Starting phenix.real_space_refine on Fri May 16 17:30:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bdq_44465/05_2025/9bdq_44465.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bdq_44465/05_2025/9bdq_44465.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bdq_44465/05_2025/9bdq_44465.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bdq_44465/05_2025/9bdq_44465.map" model { file = "/net/cci-nas-00/data/ceres_data/9bdq_44465/05_2025/9bdq_44465.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bdq_44465/05_2025/9bdq_44465.cif" } resolution = 2.26 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= 0.000 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 96 5.16 5 C 9304 2.51 5 N 2491 2.21 5 O 2774 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 14667 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 10474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1301, 10474 Classifications: {'peptide': 1301} Link IDs: {'PCIS': 1, 'PTRANS': 49, 'TRANS': 1250} Chain breaks: 4 Chain: "B" Number of atoms: 932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 932 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 6, 'TRANS': 111} Chain: "D" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 826 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 4, 'TRANS': 98} Chain: "C" Number of atoms: 1597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1597 Classifications: {'peptide': 200} Link IDs: {'PTRANS': 8, 'TRANS': 191} Chain breaks: 2 Chain: "E" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 836 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 4, 'TRANS': 101} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 8994 SG CYS A1236 53.627 87.905 21.073 1.00 77.76 S ATOM 9017 SG CYS A1239 51.028 90.349 22.532 1.00 99.78 S ATOM 8644 SG CYS A1191 36.108 75.094 19.724 1.00 90.89 S ATOM 10201 SG CYS A1428 39.702 77.368 18.397 1.00110.76 S ATOM 10207 SG CYS A1429 37.991 75.626 20.917 1.00 91.34 S Time building chain proxies: 9.37, per 1000 atoms: 0.64 Number of scatterers: 14667 At special positions: 0 Unit cell: (107.9, 143.59, 178.45, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 96 16.00 O 2774 8.00 N 2491 7.00 C 9304 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 - 3.00 Amino acid : True - 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: 3.36 Conformation dependent library (CDL) restraints added in 1.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2301 " pdb="ZN ZN A2301 " - pdb=" NE2 HIS A1423 " pdb="ZN ZN A2301 " - pdb=" ND1 HIS A1421 " pdb="ZN ZN A2301 " - pdb=" SG CYS A1236 " pdb="ZN ZN A2301 " - pdb=" SG CYS A1239 " pdb=" ZN A2302 " pdb="ZN ZN A2302 " - pdb=" SG CYS A1429 " pdb="ZN ZN A2302 " - pdb=" SG CYS A1428 " pdb="ZN ZN A2302 " - pdb=" SG CYS A1191 " Number of angles added : 1 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3496 Finding SS restraints... Secondary structure from input PDB file: 89 helices and 11 sheets defined 64.4% alpha, 5.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.71 Creating SS restraints... Processing helix chain 'A' and resid 6 through 11 Processing helix chain 'A' and resid 23 through 33 removed outlier: 3.521A pdb=" N ALA A 33 " --> pdb=" O ALA A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 56 removed outlier: 3.907A pdb=" N SER A 47 " --> pdb=" O ASP A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 77 Processing helix chain 'A' and resid 79 through 83 Processing helix chain 'A' and resid 91 through 96 Processing helix chain 'A' and resid 105 through 137 removed outlier: 3.789A pdb=" N ILE A 121 " --> pdb=" O ALA A 117 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N LYS A 123 " --> pdb=" O ASN A 119 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N LYS A 124 " --> pdb=" O ILE A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 156 removed outlier: 3.650A pdb=" N ASP A 156 " --> pdb=" O ARG A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 163 Processing helix chain 'A' and resid 166 through 189 removed outlier: 3.665A pdb=" N LYS A 189 " --> pdb=" O LYS A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 193 removed outlier: 3.728A pdb=" N ARG A 193 " --> pdb=" O PRO A 190 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 190 through 193' Processing helix chain 'A' and resid 231 through 255 Processing helix chain 'A' and resid 256 through 259 Processing helix chain 'A' and resid 260 through 273 removed outlier: 3.962A pdb=" N ARG A 264 " --> pdb=" O PRO A 260 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ASN A 266 " --> pdb=" O ILE A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 280 Processing helix chain 'A' and resid 282 through 289 removed outlier: 4.024A pdb=" N ILE A 286 " --> pdb=" O ARG A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 300 Processing helix chain 'A' and resid 304 through 308 Processing helix chain 'A' and resid 309 through 326 removed outlier: 3.822A pdb=" N HIS A 314 " --> pdb=" O ALA A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 346 Processing helix chain 'A' and resid 349 through 355 Processing helix chain 'A' and resid 356 through 359 Processing helix chain 'A' and resid 369 through 382 removed outlier: 3.516A pdb=" N ALA A 373 " --> pdb=" O GLU A 369 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N HIS A 380 " --> pdb=" O LYS A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 409 Processing helix chain 'A' and resid 425 through 435 Processing helix chain 'A' and resid 439 through 446 Processing helix chain 'A' and resid 447 through 451 Processing helix chain 'A' and resid 482 through 486 removed outlier: 4.207A pdb=" N VAL A 486 " --> pdb=" O TRP A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 492 Processing helix chain 'A' and resid 504 through 512 Processing helix chain 'A' and resid 516 through 526 removed outlier: 3.704A pdb=" N VAL A 524 " --> pdb=" O MET A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 532 removed outlier: 3.693A pdb=" N GLU A 531 " --> pdb=" O GLY A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 573 Processing helix chain 'A' and resid 574 through 580 Processing helix chain 'A' and resid 588 through 601 removed outlier: 3.516A pdb=" N PHE A 596 " --> pdb=" O LEU A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 730 Processing helix chain 'A' and resid 731 through 747 removed outlier: 4.673A pdb=" N ILE A 737 " --> pdb=" O GLU A 733 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N PHE A 738 " --> pdb=" O SER A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 754 through 760 Processing helix chain 'A' and resid 780 through 784 removed outlier: 3.632A pdb=" N THR A 784 " --> pdb=" O LEU A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 822 Proline residue: A 812 - end of helix Processing helix chain 'A' and resid 847 through 873 Processing helix chain 'A' and resid 904 through 910 removed outlier: 3.918A pdb=" N SER A 908 " --> pdb=" O GLN A 904 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 940 Processing helix chain 'A' and resid 943 through 964 Processing helix chain 'A' and resid 972 through 982 Proline residue: A 978 - end of helix removed outlier: 3.534A pdb=" N ASN A 982 " --> pdb=" O PRO A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 992 Processing helix chain 'A' and resid 993 through 997 Processing helix chain 'A' and resid 1003 through 1009 removed outlier: 3.651A pdb=" N ILE A1007 " --> pdb=" O ASN A1003 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N PHE A1008 " --> pdb=" O LEU A1004 " (cutoff:3.500A) Processing helix chain 'A' and resid 1014 through 1029 Processing helix chain 'A' and resid 1033 through 1042 removed outlier: 4.121A pdb=" N LEU A1037 " --> pdb=" O THR A1033 " (cutoff:3.500A) Processing helix chain 'A' and resid 1049 through 1056 Processing helix chain 'A' and resid 1067 through 1083 Processing helix chain 'A' and resid 1096 through 1110 Processing helix chain 'A' and resid 1115 through 1124 Processing helix chain 'A' and resid 1126 through 1137 Processing helix chain 'A' and resid 1141 through 1147 Processing helix chain 'A' and resid 1155 through 1179 removed outlier: 5.171A pdb=" N ASP A1166 " --> pdb=" O LEU A1162 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N TYR A1167 " --> pdb=" O SER A1163 " (cutoff:3.500A) Processing helix chain 'A' and resid 1191 through 1204 Processing helix chain 'A' and resid 1204 through 1209 Processing helix chain 'A' and resid 1220 through 1224 Processing helix chain 'A' and resid 1236 through 1241 Processing helix chain 'A' and resid 1291 through 1308 Processing helix chain 'A' and resid 1311 through 1323 Processing helix chain 'A' and resid 1329 through 1337 Processing helix chain 'A' and resid 1374 through 1378 removed outlier: 3.982A pdb=" N ASP A1378 " --> pdb=" O ASP A1375 " (cutoff:3.500A) Processing helix chain 'A' and resid 1391 through 1407 Processing helix chain 'B' and resid 480 through 484 removed outlier: 4.196A pdb=" N PHE B 484 " --> pdb=" O PRO B 480 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 480 through 484' Processing helix chain 'B' and resid 489 through 502 Processing helix chain 'B' and resid 507 