Starting phenix.real_space_refine on Thu Sep 18 01:53:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mzh_45896/09_2025/9mzh_45896.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mzh_45896/09_2025/9mzh_45896.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9mzh_45896/09_2025/9mzh_45896.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mzh_45896/09_2025/9mzh_45896.map" model { file = "/net/cci-nas-00/data/ceres_data/9mzh_45896/09_2025/9mzh_45896.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mzh_45896/09_2025/9mzh_45896.cif" } resolution = 2.99 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.010 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: 4 Type Number sf(0) Gaussians S 84 5.16 5 C 8065 2.51 5 N 2153 2.21 5 O 2341 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12643 Number of models: 1 Model: "" Number of chains: 7 Chain: "B" Number of atoms: 309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 309 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 2, 'TRANS': 38} Chain: "C" Number of atoms: 355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 355 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 2, 'TRANS': 44} Chain: "D" Number of atoms: 292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 292 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 2, 'TRANS': 35} Chain: "E" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 421 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain breaks: 1 Chain: "G" Number of atoms: 434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 434 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 1, 'TRANS': 52} Chain: "H" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 979 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain breaks: 4 Chain: "A" Number of atoms: 9853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1220, 9853 Classifications: {'peptide': 1220} Link IDs: {'PTRANS': 46, 'TRANS': 1173} Chain breaks: 9 Time building chain proxies: 2.92, per 1000 atoms: 0.23 Number of scatterers: 12643 At special positions: 0 Unit cell: (110.88, 105.84, 164.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 84 16.00 O 2341 8.00 N 2153 7.00 C 8065 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: 0.96 Conformation dependent library (CDL) restraints added in 513.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3066 Ramachandran restraints generated. 1533 Oldfield, 0 Emsley, 1533 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3024 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 7 sheets defined 62.5% alpha, 5.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'B' and resid 542 through 573 removed outlier: 3.912A pdb=" N SER B 552 " --> pdb=" O ASN B 548 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 578 removed outlier: 3.532A pdb=" N LEU C 550 " --> pdb=" O ILE C 546 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLU C 551 " --> pdb=" O ILE C 547 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N SER C 552 " --> pdb=" O ASN C 548 " (cutoff:3.500A) Processing helix chain 'D' and resid 543 through 574 removed outlier: 3.614A pdb=" N ILE D 547 " --> pdb=" O ILE D 543 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASN D 548 " --> pdb=" O PRO D 544 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LYS D 549 " --> pdb=" O LYS D 545 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N MET D 574 " --> pdb=" O HIS D 570 " (cutoff:3.500A) Processing helix chain 'E' and resid 543 through 573 removed outlier: 4.030A pdb=" N ASN E 548 " --> pdb=" O PRO E 544 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LYS E 549 " --> pdb=" O LYS E 545 " (cutoff:3.500A) Processing helix chain 'E' and resid 718 through 725 removed outlier: 3.702A pdb=" N LEU E 724 " --> pdb=" O GLN E 721 " (cutoff:3.500A) Processing helix chain 'G' and resid 657 through 672 Processing helix chain 