-restraints excluded: chain A residue 1464 SER Chi-restraints excluded: chain A residue 1489 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 111 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 52 optimal weight: 0.3980 chunk 77 optimal weight: 0.6980 chunk 116 optimal weight: 5.9990 chunk 107 optimal weight: 0.9980 chunk 92 optimal weight: 10.0000 chunk 9 optimal weight: 0.3980 chunk 71 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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: 0.8249 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9142 Z= 0.174 Angle : 0.545 8.379 12450 Z= 0.261 Chirality : 0.038 0.245 1504 Planarity : 0.004 0.045 1513 Dihedral : 9.295 133.499 1300 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.85 % Allowed : 13.05 % Favored : 84.10 % 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: 2.15 (0.25), residues: 1150 helix: 1.88 (0.19), residues: 795 sheet: 1.35 (0.59), residues: 70 loop : 0.28 (0.38), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1214 HIS 0.004 0.001 HIS A1001 PHE 0.013 0.001 PHE A 552 TYR 0.010 0.001 TYR A 871 ARG 0.009 0.000 ARG A1091 ********************** 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 133 residues out of total 1007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 107 time to evaluate : 1.021 Fit side-chains revert: symmetry clash REVERT: A 225 LYS cc_start: 0.8210 (mtmt) cc_final: 0.7480 (tttp) REVERT: A 231 MET cc_start: 0.8335 (tpt) cc_final: 0.8055 (tpt) REVERT: A 239 HIS cc_start: 0.8154 (OUTLIER) cc_final: 0.7187 (m90) REVERT: A 284 SER cc_start: 0.8661 (t) cc_final: 0.8330 (m) REVERT: A 405 MET cc_start: 0.7227 (mmm) cc_final: 0.6859 (mmt) REVERT: A 520 MET cc_start: 0.7462 (OUTLIER) cc_final: 0.7078 (mtp) REVERT: A 906 TRP cc_start: 0.8653 (m-10) cc_final: 0.8373 (m-10) REVERT: A 910 MET cc_start: 0.6070 (OUTLIER) cc_final: 0.5787 (ttt) REVERT: A 1079 PHE cc_start: 0.8550 (t80) cc_final: 0.8152 (t80) REVERT: A 1123 MET cc_start: 0.8346 (tpp) cc_final: 0.7770 (tpp) REVERT: A 1128 THR cc_start: 0.8556 (OUTLIER) cc_final: 0.8194 (p) REVERT: A 1322 LYS cc_start: 0.8667 (ttpt) cc_final: 0.7968 (tptt) REVERT: A 1333 LYS cc_start: 0.8336 (mtmm) cc_final: 0.8051 (tmtt) REVERT: A 1334 PRO cc_start: 0.7572 (Cg_endo) cc_final: 0.6215 (Cg_exo) REVERT: A 1445 PHE cc_start: 0.8561 (m-80) cc_final: 0.8070 (m-80) REVERT: A 1450 ARG cc_start: 0.8586 (mtt180) cc_final: 0.7930 (mtm180) REVERT: A 1459 PHE cc_start: 0.8489 (t80) cc_final: 0.8269 (t80) outliers start: 26 outliers final: 22 residues processed: 126 average time/residue: 0.1960 time to fit residues: 35.9454 Evaluate side-chains 133 residues out of total 1007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 107 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 HIS Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 432 TRP Chi-restraints excluded: chain A residue 520 MET Chi-restraints excluded: chain A residue 524 SER Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 725 VAL Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 910 MET Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1111 THR Chi-restraints excluded: chain A residue 1128 THR Chi-restraints excluded: chain A residue 1146 GLN Chi-restraints excluded: chain A residue 1162 SER Chi-restraints excluded: chain A residue 1219 THR Chi-restraints excluded: chain A residue 1262 VAL Chi-restraints excluded: chain A residue 1355 PHE Chi-restraints excluded: chain A residue 1399 ILE Chi-restraints excluded: chain A residue 1403 LEU Chi-restraints excluded: chain A residue 1437 THR Chi-restraints excluded: chain A residue 1464 SER Chi-restraints excluded: chain A residue 1489 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 0.7980 chunk 28 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 92 optimal weight: 9.9990 chunk 38 optimal weight: 6.9990 chunk 95 optimal weight: 7.9990 chunk 11 optimal weight: 0.7980 chunk 17 optimal weight: 0.2980 chunk 81 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 ASN ** A 824 GLN ** 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 = 0.3832 r_free = 0.3832 target = 0.151588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.119469 restraints weight = 12845.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.119056 restraints weight = 8464.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.119384 restraints weight = 6550.082| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.2463 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= 0.171 Angle : 0.554 10.727 12450 Z= 0.263 Chirality : 0.038 0.222 1504 Planarity : 0.004 0.045 1513 Dihedral : 9.215 132.854 1300 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.96 % Allowed : 13.71 % 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: 2.18 (0.25), residues: 1150 helix: 1.89 (0.19), residues: 797 sheet: 1.41 (0.59), residues: 70 loop : 0.29 (0.38), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1214 HIS 0.004 0.001 HIS A1001 PHE 0.012 0.001 PHE A 552 TYR 0.011 0.001 TYR A 871 ARG 0.006 0.000 ARG A1091 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1773.98 seconds wall clock time: 33 minutes 4.19 seconds (1984.19 seconds total)