through 533 removed outlier: 3.565A pdb=" N LEU B 511 " --> pdb=" O ASP B 507 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N CYS B 512 " --> pdb=" O LEU B 508 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N GLU B 513 " --> pdb=" O GLU B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 543 removed outlier: 3.555A pdb=" N VAL B 540 " --> pdb=" O ILE B 536 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N LYS B 541 " --> pdb=" O GLU B 537 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLU B 542 " --> pdb=" O GLU B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 578 removed outlier: 4.425A pdb=" N ASN B 548 " --> pdb=" O PRO B 544 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS B 549 " --> pdb=" O LYS B 545 " (cutoff:3.500A) Processing helix chain 'D' and resid 480 through 485 removed outlier: 4.024A pdb=" N PHE D 484 " --> pdb=" O PRO D 480 " (cutoff:3.500A) Processing helix chain 'D' and resid 486 through 488 No H-bonds generated for 'chain 'D' and resid 486 through 488' Processing helix chain 'D' and resid 489 through 502 Processing helix chain 'D' and resid 511 through 539 removed outlier: 3.963A pdb=" N GLN D 539 " --> pdb=" O HIS D 535 " (cutoff:3.500A) Processing helix chain 'D' and resid 542 through 574 removed outlier: 3.531A pdb=" N MET D 574 " --> pdb=" O HIS D 570 " (cutoff:3.500A) Processing helix chain 'C' and resid 489 through 501 removed outlier: 3.743A pdb=" N ASP C 501 " --> pdb=" O ASN C 497 " (cutoff:3.500A) Processing helix chain 'C' and resid 507 through 543 Processing helix chain 'C' and resid 545 through 574 Processing helix chain 'C' and resid 604 through 609 Processing helix chain 'C' and resid 634 through 638 Processing helix chain 'C' and resid 657 through 672 removed outlier: 3.511A pdb=" N HIS C 671 " --> pdb=" O LEU C 667 " (cutoff:3.500A) Processing helix chain 'C' and resid 674 through 688 Processing helix chain 'C' and resid 690 through 707 removed outlier: 3.853A pdb=" N ILE C 694 " --> pdb=" O ASN C 690 " (cutoff:3.500A) Processing helix chain 'E' and resid 480 through 485 removed outlier: 4.454A pdb=" N PHE E 484 " --> pdb=" O PRO E 480 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N SER E 485 " --> pdb=" O SER E 481 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 480 through 485' Processing helix chain 'E' and resid 489 through 497 removed outlier: 4.206A pdb=" N THR E 493 " --> pdb=" O PHE E 489 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N ARG E 495 " --> pdb=" O HIS E 491 " (cutoff:3.500A) Processing helix chain 'E' and resid 498 through 501 removed outlier: 3.850A pdb=" N ASP E 501 " --> pdb=" O TYR E 498 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 498 through 501' Processing helix chain 'E' and resid 510 through 541 removed outlier: 3.639A pdb=" N GLU E 514 " --> pdb=" O THR E 510 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLN E 539 " --> pdb=" O HIS E 535 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS E 541 " --> pdb=" O GLU E 537 " (cutoff:3.500A) Processing helix chain 'E' and resid 542 through 573 removed outlier: 3.506A pdb=" N SER E 573 " --> pdb=" O GLY E 569 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 21 through 22 removed outlier: 6.713A pdb=" N ILE A 21 " --> pdb=" O LEU A 368 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA3, first strand: chain 'A' and resid 385 through 388 removed outlier: 8.487A pdb=" N MET E 575 " --> pdb=" O LEU C 594 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N MET E 577 " --> pdb=" O PRO C 596 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ILE C 598 " --> pdb=" O MET E 577 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLU C 593 " --> pdb=" O ILE C 578 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 418 through 419 Processing sheet with id=AA5, first strand: chain 'A' and resid 554 through 556 removed outlier: 5.283A pdb=" N VAL A 537 " --> pdb=" O VAL A 763 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N TYR A 765 " --> pdb=" O VAL A 537 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 713 through 716 Processing sheet with id=AA7, first strand: chain 'A' and resid 827 through 828 removed outlier: 3.601A pdb=" N SER A 835 " --> pdb=" O ILE A 828 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N GLU A 834 " --> pdb=" O THR A 721 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 890 through 891 Processing sheet with id=AA9, first strand: chain 'A' and resid 1113 through 1114 Processing sheet with id=AB1, first strand: chain 'A' and resid 1225 through 1231 Processing sheet with id=AB2, first strand: chain 'A' and resid 1379 through 1381 removed outlier: 4.423A pdb=" N PHE A1379 " --> pdb=" O VAL A1386 " (cutoff:3.500A) 846 hydrogen bonds defined for protein. 2424 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: 5.17 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: 1.19 - 1.31: 2491 1.31 - 1.44: 3738 1.44 - 1.56: 8552 1.56 - 1.69: 2 1.69 - 1.81: 160 Bond restraints: 14943 Sorted by residual: bond pdb=" N PRO C 544 " pdb=" CD PRO C 544 " ideal model delta sigma weight residual 1.473 1.655 -0.182 1.40e-02 5.10e+03 1.69e+02 bond pdb=" N PRO A 89 " pdb=" CD PRO A 89 " ideal model delta sigma weight residual 1.474 1.339 0.135 1.40e-02 5.10e+03 9.32e+01 bond pdb=" N PRO A 417 " pdb=" CD PRO A 417 " ideal model delta sigma weight residual 1.473 1.605 -0.132 1.40e-02 5.10e+03 8.93e+01 bond pdb=" C LYS B 541 " pdb=" O LYS B 541 " ideal model delta sigma weight residual 1.236 1.316 -0.079 1.22e-02 6.72e+03 4.25e+01 bond pdb=" C SER A 599 " pdb=" N ILE A 600 " ideal model delta sigma weight residual 1.335 1.264 0.071 1.20e-02 6.94e+03 3.51e+01 ... (remaining 14938 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.52: 19718 2.52 - 5.03: 416 5.03 - 7.55: 46 7.55 - 10.07: 12 10.07 - 12.59: 4 Bond angle restraints: 20196 Sorted by residual: angle pdb=" N GLU B 542 " pdb=" CA GLU B 542 " pdb=" C GLU B 542 " ideal model delta sigma weight residual 111.71 102.44 9.27 1.15e+00 7.56e-01 6.50e+01 angle pdb=" CA PRO A 89 " pdb=" N PRO A 89 " pdb=" CD PRO A 89 " ideal model delta sigma weight residual 111.50 121.01 -9.51 1.40e+00 5.10e-01 4.61e+01 angle pdb=" C LYS B 545 " pdb=" N ILE B 546 " pdb=" CA ILE B 546 " ideal model delta sigma weight residual 120.55 130.78 -10.23 1.60e+00 3.91e-01 4.09e+01 angle pdb=" C MET A 469 " pdb=" N TYR A 470 " pdb=" CA TYR A 470 " ideal model delta sigma weight residual 122.31 110.76 11.55 1.81e+00 3.05e-01 4.07e+01 angle pdb=" N VAL D 540 " pdb=" CA VAL D 540 " pdb=" C VAL D 540 " ideal model delta sigma weight residual 113.71 108.35 5.36 9.50e-01 1.11e+00 3.19e+01 ... (remaining 20191 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.11: 7832 18.11 - 36.23: 978 36.23 - 54.34: 269 54.34 - 72.45: 57 72.45 - 90.56: 13 Dihedral angle restraints: 9149 sinusoidal: 3775 harmonic: 5374 Sorted by residual: dihedral pdb=" CA ILE C 543 " pdb=" C ILE C 543 " pdb=" N PRO C 544 " pdb=" CA PRO C 544 " ideal model delta harmonic sigma weight residual -180.00 -151.11 -28.89 0 5.00e+00 4.00e-02 3.34e+01 dihedral pdb=" CA MET B 479 " pdb=" C MET B 479 " pdb=" N PRO B 480 " pdb=" CA PRO B 480 " ideal model delta harmonic sigma weight residual -180.00 -151.25 -28.75 0 5.00e+00 4.00e-02 3.31e+01 dihedral pdb=" C PRO D 480 " pdb=" N PRO D 480 " pdb=" CA PRO D 480 " pdb=" CB PRO D 480 " ideal model delta harmonic sigma weight residual -120.70 -109.24 -11.46 0 2.50e+00 1.60e-01 2.10e+01 ... (remaining 9146 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1566 0.041 - 0.083: 507 0.083 - 0.124: 164 0.124 - 0.165: 41 0.165 - 0.206: 17 Chirality restraints: 2295 Sorted by residual: chirality pdb=" CA HIS E 491 " pdb=" N HIS E 491 " pdb=" C HIS E 491 " pdb=" CB HIS E 491 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA ILE A1154 " pdb=" N ILE A1154 " pdb=" C ILE A1154 " pdb=" CB ILE A1154 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CA LEU A1092 " pdb=" N LEU A1092 " pdb=" C LEU A1092 " pdb=" CB LEU A1092 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 2292 not shown) Planarity restraints: 2585 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR C 487 " 0.019 2.00e-02 2.50e+03 3.75e-02 1.40e+01 pdb=" C THR C 487 " -0.065 2.00e-02 2.50e+03 pdb=" O THR C 487 " 0.024 2.00e-02 2.50e+03 pdb=" N PHE C 488 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 470 " 0.016 2.00e-02 2.50e+03 3.33e-02 1.11e+01 pdb=" C TYR A 470 " -0.058 2.00e-02 2.50e+03 pdb=" O TYR A 470 " 0.021 2.00e-02 2.50e+03 pdb=" N MET A 471 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 465 " -0.015 2.00e-02 2.50e+03 3.01e-02 9.05e+00 pdb=" C SER A 465 " 0.052 2.00e-02 2.50e+03 pdb=" O SER A 465 " -0.019 2.00e-02 2.50e+03 pdb=" N ASP A 466 " -0.018 2.00e-02 2.50e+03 ... (remaining 2582 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 542 2.71 - 3.26: 15309 3.26 - 3.80: 25180 3.80 - 4.35: 31808 4.35 - 4.90: 51988 Nonbonded interactions: 124827 Sorted by model distance: nonbonded pdb=" OD1 ASP A 203 " pdb=" N LYS A 204 " model vdw 2.162 3.120 nonbonded pdb=" OD1 ASN A1364 " pdb=" OG SER A1367 " model vdw 2.222 3.040 nonbonded pdb=" O HIS B 502 " pdb=" ND1 HIS B 502 " model vdw 2.230 3.120 nonbonded pdb=" OG1 THR A 721 " pdb=" OE1 GLU A 834 " model vdw 2.231 3.040 nonbonded pdb=" OG1 THR A 972 " pdb=" OD1 ASP A 974 " model vdw 2.232 3.040 ... (remaining 124822 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and resid 479 through 579) selection = (chain 'D' and resid 479 through 579) selection = (chain 'E' and resid 479 through 579) } 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 individual isotropic 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: 7.