'G' and resid 674 through 686 Processing helix chain 'G' and resid 690 through 704 removed outlier: 3.902A pdb=" N ILE G 694 " --> pdb=" O ASN G 690 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ILE G 704 " --> pdb=" O THR G 700 " (cutoff:3.500A) Processing helix chain 'H' and resid 1491 through 1508 removed outlier: 3.876A pdb=" N ILE H1507 " --> pdb=" O VAL H1503 " (cutoff:3.500A) Processing helix chain 'H' and resid 1538 through 1555 removed outlier: 3.688A pdb=" N LEU H1544 " --> pdb=" O GLU H1540 " (cutoff:3.500A) Processing helix chain 'H' and resid 1624 through 1641 Processing helix chain 'H' and resid 1666 through 1674 removed outlier: 3.561A pdb=" N VAL H1671 " --> pdb=" O LYS H1667 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ILE H1672 " --> pdb=" O HIS H1668 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ILE H1673 " --> pdb=" O LEU H1669 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ASP H1674 " --> pdb=" O CYS H1670 " (cutoff:3.500A) Processing helix chain 'H' and resid 1689 through 1708 removed outlier: 4.464A pdb=" N CYS H1695 " --> pdb=" O GLN H1691 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ARG H1698 " --> pdb=" O ILE H1694 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ASP H1699 " --> pdb=" O CYS H1695 " (cutoff:3.500A) Processing helix chain 'H' and resid 1710 through 1714 Processing helix chain 'A' and resid 22 through 33 removed outlier: 3.820A pdb=" N LEU A 26 " --> pdb=" O VAL A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 57 Processing helix chain 'A' and resid 60 through 77 Processing helix chain 'A' and resid 79 through 83 Processing helix chain 'A' and resid 88 through 90 No H-bonds generated for 'chain 'A' and resid 88 through 90' Processing helix chain 'A' and resid 91 through 96 Processing helix chain 'A' and resid 104 through 137 removed outlier: 3.700A pdb=" N ILE A 120 " --> pdb=" O LYS A 116 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ILE A 121 " --> pdb=" O ALA A 117 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N LYS A 123 " --> pdb=" O ASN A 119 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N LYS A 124 " --> pdb=" O ILE A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 156 removed outlier: 3.786A pdb=" N ILE A 145 " --> pdb=" O ARG A 141 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ILE A 146 " --> pdb=" O ARG A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 163 Processing helix chain 'A' and resid 166 through 189 removed outlier: 3.609A pdb=" N LYS A 189 " --> pdb=" O LYS A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 194 removed outlier: 4.381A pdb=" N SER A 194 " --> pdb=" O LYS A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 255 Processing helix chain 'A' and resid 260 through 273 removed outlier: 3.643A pdb=" N ARG A 264 " --> pdb=" O PRO A 260 " (cutoff:3.500A) removed outlier: 3.919A 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: 4.064A 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 309 through 327 removed outlier: 3.829A 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 362 removed outlier: 4.242A pdb=" N PHE A 360 " --> pdb=" O PHE A 357 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ARG A 361 " --> pdb=" O SER A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 382 removed outlier: 3.715A pdb=" N HIS A 380 " --> pdb=" O LYS A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 412 removed outlier: 3.786A pdb=" N ARG A 410 " --> pdb=" O GLY A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 434 removed outlier: 3.593A pdb=" N SER A 434 " --> pdb=" O ARG A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 446 removed outlier: 4.133A pdb=" N ASN A 446 " --> pdb=" O ASP A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 451 Processing helix chain 'A' and resid 479 through 487 removed outlier: 3.835A pdb=" N TRP A 483 " --> pdb=" O LYS