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.600 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 37.600 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.060 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:11.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 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 : 0.006 0.182 14950 Z= 0.356 Angle : 0.814 12.587 20197 Z= 0.511 Chirality : 0.049 0.206 2295 Planarity : 0.005 0.072 2585 Dihedral : 17.378 90.563 5653 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.60 % Favored : 96.35 % Rotamer: Outliers : 3.68 % Allowed : 25.63 % Favored : 70.69 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 1.43 % 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: 1.12 (0.20), residues: 1806 helix: 1.59 (0.16), residues: 1038 sheet: -0.19 (0.50), residues: 101 loop : -0.40 (0.25), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 173 HIS 0.008 0.001 HIS B 502 PHE 0.022 0.002 PHE A 399 TYR 0.038 0.001 TYR B 498 ARG 0.010 0.000 ARG A1295 Details of bonding type rmsd hydrogen bonds : bond 0.14413 ( 846) hydrogen bonds : angle 5.32582 ( 2424) metal coordination : bond 0.04001 ( 7) metal coordination : angle 2.21930 ( 1) covalent geometry : bond 0.00563 (14943) covalent geometry : angle 0.81427 (20196) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 1658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 399 time to evaluate : 1.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 SER cc_start: 0.8502 (m) cc_final: 0.8202 (p) REVERT: A 44 LYS cc_start: 0.8233 (mmtt) cc_final: 0.7854 (mmpt) REVERT: A 109 ASN cc_start: 0.8285 (m-40) cc_final: 0.7988 (m-40) REVERT: A 112 ARG cc_start: 0.7721 (mtm110) cc_final: 0.7170 (mtt90) REVERT: A 141 ARG cc_start: 0.7171 (ttt-90) cc_final: 0.6838 (ttp-110) REVERT: A 150 GLU cc_start: 0.7667 (tt0) cc_final: 0.7422 (tt0) REVERT: A 159 LYS cc_start: 0.8293 (ttpt) cc_final: 0.7954 (ttpp) REVERT: A 179 GLU cc_start: 0.8228 (mm-30) cc_final: 0.7991 (mp0) REVERT: A 191 LYS cc_start: 0.7632 (ptpp) cc_final: 0.7284 (ptmm) REVERT: A 204 LYS cc_start: 0.7965 (mttt) cc_final: 0.7633 (mttt) REVERT: A 328 PHE cc_start: 0.8075 (m-80) cc_final: 0.7821 (m-80) REVERT: A 332 LYS cc_start: 0.7695 (mttt) cc_final: 0.7409 (mmmm) REVERT: A 388 GLU cc_start: 0.7695 (tt0) cc_final: 0.7453 (tm-30) REVERT: A 419 TYR cc_start: 0.8318 (m-80) cc_final: 0.7862 (m-80) REVERT: A 436 GLU cc_start: 0.7608 (mt-10) cc_final: 0.7183 (mt-10) REVERT: A 481 ASP cc_start: 0.7837 (m-30) cc_final: 0.7497 (m-30) REVERT: A 504 ARG cc_start: 0.7568 (mtp85) cc_final: 0.7219 (mtp85) REVERT: A 511 ASN cc_start: 0.8085 (m-40) cc_final: 0.7880 (m-40) REVERT: A 533 ASP cc_start: 0.7970 (p0) cc_final: 0.7496 (t0) REVERT: A 534 GLN cc_start: 0.8094 (mm-40) cc_final: 0.7618 (mm110) REVERT: A 542 LYS cc_start: 0.7690 (tttt) cc_final: 0.7479 (tttt) REVERT: A 559 LYS cc_start: 0.8412 (mttp) cc_final: 0.8147 (mttt) REVERT: A 568 GLU cc_start: 0.7351 (mm-30) cc_final: 0.7133 (mm-30) REVERT: A 714 THR cc_start: 0.8330 (OUTLIER) cc_final: 0.7821 (m) REVERT: A 725 LYS cc_start: 0.8511 (mmtp) cc_final: 0.8246 (mmtp) REVERT: A 735 MET cc_start: 0.8543 (tpt) cc_final: 0.8340 (tpp) REVERT: A 743 ASP cc_start: 0.7870 (m-30) cc_final: 0.7546 (m-30) REVERT: A 782 GLU cc_start: 0.7538 (mp0) cc_final: 0.7012 (mp0) REVERT: A 841 LYS cc_start: 0.8128 (mmtm) cc_final: 0.7614 (mmtm) REVERT: A 853 GLU cc_start: 0.7430 (tp30) cc_final: 0.7168 (tp30) REVERT: A 907 LYS cc_start: 0.8646 (tttt) cc_final: 0.8367 (tttp) REVERT: A 1070 LYS cc_start: 0.7303 (ttpt) cc_final: 0.7083 (ttmm) REVERT: A 1073 LYS cc_start: 0.7641 (mmtp) cc_final: 0.7411 (mmtp) REVERT: A 1096 LYS cc_start: 0.7645 (mtmt) cc_final: 0.7375 (ptpp) REVERT: A 1132 GLU cc_start: 0.7028 (tp30) cc_final: 0.6747 (tp30) REVERT: A 1217 GLU cc_start: 0.7940 (mp0) cc_final: 0.7657 (mm-30) REVERT: A 1220 ASP cc_start: 0.7934 (t70) cc_final: 0.7718 (t0) REVERT: A 1259 GLN cc_start: 0.7666 (mm-40) cc_final: 0.7343 (tp40) REVERT: A 1313 GLU cc_start: 0.6811 (mm-30) cc_final: 0.6306 (tp30) REVERT: A 1374 ASN cc_start: 0.7093 (m-40) cc_final: 0.6884 (m-40) REVERT: B 491 HIS cc_start: 0.6784 (OUTLIER) cc_final: 0.6491 (p-80) REVERT: B 494 ASP cc_start: 0.7228 (OUTLIER) cc_final: 0.7014 (t70) REVERT: D 575 MET cc_start: 0.7446 (mmm) cc_final: 0.7226 (mmm) REVERT: C 594 LEU cc_start: 0.7687 (mt) cc_final: 0.7179 (mt) REVERT: E 479 MET cc_start: 0.4319 (ptt) cc_final: 0.4093 (ptt) outliers start: 61 outliers final: 25 residues processed: 447 average time/residue: 1.2980 time to fit residues: 634.4077 Evaluate side-chains 393 residues out of total 1658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 365 time to evaluate : 1.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 712 PHE Chi-restraints excluded: chain A residue 714 THR Chi-restraints excluded: chain A residue 802 SER Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1025 ARG Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1079 THR Chi-restraints excluded: chain A residue 1180 ARG Chi-restraints excluded: chain A residue 1294 LEU Chi-restraints excluded: chain A residue 1451 VAL Chi-restraints excluded: chain B residue 491 HIS Chi-restraints excluded: chain B residue 494 ASP Chi-restraints excluded: chain B residue 512 CYS Chi-restraints excluded: chain B residue 541 LYS Chi-restraints excluded: chain B residue 542 GLU Chi-restraints excluded: chain B residue 543 ILE Chi-restraints excluded: chain B residue 545 LYS Chi-restraints excluded: chain B residue 559 LYS Chi-restraints excluded: chain B residue 572 VAL Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 547 ILE Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 545 LYS Chi-restraints excluded: chain C residue 573 SER Chi-restraints excluded: chain C residue 690 ASN Chi-restraints excluded: chain E residue 506 TYR Chi-restraints excluded: chain E residue 552 SER Chi-restraints excluded: chain E residue 560 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 152 optimal weight: 0.9990 chunk 137 optimal weight: 0.9980 chunk 76 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 92 optimal weight: 0.1980 chunk 73 optimal weight: 0.9980 chunk 141 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 chunk 105 optimal weight: 0.6980 chunk 164 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 ASN A1169 GLN A1179 ASN A1183 ASN A1324 GLN E 499 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.158780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.133536 restraints weight = 19787.773| |-----------------------------------------------------------------------------| r_work (start): 0.3865 rms_B_bonded: 1.59 r_work: 0.3757 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3610 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 14950 Z= 0.232 Angle : 0.657 11.834 20197 Z= 0.338 Chirality : 0.046 0.180 2295 Planarity : 0.005 0.098 2585 Dihedral : 6.500 64.538 2023 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.21 % Favored : 96.73 % Rotamer: Outliers : 5.01 % Allowed : 25.69 % Favored : 69.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: 1.24 (0.20), residues: 1806 helix: 1.71 (0.16), residues: 1043 sheet: -0.29 (0.54), residues: 99 loop : -0.38 (0.25), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 447 HIS 0.007 0.001 HIS A 149 PHE 0.024 0.002 PHE A 399 TYR 0.026 0.002 TYR B 498 ARG 0.004 0.001 ARG A1295 Details of bonding type rmsd hydrogen bonds : bond 0.04841 ( 846) hydrogen bonds : angle 4.33945 ( 2424) metal coordination : bond 0.01358 ( 7) metal coordination : angle 6.35739 ( 1) covalent geometry : bond 0.00563 (14943) covalent geometry : angle 0.65593 (20196) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 1658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 379 time to evaluate : 1.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 LYS cc_start: 0.8397 (mmtt) cc_final: 0.8160 (mmpt) REVERT: A 109 ASN cc_start: 0.8262 (m-40) cc_final: 0.8045 (m-40) REVERT: A 112 ARG cc_start: 0.7777 (mtm110) cc_final: 0.7515 (mtt90) REVERT: A 210 LEU cc_start: 0.8648 (pp) cc_final: 0.8444 (pp) REVERT: A 441 ASP cc_start: 0.7840 (t0) cc_final: 0.7613 (t0) REVERT: A 714 THR cc_start: 0.8570 (OUTLIER) cc_final: 0.8259 (m) REVERT: A 782 GLU cc_start: 0.7556 (mp0) cc_final: 0.7324 (mp0) REVERT: A 841 LYS cc_start: 0.8565 (mmtm) cc_final: 0.8325 (mmtm) REVERT: A 907 LYS cc_start: 0.8682 (tttt) cc_final: 0.8149 (ttpp) REVERT: A 1073 LYS cc_start: 0.8167 (mmtp) cc_final: 0.7950 (mmtp) REVERT: A 1078 ARG cc_start: 0.8108 (mtt180) cc_final: 0.7880 (mtt-85) REVERT: A 1132 GLU cc_start: 0.7797 (tp30) cc_final: 0.7564 (tp30) REVERT: A 1166 ASP cc_start: 0.7790 (OUTLIER) cc_final: 0.7574 (t70) REVERT: A 1205 ARG cc_start: 0.7832 (OUTLIER) cc_final: 0.7577 (ttp-170) REVERT: A 1235 GLU cc_start: 0.6823 (mp0) cc_final: 0.6616 (mp0) REVERT: A 1259 GLN cc_start: 0.7631 (OUTLIER) cc_final: 0.7394 (tp40) REVERT: A 1374 ASN cc_start: 0.8316 (m-40) cc_final: 0.8001 (m-40) REVERT: B 491 HIS cc_start: 0.7032 (OUTLIER) cc_final: 0.6621 (p-80) REVERT: D 531 MET cc_start: 0.7502 (tmm) cc_final: 0.7288 (tpt) REVERT: D 577 MET cc_start: 0.6737 (tmt) cc_final: 0.6439 (tmt) REVERT: C 545 LYS cc_start: 0.7001 (OUTLIER) cc_final: 0.6620 (ptmt) REVERT: C 546 ILE cc_start: 0.7155 (mp) cc_final: 0.6875 (mt) REVERT: C 694 ILE cc_start: 0.7941 (OUTLIER) cc_final: 0.7685 (mt) REVERT: C 695 GLN cc_start: 0.7518 (OUTLIER) cc_final: 0.7309 (mm-40) REVERT: E 479 MET cc_start: 0.4338 (ptt) cc_final: 0.4109 (ptt) REVERT: E 518 MET cc_start: 0.4187 (OUTLIER) cc_final: 0.3686 (ppp) outliers start: 83 outliers final: 25 residues processed: 437 average time/residue: 1.3527 time to fit residues: 643.8999 Evaluate side-chains 396 residues out of total 1658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 362 time to evaluate : 1.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 714 THR Chi-restraints excluded: chain A residue 855 CYS Chi-restraints excluded: chain A residue 1025 ARG Chi-restraints excluded: chain A residue 1084 SER Chi-restraints excluded: chain A residue 1137 LEU Chi-restraints excluded: chain A residue 1142 LYS Chi-restraints excluded: chain A residue 1166 ASP Chi-restraints excluded: chain A residue 1190 THR Chi-restraints excluded: chain A residue 1205 ARG Chi-restraints excluded: chain A residue 1259 GLN Chi-restraints excluded: chain A residue 1451 VAL Chi-restraints excluded: chain B residue 491 HIS Chi-restraints excluded: chain B residue 499 HIS Chi-restraints excluded: chain B residue 512 CYS Chi-restraints excluded: chain B residue 541 LYS Chi-restraints excluded: chain B residue 542 GLU Chi-restraints excluded: chain B residue 543 ILE Chi-restraints excluded: chain B residue 545 LYS Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 535 HIS Chi-restraints excluded: chain C residue 518 MET Chi-restraints excluded: chain C residue 523 SER Chi-restraints excluded: chain C residue 545 LYS Chi-restraints excluded: chain C residue 690 ASN Chi-restraints excluded: chain C residue 694 ILE Chi-restraints excluded: chain C residue 695 GLN Chi-restraints excluded: chain E residue 491 HIS Chi-restraints excluded: chain E residue 506 TYR Chi-restraints excluded: chain E residue 518 MET Chi-restraints excluded: chain E residue 531 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 29 optimal weight: 0.9990 chunk 75 optimal weight: 0.7980 chunk 57 optimal weight: 0.5980 chunk 131 optimal weight: 4.9990 chunk 139 optimal weight: 0.5980 chunk 87 optimal weight: 0.8980 chunk 40 optimal weight: 0.5980 chunk 58 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 chunk 148 optimal weight: 0.6980 chunk 59 optimal weight: 8.9990 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 119 ASN A 534 GLN A 951 ASN A1011 ASN A1183 ASN A1324 GLN C 651 GLN E 539 GLN E 548 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.158673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.133464 restraints weight = 19833.355| |-----------------------------------------------------------------------------| r_work (start): 0.3861 rms_B_bonded: 1.60 r_work: 0.3753 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3604 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 14950 Z= 0.220 Angle : 0.627 11.054 20197 Z= 0.321 Chirality : 0.046 0.189 2295 Planarity : 0.005 0.097 2585 Dihedral : 5.876 59.697 1998 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.10 % Favored : 96.84 % Rotamer: Outliers : 4.58 % Allowed : 26.00 % Favored : 69.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: 1.24 (0.20), residues: 1806 helix: 1.77 (0.16), residues: 1043 sheet: -0.25 (0.53), residues: 96 loop : -0.49 (0.25), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 806 HIS 0.005 0.001 HIS A1120 PHE 0.024 0.002 PHE A 399 TYR 0.023 0.002 TYR B 498 ARG 0.004 0.000 ARG C 532 Details of bonding type rmsd hydrogen bonds : bond 0.04690 ( 846) hydrogen bonds : angle 4.25889 ( 2424) metal coordination : bond 0.00956 ( 7) metal coordination : angle 6.15098 ( 1) covalent geometry : bond 0.00537 (14943) covalent geometry : angle 0.62516 (20196) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 1658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 370 time to evaluate : 1.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 GLU cc_start: 0.7887 (pt0) cc_final: 0.7648 (pt0) REVERT: A 84 MET cc_start: 0.8244 (tpp) cc_final: 0.7763 (tpp) REVERT: A 112 ARG cc_start: 0.7828 (mtm110) cc_final: 0.7552 (mtt90) REVERT: A 286 ILE cc_start: 0.8398 (OUTLIER) cc_final: 0.8150 (mt) REVERT: A 385 LYS cc_start: 0.8868 (OUTLIER) cc_final: 0.8617 (mttt) REVERT: A 460 GLU cc_start: 0.7759 (pm20) cc_final: 0.7457 (pm20) REVERT: A 568 GLU cc_start: 0.7230 (mm-30) cc_final: 0.7013 (tp30) REVERT: A 714 THR cc_start: 0.8599 (OUTLIER) cc_final: 0.8281 (m) REVERT: A 782 GLU cc_start: 0.7571 (mp0) cc_final: 0.7342 (mp0) REVERT: A 841 LYS cc_start: 0.8571 (mmtm) cc_final: 0.8329 (mmtm) REVERT: A 889 PHE cc_start: 0.7435 (OUTLIER) cc_final: 0.6676 (t80) REVERT: A 907 LYS cc_start: 0.8636 (tttt) cc_final: 0.8432 (tttp) REVERT: A 1012 ILE cc_start: 0.7893 (mm) cc_final: 0.7691 (tp) REVERT: A 1078 ARG cc_start: 0.8130 (mtt180) cc_final: 0.7880 (mtt-85) REVERT: A 1132 GLU cc_start: 0.7788 (tp30) cc_final: 0.7529 (tp30) REVERT: A 1166 ASP cc_start: 0.7798 (OUTLIER) cc_final: 0.7597 (t0) REVERT: A 1205 ARG cc_start: 0.7814 (OUTLIER) cc_final: 0.7560 (ttp-170) REVERT: A 1234 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7802 (pp) REVERT: A 1235 GLU cc_start: 0.6863 (mp0) cc_final: 0.6626 (mp0) REVERT: A 1313 GLU cc_start: 0.7494 (mm-30) cc_final: 0.7175 (tm-30) REVERT: C 545 LYS cc_start: 0.7313 (OUTLIER) cc_final: 0.7090 (pmmt) REVERT: C 546 ILE cc_start: 0.7269 (mp) cc_final: 0.7066 (mt) REVERT: C 691 ASP cc_start: 0.7691 (m-30) cc_final: 0.7216 (m-30) REVERT: E 479 MET cc_start: 0.3899 (ptt) cc_final: 0.3677 (ptt) REVERT: E 536 ILE cc_start: 0.6808 (OUTLIER) cc_final: 0.6595 (tt) outliers start: 76 outliers final: 38 residues processed: 419 average time/residue: 1.3574 time to fit residues: 621.9914 Evaluate side-chains 409 residues out of total 1658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 362 time to evaluate : 1.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 317 LYS Chi-restraints excluded: chain A residue 385 LYS Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 714 THR Chi-restraints excluded: chain A residue 798 ILE Chi-restraints excluded: chain A residue 822 ASN Chi-restraints excluded: chain A residue 838 ILE Chi-restraints excluded: chain A residue 855 CYS Chi-restraints excluded: chain A residue 883 ILE Chi-restraints excluded: chain A residue 889 PHE Chi-restraints excluded: chain A residue 933 THR Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 1025 ARG Chi-restraints excluded: chain A residue 1084 SER Chi-restraints excluded: chain A residue 1142 LYS Chi-restraints excluded: chain A residue 1166 ASP Chi-restraints excluded: chain A residue 1205 ARG Chi-restraints excluded: chain A residue 1234 LEU Chi-restraints excluded: chain A residue 1330 LEU Chi-restraints excluded: chain A residue 1451 VAL Chi-restraints excluded: chain A residue 1456 LEU Chi-restraints excluded: chain B residue 499 HIS Chi-restraints excluded: chain B residue 531 MET Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 541 LYS Chi-restraints excluded: chain B residue 542 GLU Chi-restraints excluded: chain B residue 545 LYS Chi-restraints excluded: chain B residue 559 LYS Chi-restraints excluded: chain B residue 572 VAL Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 522 ASN Chi-restraints excluded: chain D residue 535 HIS Chi-restraints excluded: chain D residue 536 ILE Chi-restraints excluded: chain C residue 518 MET Chi-restraints excluded: chain C residue 523 SER Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 545 LYS Chi-restraints excluded: chain C residue 567 ILE Chi-restraints excluded: chain C residue 607 SER Chi-restraints excluded: chain C residue 685 LEU Chi-restraints excluded: chain C residue 690 ASN Chi-restraints excluded: chain E residue 491 HIS Chi-restraints excluded: chain E residue 506 TYR Chi-restraints excluded: chain E residue 518 MET Chi-restraints excluded: chain E residue 531 MET Chi-restraints excluded: chain E residue 536 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 105 optimal weight: 0.5980 chunk 17 optimal weight: 0.2980 chunk 72 optimal weight: 0.9990 chunk 21 optimal weight: 0.4980 chunk 146 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 chunk 131 optimal weight: 0.0050 chunk 115 optimal weight: 1.9990 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 ASN A 534 GLN A1011 ASN A1182 GLN A1183 ASN A1241 GLN ** A1256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1324 GLN C 648 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.159467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.134124 restraints weight = 19653.692| |-----------------------------------------------------------------------------| r_work (start): 0.3864 rms_B_bonded: 1.60 r_work: 0.3762 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3619 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 14950 Z= 0.180 Angle : 0.606 10.406 20197 Z= 0.310 Chirality : 0.044 0.180 2295 Planarity : 0.004 0.095 2585 Dihedral : 5.606 54.779 1993 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.05 % Favored : 96.90 % Rotamer: Outliers : 4.10 % Allowed : 26.18 % Favored : 69.