A 480 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N ASP A 484 " --> pdb=" O ASP A 481 " (cutoff:3.500A) removed outlier: 4.127A 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 510 removed outlier: 3.694A pdb=" N VAL A 510 " --> pdb=" O VAL A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 526 removed outlier: 3.724A pdb=" N VAL A 524 " --> pdb=" O MET A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 573 Processing helix chain 'A' and resid 574 through 581 removed outlier: 3.965A pdb=" N GLU A 581 " --> pdb=" O TYR A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 731 through 747 removed outlier: 4.169A pdb=" N ILE A 737 " --> pdb=" O GLU A 733 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N PHE A 738 " --> pdb=" O SER A 734 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ARG A 741 " --> pdb=" O ILE A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 753 through 760 removed outlier: 3.815A pdb=" N LYS A 757 " --> pdb=" O ASN A 753 " (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 874 Processing helix chain 'A' and resid 904 through 912 removed outlier: 4.013A pdb=" N SER A 908 " --> pdb=" O GLN A 904 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG A 911 " --> pdb=" O LYS A 907 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 940 Processing helix chain 'A' and resid 943 through 965 Processing helix chain 'A' and resid 972 through 982 Proline residue: A 978 - end of helix Processing helix chain 'A' and resid 982 through 992 Processing helix chain 'A' and resid 1014 through 1029 Processing helix chain 'A' and resid 1034 through 1042 removed outlier: 4.120A pdb=" N GLN A1038 " --> pdb=" O GLU A1034 " (cutoff:3.500A) Processing helix chain 'A' and resid 1049 through 1056 Processing helix chain 'A' and resid 1068 through 1073 Processing helix chain 'A' and resid 1074 through 1083 removed outlier: 3.912A pdb=" N THR A1079 " --> pdb=" O ILE A1075 " (cutoff:3.500A) Processing helix chain 'A' and resid 1096 through 1110 Processing helix chain 'A' and resid 1115 through 1126 Processing helix chain 'A' and resid 1126 through 1138 removed outlier: 3.663A pdb=" N LEU A1137 " --> pdb=" O GLU A1133 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU A1138 " --> pdb=" O ILE A1134 " (cutoff:3.500A) Processing helix chain 'A' and resid 1158 through 1163 Processing helix chain 'A' and resid 1164 through 1178 Processing helix chain 'A' and resid 1191 through 1209 removed outlier: 5.407A pdb=" N GLU A1206 " --> pdb=" O HIS A1202 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N LEU A1207 " --> pdb=" O MET A1203 " (cutoff:3.500A) Processing helix chain 'A' and resid 1220 through 1224 Processing helix chain 'A' and resid 1236 through 1242 removed outlier: 3.637A pdb=" N GLU A1240 " --> pdb=" O CYS A1236 " (cutoff:3.500A) Processing helix chain 'A' and resid 1293 through 1308 Processing helix chain 'A' and resid 1312 through 1323 removed outlier: 3.795A pdb=" N GLU A1317 " --> pdb=" O GLU A1313 " (cutoff:3.500A) Processing helix chain 'A' and resid 1391 through 1407 Processing sheet with id=AA1, first strand: chain 'E' and resid 575 through 576 removed outlier: 3.519A pdb=" N ILE E 576 " --> pdb=" O LYS E 711 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE E 714 " --> pdb=" O MET B 575 " (cutoff:3.500A) 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 553 through 556 removed outlier: 3.818A pdb=" N PHE A 553 " --> pdb=" O SER A 540 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N VAL A 537 " --> pdb=" O VAL A 763 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N TYR A 765 " --> pdb=" O VAL A 537 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 824 through 825 removed outlier: 3.721A pdb=" N ARG A 824 " --> pdb=" O THR A 839 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 888 through 891 Processing sheet with id=AA6, first strand: chain 'A' and resid 1113 through 1114 Processing sheet with id=AA7, first strand: chain 'A' and resid 1225 through 1230 712 hydrogen bonds defined for protein. 