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: 1.28 (0.20), residues: 1806 helix: 1.81 (0.16), residues: 1044 sheet: -0.48 (0.54), residues: 90 loop : -0.46 (0.25), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 806 HIS 0.004 0.001 HIS A1120 PHE 0.024 0.001 PHE B 488 TYR 0.021 0.001 TYR B 498 ARG 0.004 0.000 ARG A 282 Details of bonding type rmsd hydrogen bonds : bond 0.04380 ( 846) hydrogen bonds : angle 4.21290 ( 2424) metal coordination : bond 0.00787 ( 7) metal coordination : angle 5.52634 ( 1) covalent geometry : bond 0.00435 (14943) covalent geometry : angle 0.60486 (20196) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 1658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 362 time to evaluate : 1.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.8242 (tpp) cc_final: 0.7751 (tpp) REVERT: A 385 LYS cc_start: 0.8835 (OUTLIER) cc_final: 0.8599 (mttt) REVERT: A 460 GLU cc_start: 0.7775 (pm20) cc_final: 0.7486 (pm20) REVERT: A 714 THR cc_start: 0.8543 (OUTLIER) cc_final: 0.8227 (m) REVERT: A 782 GLU cc_start: 0.7569 (mp0) cc_final: 0.7342 (mp0) REVERT: A 841 LYS cc_start: 0.8550 (mmtm) cc_final: 0.8306 (mmtm) REVERT: A 1078 ARG cc_start: 0.8076 (mtt180) cc_final: 0.7795 (mtt-85) REVERT: A 1132 GLU cc_start: 0.7758 (tp30) cc_final: 0.7461 (tp30) REVERT: A 1166 ASP cc_start: 0.7745 (OUTLIER) cc_final: 0.7542 (t70) REVERT: A 1205 ARG cc_start: 0.7790 (OUTLIER) cc_final: 0.7543 (ttp-170) REVERT: A 1234 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7882 (pp) REVERT: A 1235 GLU cc_start: 0.6832 (mp0) cc_final: 0.6599 (mp0) REVERT: A 1313 GLU cc_start: 0.7474 (mm-30) cc_final: 0.7203 (tm-30) REVERT: B 543 ILE cc_start: 0.6899 (OUTLIER) cc_final: 0.6687 (tt) REVERT: D 531 MET cc_start: 0.7545 (tmm) cc_final: 0.7247 (tpt) REVERT: C 546 ILE cc_start: 0.7290 (mp) cc_final: 0.7060 (mt) REVERT: C 691 ASP cc_start: 0.7696 (m-30) cc_final: 0.7030 (m-30) REVERT: E 479 MET cc_start: 0.3901 (ptt) cc_final: 0.3697 (ptt) outliers start: 68 outliers final: 36 residues processed: 408 average time/residue: 1.3363 time to fit residues: 595.6521 Evaluate side-chains 398 residues out of total 1658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 356 time to evaluate : 1.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 317 LYS Chi-restraints excluded: chain A residue 385 LYS Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 714 THR Chi-restraints excluded: chain A residue 855 CYS Chi-restraints excluded: chain A residue 933 THR Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 1025 ARG Chi-restraints excluded: chain A residue 1084 SER Chi-restraints excluded: chain A residue 1142 LYS Chi-restraints excluded: chain A residue 1166 ASP Chi-restraints excluded: chain A residue 1205 ARG Chi-restraints excluded: chain A residue 1234 LEU Chi-restraints excluded: chain A residue 1236 CYS Chi-restraints excluded: chain A residue 1330 LEU Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain B residue 499 HIS Chi-restraints excluded: chain B residue 531 MET Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 541 LYS Chi-restraints excluded: chain B residue 542 GLU Chi-restraints excluded: chain B residue 543 ILE Chi-restraints excluded: chain B residue 545 LYS Chi-restraints excluded: chain B residue 559 LYS Chi-restraints excluded: chain D residue 478 ILE Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 522 ASN Chi-restraints excluded: chain D residue 535 HIS Chi-restraints excluded: chain D residue 536 ILE Chi-restraints excluded: chain C residue 518 MET Chi-restraints excluded: chain C residue 523 SER Chi-restraints excluded: chain C residue 545 LYS Chi-restraints excluded: chain C residue 567 ILE Chi-restraints excluded: chain C residue 631 VAL Chi-restraints excluded: chain C residue 685 LEU Chi-restraints excluded: chain C residue 690 ASN Chi-restraints excluded: chain E residue 491 HIS Chi-restraints excluded: chain E residue 506 TYR Chi-restraints excluded: chain E residue 518 MET Chi-restraints excluded: chain E residue 531 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 176 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 138 optimal weight: 0.9990 chunk 113 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 108 optimal weight: 0.5980 chunk 178 optimal weight: 0.2980 chunk 179 optimal weight: 0.9980 chunk 110 optimal weight: 0.0980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 ASN A 534 GLN A1011 ASN A1183 ASN A1324 GLN ** A1374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 648 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.159259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.133913 restraints weight = 19925.849| |-----------------------------------------------------------------------------| r_work (start): 0.3865 rms_B_bonded: 1.62 r_work: 0.3758 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3608 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 14950 Z= 0.205 Angle : 0.618 11.288 20197 Z= 0.314 Chirality : 0.045 0.195 2295 Planarity : 0.004 0.092 2585 Dihedral : 5.490 55.348 1992 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.21 % Favored : 96.73 % Rotamer: Outliers : 4.58 % Allowed : 26.18 % Favored : 69.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: 1.24 (0.20), residues: 1806 helix: 1.78 (0.16), residues: 1046 sheet: -0.56 (0.54), residues: 90 loop : -0.47 (0.25), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 806 HIS 0.005 0.001 HIS A1120 PHE 0.025 0.002 PHE A 399 TYR 0.019 0.002 TYR B 498 ARG 0.004 0.000 ARG A 824 Details of bonding type rmsd hydrogen bonds : bond 0.04466 ( 846) hydrogen bonds : angle 4.23039 ( 2424) metal coordination : bond 0.01565 ( 7) metal coordination : angle 11.28763 ( 1) covalent geometry : bond 0.00502 (14943) covalent geometry : angle 0.61258 (20196) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 1658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 365 time to evaluate : 1.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.8259 (tpp) cc_final: 0.7774 (tpp) REVERT: A 385 LYS cc_start: 0.8855 (OUTLIER) cc_final: 0.8630 (mttt) REVERT: A 460 GLU cc_start: 0.7801 (pm20) cc_final: 0.7516 (pm20) REVERT: A 714 THR cc_start: 0.8583 (OUTLIER) cc_final: 0.8269 (m) REVERT: A 782 GLU cc_start: 0.7593 (mp0) cc_final: 0.7370 (mp0) REVERT: A 841 LYS cc_start: 0.8502 (mmtm) cc_final: 0.8257 (mmtm) REVERT: A 1032 MET cc_start: 0.8185 (OUTLIER) cc_final: 0.7981 (mtm) REVERT: A 1078 ARG cc_start: 0.8092 (mtt180) cc_final: 0.7806 (mtt-85) REVERT: A 1132 GLU cc_start: 0.7727 (tp30) cc_final: 0.7427 (tp30) REVERT: A 1166 ASP cc_start: 0.7778 (OUTLIER) cc_final: 0.7572 (t0) REVERT: A 1205 ARG cc_start: 0.7828 (OUTLIER) cc_final: 0.7582 (ttp-170) REVERT: C 578 ILE cc_start: 0.8196 (pp) cc_final: 0.7983 (mp) REVERT: E 479 MET cc_start: 0.3939 (ptt) cc_final: 0.3734 (ptt) outliers start: 76 outliers final: 41 residues processed: 411 average time/residue: 1.4027 time to fit residues: 627.3781 Evaluate side-chains 406 residues out of total 1658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 360 time to evaluate : 2.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 219 LYS Chi-restraints excluded: chain A residue 385 LYS Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 714 THR Chi-restraints excluded: chain A residue 822 ASN Chi-restraints excluded: chain A residue 855 CYS Chi-restraints excluded: chain A residue 933 THR Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 1025 ARG Chi-restraints excluded: chain A residue 1032 MET Chi-restraints excluded: chain A residue 1084 SER Chi-restraints excluded: chain A residue 1142 LYS Chi-restraints excluded: chain A residue 1166 ASP Chi-restraints excluded: chain A residue 1168 ASN Chi-restraints excluded: chain A residue 1205 ARG Chi-restraints excluded: chain A residue 1330 LEU Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain A residue 1451 VAL Chi-restraints excluded: chain A residue 1456 LEU Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 499 HIS Chi-restraints excluded: chain B residue 531 MET Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 541 LYS Chi-restraints excluded: chain B residue 542 GLU Chi-restraints excluded: chain B residue 543 ILE Chi-restraints excluded: chain B residue 545 LYS Chi-restraints excluded: chain B residue 559 LYS Chi-restraints excluded: chain B residue 572 VAL Chi-restraints excluded: chain D residue 478 ILE Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 527 ILE Chi-restraints excluded: chain D residue 535 HIS Chi-restraints excluded: chain D residue 536 ILE Chi-restraints excluded: chain C residue 518 MET Chi-restraints excluded: chain C residue 523 SER Chi-restraints excluded: chain C residue 567 ILE Chi-restraints excluded: chain C residue 577 MET Chi-restraints excluded: chain C residue 607 SER Chi-restraints excluded: chain C residue 690 ASN Chi-restraints excluded: chain E residue 491 HIS Chi-restraints excluded: chain E residue 506 TYR Chi-restraints excluded: chain E residue 518 MET Chi-restraints excluded: chain E residue 531 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 75 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 50 optimal weight: 0.5980 chunk 168 optimal weight: 0.8980 chunk 78 optimal weight: 0.7980 chunk 74 optimal weight: 0.5980 chunk 48 optimal weight: 0.0870 chunk 136 optimal weight: 0.3980 chunk 116 optimal weight: 0.9980 chunk 111 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN A 119 ASN A 139 GLN A 331 GLN A 534 GLN A1011 ASN A1183 ASN A1256 GLN A1324 GLN C 648 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.159923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.134592 restraints weight = 19801.331| |-----------------------------------------------------------------------------| r_work (start): 0.3873 rms_B_bonded: 1.63 r_work: 0.3767 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3617 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 14950 Z= 0.177 Angle : 0.611 10.351 20197 Z= 0.309 Chirality : 0.044 0.181 2295 Planarity : 0.004 0.090 2585 Dihedral : 5.317 55.993 1988 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.10 % Favored : 96.84 % Rotamer: Outliers : 4.34 % Allowed : 27.08 % Favored : 68.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: 1.29 (0.20), residues: 1806 helix: 1.82 (0.16), residues: 1047 sheet: -0.59 (0.53), residues: 90 loop : -0.46 (0.25), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 806 HIS 0.004 0.001 HIS A1120 PHE 0.024 0.001 PHE A 399 TYR 0.018 0.001 TYR B 498 ARG 0.006 0.000 ARG B 532 Details of bonding type rmsd hydrogen bonds : bond 0.04272 ( 846) hydrogen bonds : angle 4.16627 ( 2424) metal coordination : bond 0.01298 ( 7) metal coordination : angle 10.35098 ( 1) covalent geometry : bond 0.00430 (14943) covalent geometry : angle 0.60630 (20196) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 1658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 364 time to evaluate : 1.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.8249 (tpp) cc_final: 0.7770 (tpp) REVERT: A 460 GLU cc_start: 0.7791 (pm20) cc_final: 0.7508 (pm20) REVERT: A 714 THR cc_start: 0.8559 (OUTLIER) cc_final: 0.8260 (m) REVERT: A 782 GLU cc_start: 0.7592 (mp0) cc_final: 0.7367 (mp0) REVERT: A 841 LYS cc_start: 0.8501 (mmtm) cc_final: 0.8257 (mmtm) REVERT: A 1078 ARG cc_start: 0.8085 (mtt180) cc_final: 0.7799 (mtt-85) REVERT: A 1132 GLU cc_start: 0.7716 (tp30) cc_final: 0.7408 (tp30) REVERT: A 1166 ASP cc_start: 0.7758 (OUTLIER) cc_final: 0.7546 (t70) REVERT: A 1205 ARG cc_start: 0.7835 (OUTLIER) cc_final: 0.7574 (ttp-110) REVERT: B 509 GLU cc_start: 0.5467 (OUTLIER) cc_final: 0.4556 (pm20) REVERT: D 531 MET cc_start: 0.7550 (tmm) cc_final: 0.7204 (tpt) REVERT: C 546 ILE cc_start: 0.7377 (mp) cc_final: 0.7158 (mt) REVERT: E 479 MET cc_start: 0.3916 (ptt) cc_final: 0.3708 (ptt) outliers start: 72 outliers final: 44 residues processed: 407 average time/residue: 1.3182 time to fit residues: 586.4477 Evaluate side-chains 405 residues out of total 1658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 357 time to evaluate : 1.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 219 LYS Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 714 THR Chi-restraints excluded: chain A residue 822 ASN Chi-restraints excluded: chain A residue 855 CYS Chi-restraints excluded: chain A residue 907 LYS Chi-restraints excluded: chain A residue 933 THR Chi-restraints excluded: chain A residue 1025 ARG Chi-restraints excluded: chain A residue 1084 SER Chi-restraints excluded: chain A residue 1142 LYS Chi-restraints excluded: chain A residue 1166 ASP Chi-restraints excluded: chain A residue 1205 ARG Chi-restraints excluded: chain A residue 1218 VAL Chi-restraints excluded: chain A residue 1323 SER Chi-restraints excluded: chain A residue 1330 LEU Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain A residue 1456 LEU Chi-restraints excluded: chain B residue 499 HIS Chi-restraints excluded: chain B residue 509 GLU Chi-restraints excluded: chain B residue 531 MET Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 541 LYS Chi-restraints excluded: chain B residue 542 GLU Chi-restraints excluded: chain B residue 543 ILE Chi-restraints excluded: chain B residue 559 LYS Chi-restraints excluded: chain B residue 572 VAL Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 527 ILE Chi-restraints excluded: chain D residue 535 HIS Chi-restraints excluded: chain D residue 536 ILE Chi-restraints excluded: chain C residue 518 MET Chi-restraints excluded: chain C residue 520 VAL Chi-restraints excluded: chain C residue 523 SER Chi-restraints excluded: chain C residue 567 ILE Chi-restraints excluded: chain C residue 577 MET Chi-restraints excluded: chain C residue 607 SER Chi-restraints excluded: chain C residue 685 LEU Chi-restraints excluded: chain C residue 690 ASN Chi-restraints excluded: chain E residue 491 HIS Chi-restraints excluded: chain E residue 506 TYR Chi-restraints excluded: chain E residue 518 MET Chi-restraints excluded: chain E residue 531 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 129 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 122 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 128 optimal weight: 0.4980 chunk 91 optimal weight: 0.5980 chunk 73 optimal weight: 0.5980 chunk 179 optimal weight: 0.0980 chunk 80 optimal weight: 1.9990 chunk 48 optimal weight: 0.0870 chunk 161 optimal weight: 0.0970 overall best weight: 0.2756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN A 119 ASN A 331 GLN A 534 GLN A 896 HIS A1011 ASN A1183 ASN A1324 GLN ** A1374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 648 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.160879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.135675 restraints weight = 19803.379| |-----------------------------------------------------------------------------| r_work (start): 0.3883 rms_B_bonded: 1.63 r_work: 0.3783 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3637 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 14950 Z= 0.137 Angle : 0.596 10.042 20197 Z= 0.302 Chirality : 0.042 0.156 2295 Planarity : 0.004 0.088 2585 Dihedral : 5.123 57.001 1984 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.99 % Favored : 96.95 % Rotamer: Outliers : 4.16 % Allowed : 27.93 % Favored : 67.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: 1.39 (0.20), residues: 1806 helix: 1.92 (0.16), residues: 1043 sheet: -0.51 (0.54), residues: 90 loop : -0.43 (0.25), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 806 HIS 0.005 0.001 HIS C 491 PHE 0.023 0.001 PHE A 399 TYR 0.018 0.001 TYR B 498 ARG 0.008 0.000 ARG A 141 Details of bonding type rmsd hydrogen bonds : bond 0.03944 ( 846) hydrogen bonds : angle 4.09137 ( 2424) metal coordination : bond 0.00787 ( 7) metal coordination : angle 7.91261 ( 1) covalent geometry : bond 0.00324 (14943) covalent geometry : angle 0.59309 (20196) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 1658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 373 time to evaluate : 1.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.8214 (tpp) cc_final: 0.7737 (tpp) REVERT: A 385 LYS cc_start: 0.8827 (OUTLIER) cc_final: 0.8608 (mttt) REVERT: A 460 GLU cc_start: 0.7756 (pm20) cc_final: 0.7477 (pm20) REVERT: A 568 GLU cc_start: 0.7156 (OUTLIER) cc_final: 0.6943 (mp0) REVERT: A 714 THR cc_start: 0.8491 (OUTLIER) cc_final: 0.8185 (m) REVERT: A 841 LYS cc_start: 0.8506 (mmtm) cc_final: 0.8259 (mmtm) REVERT: A 1205 ARG cc_start: 0.7770 (OUTLIER) cc_final: 0.7529 (ttp-170) REVERT: A 1214 TYR cc_start: 0.8727 (t80) cc_final: 0.8462 (t80) REVERT: B 509 GLU cc_start: 0.5323 (OUTLIER) cc_final: 0.4458 (pm20) REVERT: C 536 ILE cc_start: 0.7962 (OUTLIER) cc_final: 0.7547 (tp) REVERT: C 546 ILE cc_start: 0.7341 (mp) cc_final: 0.7139 (mt) REVERT: C 669 ARG cc_start: 0.7952 (mtt90) cc_final: 0.7511 (mtt180) REVERT: E 479 MET cc_start: 0.3625 (ptt) cc_final: 0.3404 (ptt) outliers start: 69 outliers final: 42 residues processed: 417 average time/residue: 1.3508 time to fit residues: 615.4993 Evaluate side-chains 409 residues out of total 1658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 361 time to evaluate : 1.