2031 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.18 Time building geometry restraints manager: 1.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 4097 1.35 - 1.46: 2805 1.46 - 1.58: 5829 1.58 - 1.70: 0 1.70 - 1.82: 137 Bond restraints: 12868 Sorted by residual: bond pdb=" CB ARG A 141 " pdb=" CG ARG A 141 " ideal model delta sigma weight residual 1.520 1.554 -0.034 3.00e-02 1.11e+03 1.26e+00 bond pdb=" CB LYS C 559 " pdb=" CG LYS C 559 " ideal model delta sigma weight residual 1.520 1.551 -0.031 3.00e-02 1.11e+03 1.05e+00 bond pdb=" CB LYS A 332 " pdb=" CG LYS A 332 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 1.03e+00 bond pdb=" CB LYS A 498 " pdb=" CG LYS A 498 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 9.76e-01 bond pdb=" CB GLU A 881 " pdb=" CG GLU A 881 " ideal model delta sigma weight residual 1.520 1.548 -0.028 3.00e-02 1.11e+03 8.67e-01 ... (remaining 12863 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 17183 2.03 - 4.06: 130 4.06 - 6.09: 38 6.09 - 8.12: 10 8.12 - 10.15: 4 Bond angle restraints: 17365 Sorted by residual: angle pdb=" C ASP A 788 " pdb=" CA ASP A 788 " pdb=" CB ASP A 788 " ideal model delta sigma weight residual 116.34 109.15 7.19 1.40e+00 5.10e-01 2.63e+01 angle pdb=" CA LYS C 559 " pdb=" CB LYS C 559 " pdb=" CG LYS C 559 " ideal model delta sigma weight residual 114.10 121.15 -7.05 2.00e+00 2.50e-01 1.24e+01 angle pdb=" CB MET H1633 " pdb=" CG MET H1633 " pdb=" SD MET H1633 " ideal model delta sigma weight residual 112.70 122.41 -9.71 3.00e+00 1.11e-01 1.05e+01 angle pdb=" CA GLU H1505 " pdb=" CB GLU H1505 " pdb=" CG GLU H1505 " ideal model delta sigma weight residual 114.10 120.12 -6.02 2.00e+00 2.50e-01 9.05e+00 angle pdb=" CA LEU C 557 " pdb=" CB LEU C 557 " pdb=" CG LEU C 557 " ideal model delta sigma weight residual 116.30 126.45 -10.15 3.50e+00 8.16e-02 8.40e+00 ... (remaining 17360 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 6567 17.89 - 35.78: 985 35.78 - 53.67: 265 53.67 - 71.57: 43 71.57 - 89.46: 22 Dihedral angle restraints: 7882 sinusoidal: 3251 harmonic: 4631 Sorted by residual: dihedral pdb=" CA GLU H1505 " pdb=" C GLU H1505 " pdb=" N ILE H1506 " pdb=" CA ILE H1506 " ideal model delta harmonic sigma weight residual 180.00 156.32 23.68 0 5.00e+00 4.00e-02 2.24e+01 dihedral pdb=" CB GLU A 322 " pdb=" CG GLU A 322 " pdb=" CD GLU A 322 " pdb=" OE1 GLU A 322 " ideal model delta sinusoidal sigma weight residual 0.00 87.54 -87.54 1 3.00e+01 1.11e-03 1.02e+01 dihedral pdb=" CB GLU A 303 " pdb=" CG GLU A 303 " pdb=" CD GLU A 303 " pdb=" OE1 GLU A 303 " ideal model delta sinusoidal sigma weight residual 0.00 -85.01 85.01 1 3.00e+01 1.11e-03 9.74e+00 ... (remaining 7879 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1400 0.035 - 0.070: 428 0.070 - 0.106: 132 0.106 - 0.141: 33 0.141 - 0.176: 3 Chirality restraints: 1996 Sorted by residual: chirality pdb=" CG LEU A1123 " pdb=" CB LEU A1123 " pdb=" CD1 LEU A1123 " pdb=" CD2 LEU A1123 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 7.75e-01 chirality pdb=" CA ILE A1445 " pdb=" N ILE A1445 " pdb=" C ILE A1445 " pdb=" CB ILE A1445 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.67e-01 chirality pdb=" CB ILE A 828 " pdb=" CA ILE A 828 " pdb=" CG1 ILE A 828 " pdb=" CG2 ILE A 828 " both_signs ideal model delta sigma weight residual False 2.64 2.79 -0.15 2.00e-01 2.50e+01 5.53e-01 ... (remaining 1993 not shown) Planarity restraints: 2183 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN H1689 " 0.043 5.00e-02 4.00e+02 6.61e-02 7.00e+00 pdb=" N PRO H1690 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO H1690 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO H1690 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 543 " -0.031 5.00e-02 4.00e+02 4.65e-02 3.45e+00 pdb=" N PRO B 544 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO B 544 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 544 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP H1538 " 0.027 5.00e-02 4.00e+02 4.15e-02 2.76e+00 pdb=" N PRO H1539 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO H1539 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO H1539 " 0.023 5.00e-02 4.00e+02 ... (remaining 2180 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 179 2.67 - 3.23: 11767 3.23 - 3.79: 20010 3.79 - 4.34: 26232 4.34 - 4.90: 44170 Nonbonded interactions: 102358 Sorted by model distance: nonbonded pdb=" O ALA H1543 " pdb=" OG SER H1631 " model vdw 2.115 3.040 nonbonded pdb=" OG SER A 324 " pdb=" NH1 ARG A 334 " model vdw 2.137 3.120 nonbonded pdb=" OD1 ASN B 561 " pdb=" OG1 THR C 560 " model vdw 2.144 3.040 nonbonded pdb=" OG SER A1192 " pdb=" OE1 GLU A1223 " model vdw 2.190 3.040 nonbonded pdb=" OH TYR A1214 " pdb=" O VAL A1433 " model vdw 2.214 3.040 ... (remaining 102353 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 542 through 579) selection = (chain 'C' and resid 542 through 579) selection = chain 'D' } 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: 3.800 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.300 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 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 : 0.002 0.034 12868 Z= 0.099 Angle : 0.533 10.147 17365 Z= 0.262 Chirality : 0.039 0.176 1996 Planarity : 0.004 0.066 2183 Dihedral : 18.389 89.457 4858 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.00 % Favored : 96.93 % Rotamer: Outliers : 0.14 % Allowed : 34.41 % Favored : 65.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.98 (0.23), residues: 1533 helix: 2.23 (0.18), residues: 889 sheet: 0.47 (0.65), residues: 81 loop : 0.00 (0.27), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 555 TYR 0.012 0.001 TYR A 284 PHE 0.008 0.001 PHE A1093 TRP 0.011 0.001 TRP A1248 HIS 0.004 0.000 HIS A1423 Details of bonding type rmsd covalent geometry : bond 0.00211 (12868) covalent geometry : angle 0.53289 (17365) hydrogen bonds : bond 0.14011 ( 712) hydrogen bonds : angle 5.09596 ( 2031) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3066 Ramachandran restraints generated. 1533 Oldfield, 0 Emsley, 1533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3066 Ramachandran restraints generated. 1533 Oldfield, 0 Emsley, 1533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 331 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 565 SER cc_start: 0.8792 (t) cc_final: 0.8298 (p) REVERT: H 1637 MET cc_start: 0.7304 (mtp) cc_final: 0.6956 (mmp) REVERT: A 101 GLN cc_start: 0.8700 (mt0) cc_final: 0.8134 (mp10) REVERT: A 189 LYS cc_start: 0.6483 (mtmt) cc_final: 0.6230 (mtmt) REVERT: A 204 LYS cc_start: 0.8032 (mmtm) cc_final: 0.7163 (pttm) REVERT: A 221 ASP cc_start: 0.6977 (m-30) cc_final: 0.6432 (p0) REVERT: A 332 LYS cc_start: 0.6837 (tppt) cc_final: 0.6411 (mptt) REVERT: A 392 ILE cc_start: 0.7939 (tt) cc_final: 0.7279 (mt) REVERT: A 503 ARG cc_start: 0.6869 (mtt180) cc_final: 0.6305 (mtm180) REVERT: A 542 LYS cc_start: 0.6924 (tptt) cc_final: 0.6250 (pmtt) REVERT: A 725 LYS cc_start: 0.8357 (mttm) cc_final: 0.8098 (mtmt) REVERT: A 799 GLU cc_start: 0.7897 (tt0) cc_final: 0.7309 (pm20) REVERT: A 864 GLU cc_start: 0.8076 (tt0) cc_final: 0.7840 (tp30) REVERT: A 893 LYS cc_start: 0.8487 (mtpt) cc_final: 0.8198 (mtmt) REVERT: A 922 GLU cc_start: 0.8055 (mt-10) cc_final: 0.7792 (mt-10) REVERT: A 972 THR cc_start: 0.7342 (m) cc_final: 0.6894 (p) REVERT: A 1011 ASN cc_start: 0.7862 (t0) cc_final: 0.7107 (p0) REVERT: A 1128 THR cc_start: 0.5979 (m) cc_final: 0.5668 (p) REVERT: A 1168 ASN cc_start: 0.8193 (t0) cc_final: 0.7979 (m110) REVERT: A 1189 ASN cc_start: 0.7566 (m-40) cc_final: 0.6828 (t0) REVERT: A 1295 ARG cc_start: 0.8182 (ptp-170) cc_final: 0.7887 (mmt-90) REVERT: A 1299 ARG cc_start: 0.7173 (tpt170) cc_final: 0.6926 (tpt170) REVERT: A 1308 TYR cc_start: 0.6627 (m-80) cc_final: 0.6191 (m-80) outliers start: 2 outliers final: 3 residues processed: 333 average time/residue: 0.5702 time to fit residues: 206.3570 Evaluate side-chains 224 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 221 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 1665 THR Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain A residue 1328 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 5.