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 317 LYS Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 385 LYS Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain A residue 482 GLU Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 568 GLU Chi-restraints excluded: chain A residue 714 THR Chi-restraints excluded: chain A residue 822 ASN Chi-restraints excluded: chain A residue 855 CYS Chi-restraints excluded: chain A residue 907 LYS Chi-restraints excluded: chain A residue 933 THR Chi-restraints excluded: chain A residue 1025 ARG Chi-restraints excluded: chain A residue 1084 SER Chi-restraints excluded: chain A residue 1142 LYS Chi-restraints excluded: chain A residue 1205 ARG Chi-restraints excluded: chain A residue 1218 VAL Chi-restraints excluded: chain A residue 1323 SER Chi-restraints excluded: chain A residue 1330 LEU Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain A residue 1451 VAL Chi-restraints excluded: chain A residue 1456 LEU Chi-restraints excluded: chain B residue 499 HIS Chi-restraints excluded: chain B residue 509 GLU Chi-restraints excluded: chain B residue 531 MET Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 541 LYS Chi-restraints excluded: chain B residue 543 ILE Chi-restraints excluded: chain B residue 559 LYS Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 522 ASN Chi-restraints excluded: chain D residue 527 ILE Chi-restraints excluded: chain D residue 535 HIS Chi-restraints excluded: chain D residue 536 ILE Chi-restraints excluded: chain C residue 518 MET Chi-restraints excluded: chain C residue 520 VAL Chi-restraints excluded: chain C residue 523 SER Chi-restraints excluded: chain C residue 536 ILE Chi-restraints excluded: chain C residue 577 MET Chi-restraints excluded: chain C residue 607 SER Chi-restraints excluded: chain C residue 685 LEU Chi-restraints excluded: chain C residue 690 ASN Chi-restraints excluded: chain E residue 491 HIS Chi-restraints excluded: chain E residue 506 TYR Chi-restraints excluded: chain E residue 518 MET Chi-restraints excluded: chain E residue 531 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 110 optimal weight: 0.9980 chunk 135 optimal weight: 2.9990 chunk 180 optimal weight: 0.9990 chunk 89 optimal weight: 0.6980 chunk 90 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 chunk 158 optimal weight: 0.6980 chunk 28 optimal weight: 0.5980 chunk 58 optimal weight: 0.6980 chunk 117 optimal weight: 0.2980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN A 119 ASN A 331 GLN A 534 GLN A1011 ASN A1183 ASN A1324 GLN C 648 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.159870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.134482 restraints weight = 19680.050| |-----------------------------------------------------------------------------| r_work (start): 0.3870 rms_B_bonded: 1.62 r_work: 0.3763 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3614 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 14950 Z= 0.208 Angle : 0.649 11.131 20197 Z= 0.328 Chirality : 0.045 0.181 2295 Planarity : 0.004 0.085 2585 Dihedral : 5.026 56.249 1981 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.43 % Favored : 96.51 % Rotamer: Outliers : 4.52 % Allowed : 27.50 % Favored : 67.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: 1.28 (0.20), residues: 1806 helix: 1.78 (0.16), residues: 1048 sheet: -0.56 (0.53), residues: 90 loop : -0.40 (0.25), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 806 HIS 0.005 0.001 HIS A1120 PHE 0.025 0.002 PHE A 399 TYR 0.017 0.002 TYR B 498 ARG 0.008 0.000 ARG A 824 Details of bonding type rmsd hydrogen bonds : bond 0.04405 ( 846) hydrogen bonds : angle 4.18905 ( 2424) metal coordination : bond 0.01227 ( 7) metal coordination : angle 9.35638 ( 1) covalent geometry : bond 0.00508 (14943) covalent geometry : angle 0.64551 (20196) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 1658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 369 time to evaluate : 1.566 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.8185 (tpp) cc_final: 0.7701 (tpp) REVERT: A 289 MET cc_start: 0.7932 (mmm) cc_final: 0.7695 (mmm) REVERT: A 460 GLU cc_start: 0.7775 (pm20) cc_final: 0.7496 (pm20) REVERT: A 568 GLU cc_start: 0.7174 (OUTLIER) cc_final: 0.6946 (mp0) REVERT: A 714 THR cc_start: 0.8575 (OUTLIER) cc_final: 0.8258 (m) REVERT: A 815 PHE cc_start: 0.8573 (m-80) cc_final: 0.8234 (m-80) REVERT: A 841 LYS cc_start: 0.8533 (mmtm) cc_final: 0.8276 (mmtm) REVERT: A 1205 ARG cc_start: 0.7846 (OUTLIER) cc_final: 0.7585 (ttp-170) REVERT: A 1225 MET cc_start: 0.8551 (mmm) cc_final: 0.8119 (mtt) REVERT: A 1438 GLN cc_start: 0.7801 (OUTLIER) cc_final: 0.7551 (tm-30) REVERT: B 509 GLU cc_start: 0.5456 (OUTLIER) cc_final: 0.4563 (pm20) REVERT: D 531 MET cc_start: 0.7504 (tmm) cc_final: 0.7060 (tpt) REVERT: C 669 ARG cc_start: 0.7995 (mtt90) cc_final: 0.7572 (mtt180) REVERT: C 694 ILE cc_start: 0.8001 (OUTLIER) cc_final: 0.7746 (mt) REVERT: E 479 MET cc_start: 0.3821 (ptt) cc_final: 0.3609 (ptt) outliers start: 75 outliers final: 40 residues processed: 418 average time/residue: 1.3482 time to fit residues: 615.4769 Evaluate side-chains 409 residues out of total 1658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 363 time to evaluate : 1.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 482 GLU Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 568 GLU Chi-restraints excluded: chain A residue 714 THR Chi-restraints excluded: chain A residue 822 ASN Chi-restraints excluded: chain A residue 855 CYS Chi-restraints excluded: chain A residue 907 LYS Chi-restraints excluded: chain A residue 933 THR Chi-restraints excluded: chain A residue 991 LEU Chi-restraints excluded: chain A residue 1025 ARG Chi-restraints excluded: chain A residue 1084 SER Chi-restraints excluded: chain A residue 1142 LYS Chi-restraints excluded: chain A residue 1205 ARG Chi-restraints excluded: chain A residue 1218 VAL Chi-restraints excluded: chain A residue 1330 LEU Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain A residue 1438 GLN Chi-restraints excluded: chain A residue 1451 VAL Chi-restraints excluded: chain A residue 1456 LEU Chi-restraints excluded: chain B residue 499 HIS Chi-restraints excluded: chain B residue 509 GLU Chi-restraints excluded: chain B residue 531 MET Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 541 LYS Chi-restraints excluded: chain B residue 543 ILE Chi-restraints excluded: chain B residue 559 LYS Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 522 ASN Chi-restraints excluded: chain D residue 527 ILE Chi-restraints excluded: chain D residue 535 HIS Chi-restraints excluded: chain D residue 536 ILE Chi-restraints excluded: chain C residue 518 MET Chi-restraints excluded: chain C residue 520 VAL Chi-restraints excluded: chain C residue 530 ASP Chi-restraints excluded: chain C residue 567 ILE Chi-restraints excluded: chain C residue 577 MET Chi-restraints excluded: chain C residue 607 SER Chi-restraints excluded: chain C residue 682 ILE Chi-restraints excluded: chain C residue 685 LEU Chi-restraints excluded: chain C residue 690 ASN Chi-restraints excluded: chain C residue 694 ILE Chi-restraints excluded: chain E residue 493 THR Chi-restraints excluded: chain E residue 506 TYR Chi-restraints excluded: chain E residue 518 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 55 optimal weight: 0.0370 chunk 24 optimal weight: 0.5980 chunk 118 optimal weight: 0.8980 chunk 167 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 91 optimal weight: 0.7980 chunk 79 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 chunk 143 optimal weight: 4.9990 chunk 16 optimal weight: 0.4980 chunk 178 optimal weight: 0.0970 overall best weight: 0.3656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN A 119 ASN A 331 GLN A 427 HIS A1011 ASN A1182 GLN A1183 ASN A1324 GLN A1371 ASN D 499 HIS C 648 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.160642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.135360 restraints weight = 19603.793| |-----------------------------------------------------------------------------| r_work (start): 0.3883 rms_B_bonded: 1.62 r_work: 0.3778 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3631 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 14950 Z= 0.158 Angle : 0.634 10.201 20197 Z= 0.323 Chirality : 0.043 0.156 2295 Planarity : 0.004 0.083 2585 Dihedral : 5.014 56.877 1981 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.32 % Favored : 96.62 % Rotamer: Outliers : 3.62 % Allowed : 29.07 % Favored : 67.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: 1.34 (0.20), residues: 1806 helix: 1.89 (0.16), residues: 1037 sheet: -0.55 (0.53), residues: 90 loop : -0.44 (0.25), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 806 HIS 0.004 0.001 HIS A1120 PHE 0.031 0.001 PHE B 488 TYR 0.018 0.001 TYR B 498 ARG 0.008 0.000 ARG A 824 Details of bonding type rmsd hydrogen bonds : bond 0.04141 ( 846) hydrogen bonds : angle 4.17188 ( 2424) metal coordination : bond 0.00920 ( 7) metal coordination : angle 8.10190 ( 1) covalent geometry : bond 0.00379 (14943) covalent geometry : angle 0.63160 (20196) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 1658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 365 time to evaluate : 1.