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H1548 GLN A 55 HIS A 314 HIS ** A 840 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 904 GLN ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 968 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.170906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.138588 restraints weight = 17161.601| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 2.25 r_work: 0.3604 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3470 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12868 Z= 0.157 Angle : 0.589 7.989 17365 Z= 0.298 Chirality : 0.043 0.156 1996 Planarity : 0.004 0.047 2183 Dihedral : 4.988 127.127 1693 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.26 % Favored : 96.67 % Rotamer: Outliers : 6.81 % Allowed : 30.90 % Favored : 62.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.78 (0.22), residues: 1533 helix: 2.03 (0.18), residues: 899 sheet: 0.26 (0.57), residues: 88 loop : -0.02 (0.28), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 334 TYR 0.021 0.002 TYR A 284 PHE 0.012 0.001 PHE A 399 TRP 0.017 0.001 TRP A1248 HIS 0.007 0.001 HIS A 55 Details of bonding type rmsd covalent geometry : bond 0.00373 (12868) covalent geometry : angle 0.58861 (17365) hydrogen bonds : bond 0.03903 ( 712) hydrogen bonds : angle 4.23756 ( 2031) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3066 Ramachandran restraints generated. 1533 Oldfield, 0 Emsley, 1533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3066 Ramachandran restraints generated. 1533 Oldfield, 0 Emsley, 1533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 220 time to evaluate : 0.635 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 562 THR cc_start: 0.7243 (OUTLIER) cc_final: 0.6797 (t) REVERT: B 565 SER cc_start: 0.8605 (t) cc_final: 0.8038 (p) REVERT: C 562 THR cc_start: 0.8111 (OUTLIER) cc_final: 0.7828 (t) REVERT: C 575 MET cc_start: 0.8002 (mtp) cc_final: 0.7790 (mmt) REVERT: E 553 ILE cc_start: 0.5213 (OUTLIER) cc_final: 0.4863 (tt) REVERT: H 1554 TRP cc_start: 0.7367 (m-90) cc_final: 0.7112 (m-90) REVERT: H 1637 MET cc_start: 0.7293 (mtp) cc_final: 0.6314 (mmp) REVERT: H 1659 LEU cc_start: 0.7106 (OUTLIER) cc_final: 0.6645 (pt) REVERT: H 1692 GLU cc_start: 0.6047 (OUTLIER) cc_final: 0.5821 (tm-30) REVERT: A 58 ARG cc_start: 0.5969 (OUTLIER) cc_final: 0.5478 (mtp-110) REVERT: A 101 GLN cc_start: 0.8781 (mt0) cc_final: 0.8218 (mp10) REVERT: A 103 MET cc_start: 0.8717 (OUTLIER) cc_final: 0.8379 (mtm) REVERT: A 189 LYS cc_start: 0.6339 (mtmt) cc_final: 0.6004 (mtmt) REVERT: A 221 ASP cc_start: 0.6970 (m-30) cc_final: 0.6421 (p0) REVERT: A 332 LYS cc_start: 0.6933 (tppt) cc_final: 0.6542 (mptt) REVERT: A 441 ASP cc_start: 0.7393 (t0) cc_final: 0.7167 (t0) REVERT: A 471 MET cc_start: 0.7555 (OUTLIER) cc_final: 0.7294 (mmm) REVERT: A 503 ARG cc_start: 0.7251 (mtt180) cc_final: 0.6807 (mtm180) REVERT: A 551 ARG cc_start: 0.4897 (OUTLIER) cc_final: 0.4116 (mtp180) REVERT: A 725 LYS cc_start: 0.8310 (mttm) cc_final: 0.8034 (mtmt) REVERT: A 893 LYS cc_start: 0.8517 (mtpt) cc_final: 0.8209 (mtmt) REVERT: A 904 GLN cc_start: 0.8255 (pt0) cc_final: 0.7760 (pt0) REVERT: A 972 THR cc_start: 0.7420 (OUTLIER) cc_final: 0.7040 (p) REVERT: A 1011 ASN cc_start: 0.8054 (t0) cc_final: 0.7146 (p0) REVERT: A 