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.8237 (tpp) cc_final: 0.7827 (tpp) REVERT: A 191 LYS cc_start: 0.8106 (ptmt) cc_final: 0.7863 (ptmm) REVERT: A 289 MET cc_start: 0.7964 (mmm) cc_final: 0.7716 (mmm) REVERT: A 460 GLU cc_start: 0.7759 (pm20) cc_final: 0.7476 (pm20) REVERT: A 714 THR cc_start: 0.8539 (OUTLIER) cc_final: 0.8215 (m) REVERT: A 815 PHE cc_start: 0.8526 (m-80) cc_final: 0.8162 (m-80) REVERT: A 841 LYS cc_start: 0.8523 (mmtm) cc_final: 0.8259 (mmtm) REVERT: A 1205 ARG cc_start: 0.7792 (OUTLIER) cc_final: 0.7540 (ttp-110) REVERT: A 1214 TYR cc_start: 0.8722 (t80) cc_final: 0.8473 (t80) REVERT: A 1438 GLN cc_start: 0.7770 (OUTLIER) cc_final: 0.7516 (tm-30) REVERT: B 509 GLU cc_start: 0.5393 (OUTLIER) cc_final: 0.4496 (pm20) REVERT: D 531 MET cc_start: 0.7546 (tmm) cc_final: 0.7108 (tpt) REVERT: C 536 ILE cc_start: 0.7955 (OUTLIER) cc_final: 0.7538 (tp) REVERT: C 669 ARG cc_start: 0.7993 (mtt90) cc_final: 0.7555 (mtt180) outliers start: 60 outliers final: 37 residues processed: 402 average time/residue: 1.3700 time to fit residues: 600.7906 Evaluate side-chains 399 residues out of total 1658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 357 time to evaluate : 1.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 279 MET Chi-restraints excluded: chain A residue 482 GLU Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 714 THR Chi-restraints excluded: chain A residue 822 ASN Chi-restraints excluded: chain A residue 855 CYS Chi-restraints excluded: chain A residue 907 LYS Chi-restraints excluded: chain A residue 933 THR Chi-restraints excluded: chain A residue 991 LEU Chi-restraints excluded: chain A residue 1025 ARG Chi-restraints excluded: chain A residue 1084 SER Chi-restraints excluded: chain A residue 1142 LYS Chi-restraints excluded: chain A residue 1205 ARG Chi-restraints excluded: chain A residue 1218 VAL Chi-restraints excluded: chain A residue 1323 SER Chi-restraints excluded: chain A residue 1330 LEU Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain A residue 1438 GLN Chi-restraints excluded: chain A residue 1451 VAL Chi-restraints excluded: chain A residue 1456 LEU Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 499 HIS Chi-restraints excluded: chain B residue 509 GLU Chi-restraints excluded: chain B residue 531 MET Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 541 LYS Chi-restraints excluded: chain B residue 543 ILE Chi-restraints excluded: chain B residue 559 LYS Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 527 ILE Chi-restraints excluded: chain D residue 535 HIS Chi-restraints excluded: chain C residue 518 MET Chi-restraints excluded: chain C residue 520 VAL Chi-restraints excluded: chain C residue 536 ILE Chi-restraints excluded: chain C residue 577 MET Chi-restraints excluded: chain C residue 607 SER Chi-restraints excluded: chain C residue 685 LEU Chi-restraints excluded: chain C residue 690 ASN Chi-restraints excluded: chain E residue 506 TYR Chi-restraints excluded: chain E residue 518 MET Chi-restraints excluded: chain E residue 549 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 73 optimal weight: 0.4980 chunk 49 optimal weight: 1.9990 chunk 117 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 chunk 119 optimal weight: 0.0070 chunk 82 optimal weight: 0.6980 chunk 77 optimal weight: 0.5980 chunk 129 optimal weight: 0.0070 chunk 31 optimal weight: 0.5980 chunk 8 optimal weight: 0.0970 overall best weight: 0.2414 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN A 119 ASN A 331 GLN A 427 HIS ** A 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1011 ASN ** A1066 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1182 GLN A1183 ASN A1324 GLN A1371 ASN C 648 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.161405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.136222 restraints weight = 19750.907| |-----------------------------------------------------------------------------| r_work (start): 0.3895 rms_B_bonded: 1.62 r_work: 0.3790 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3643 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.2800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14950 Z= 0.138 Angle : 0.625 9.937 20197 Z= 0.318 Chirality : 0.042 0.175 2295 Planarity : 0.004 0.052 2585 Dihedral : 4.971 57.292 1981 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.83 % Allowed : 29.67 % Favored : 67.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: 1.40 (0.20), residues: 1806 helix: 1.93 (0.16), residues: 1038 sheet: -0.41 (0.54), residues: 90 loop : -0.42 (0.25), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 806 HIS 0.004 0.001 HIS A 756 PHE 0.023 0.001 PHE B 488 TYR 0.017 0.001 TYR B 498 ARG 0.015 0.001 ARG A1078 Details of bonding type rmsd hydrogen bonds : bond 0.03941 ( 846) hydrogen bonds : angle 4.12329 ( 2424) metal coordination : bond 0.00737 ( 7) metal coordination : angle 7.22732 ( 1) covalent geometry : bond 0.00321 (14943) covalent geometry : angle 0.62245 (20196) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 1658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 363 time to evaluate : 1.525 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.8231 (tpp) cc_final: 0.7859 (tpp) REVERT: A 289 MET cc_start: 0.7909 (mmm) cc_final: 0.7677 (mmm) REVERT: A 460 GLU cc_start: 0.7736 (pm20) cc_final: 0.7454 (pm20) REVERT: A 714 THR cc_start: 0.8478 (OUTLIER) cc_final: 0.8151 (m) REVERT: A 815 PHE cc_start: 0.8453 (m-80) cc_final: 0.8127 (m-10) REVERT: A 841 LYS cc_start: 0.8520 (mmtm) cc_final: 0.8256 (mmtm) REVERT: A 1205 ARG cc_start: 0.7787 (OUTLIER) cc_final: 0.7544 (ttp-170) REVERT: A 1214 TYR cc_start: 0.8713 (t80) cc_final: 0.8481 (t80) REVERT: B 509 GLU cc_start: 0.5354 (OUTLIER) cc_final: 0.4443 (pm20) REVERT: C 536 ILE cc_start: 0.7951 (OUTLIER) cc_final: 0.7525 (tp) REVERT: C 669 ARG cc_start: 0.7971 (mtt90) cc_final: 0.7535 (mtt180) outliers start: 47 outliers final: 32 residues processed: 391 average time/residue: 1.4205 time to fit residues: 607.6939 Evaluate side-chains 392 residues out of total 1658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 356 time to evaluate : 1.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 279 MET Chi-restraints excluded: chain A residue 482 GLU Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 714 THR Chi-restraints excluded: chain A residue 822 ASN Chi-restraints excluded: chain A residue 855 CYS Chi-restraints excluded: chain A residue 907 LYS Chi-restraints excluded: chain A residue 933 THR Chi-restraints excluded: chain A residue 1025 ARG Chi-restraints excluded: chain A residue 1084 SER Chi-restraints excluded: chain A residue 1142 LYS Chi-restraints excluded: chain A residue 1205 ARG Chi-restraints excluded: chain A residue 1218 VAL Chi-restraints excluded: chain A residue 1330 LEU Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain A residue 1451 VAL Chi-restraints excluded: chain A residue 1456 LEU Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 499 HIS Chi-restraints excluded: chain B residue 509 GLU Chi-restraints excluded: chain B residue 531 MET Chi-restraints excluded: chain B residue 541 LYS Chi-restraints excluded: chain B residue 543 ILE Chi-restraints excluded: chain B residue 559 LYS Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 527 ILE Chi-restraints excluded: chain D residue 535 HIS Chi-restraints excluded: chain C residue 518 MET Chi-restraints excluded: chain C residue 520 VAL Chi-restraints excluded: chain C residue 536 ILE Chi-restraints excluded: chain C residue 577 MET Chi-restraints excluded: chain C residue 685 LEU Chi-restraints excluded: chain C residue 690 ASN Chi-restraints excluded: chain E residue 506 TYR Chi-restraints excluded: chain E residue 518 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 156 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 147 optimal weight: 0.1980 chunk 126 optimal weight: 2.9990 chunk 6 optimal weight: 0.0970 chunk 135 optimal weight: 1.9990 chunk 155 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 chunk 25 optimal weight: 0.1980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN A 119 ASN A 331 GLN A 427 HIS ** A 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1011 ASN A1086 ASN A1183 ASN A1371 ASN C 648 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.160661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.135283 restraints weight = 19749.879| |-----------------------------------------------------------------------------| r_work (start): 0.3876 rms_B_bonded: 1.64 r_work: 0.3775 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3630 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14950 Z= 0.180 Angle : 0.661 11.793 20197 Z= 0.334 Chirality : 0.044 0.166 2295 Planarity : 0.004 0.053 2585 Dihedral : 5.035 56.849 1981 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.71 % Allowed : 29.92 % Favored : 67.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: 1.36 (0.20), residues: 1806 helix: 1.88 (0.16), residues: 1040 sheet: -0.35 (0.52), residues: 95 loop : -0.43 (0.25), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 806 HIS 0.005 0.001 HIS A1120 PHE 0.024 0.002 PHE A 399 TYR 0.020 0.002 TYR A 470 ARG 0.008 0.000 ARG A 824 Details of bonding type rmsd hydrogen bonds : bond 0.04209 ( 846) hydrogen bonds : angle 4.17677 ( 2424) metal coordination : bond 0.00921 ( 7) metal coordination : angle 8.48819 ( 1) covalent geometry : bond 0.00435 (14943) covalent geometry : angle 0.65830 (20196) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18931.71 seconds wall clock time: 328 minutes 28.37 seconds (19708.37 seconds total)