1066 GLN cc_start: 0.7056 (pp30) cc_final: 0.6845 (pp30) REVERT: A 1168 ASN cc_start: 0.8338 (t0) cc_final: 0.8117 (m110) REVERT: A 1189 ASN cc_start: 0.7480 (m-40) cc_final: 0.6726 (t0) REVERT: A 1206 GLU cc_start: 0.8384 (tm-30) cc_final: 0.8110 (tm-30) REVERT: A 1292 LYS cc_start: 0.6702 (OUTLIER) cc_final: 0.5338 (pptt) REVERT: A 1295 ARG cc_start: 0.8234 (ptp-170) cc_final: 0.7955 (mmt-90) REVERT: A 1299 ARG cc_start: 0.7163 (tpt170) cc_final: 0.6928 (tpt170) REVERT: A 1308 TYR cc_start: 0.6898 (m-80) cc_final: 0.6366 (m-80) REVERT: A 1319 TRP cc_start: 0.7742 (t60) cc_final: 0.7531 (t60) REVERT: A 1432 GLU cc_start: 0.5288 (OUTLIER) cc_final: 0.4203 (pm20) outliers start: 97 outliers final: 27 residues processed: 290 average time/residue: 0.6039 time to fit residues: 190.5116 Evaluate side-chains 232 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 193 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 562 THR Chi-restraints excluded: chain C residue 556 VAL Chi-restraints excluded: chain C residue 562 THR Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain C residue 576 ILE Chi-restraints excluded: chain E residue 553 ILE Chi-restraints excluded: chain E residue 572 VAL Chi-restraints excluded: chain E residue 573 SER Chi-restraints excluded: chain G residue 704 ILE Chi-restraints excluded: chain H residue 1634 ILE Chi-restraints excluded: chain H residue 1659 LEU Chi-restraints excluded: chain H residue 1692 GLU Chi-restraints excluded: chain H residue 1709 THR Chi-restraints excluded: chain H residue 1712 ARG Chi-restraints excluded: chain A residue 58 ARG Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 471 MET Chi-restraints excluded: chain A residue 551 ARG Chi-restraints excluded: chain A residue 853 GLU Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 970 THR Chi-restraints excluded: chain A residue 972 THR Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1033 THR Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1062 LEU Chi-restraints excluded: chain A residue 1109 MET Chi-restraints excluded: chain A residue 1292 LYS Chi-restraints excluded: chain A residue 1328 ILE Chi-restraints excluded: chain A residue 1432 GLU Chi-restraints excluded: chain A residue 1439 VAL Chi-restraints excluded: chain A residue 1443 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 61 optimal weight: 0.1980 chunk 120 optimal weight: 0.9990 chunk 55 optimal weight: 0.5980 chunk 130 optimal weight: 0.9990 chunk 138 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 134 optimal weight: 0.6980 chunk 125 optimal weight: 4.9990 chunk 21 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 722 GLN A 66 GLN A 840 GLN ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1165 HIS A1182 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.171284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.139155 restraints weight = 17217.064| |-----------------------------------------------------------------------------| r_work (start): 0.3741 rms_B_bonded: 2.10 r_work: 0.3619 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3487 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12868 Z= 0.121 Angle : 0.538 7.679 17365 Z= 0.272 Chirality : 0.041 0.146 1996 Planarity : 0.004 0.049 2183 Dihedral : 3.834 24.597 1690 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.87 % Favored : 97.06 % Rotamer: Outliers : 5.83 % Allowed : 31.53 % Favored : 62.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.81 (0.22), residues: 1533 helix: 2.06 (0.18), residues: 892 sheet: 0.20 (0.55), residues: 88 loop : 0.01 (0.27), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 334 TYR 0.015 0.001 TYR A 284 PHE 0.013 0.001 PHE A 357 TRP 0.015 0.001 TRP A1248 HIS 0.003 0.001 HIS A 778 Details of bonding type rmsd covalent geometry : bond 0.00284 (12868) covalent geometry : angle 0.53786 (17365) hydrogen bonds : bond 0.03515 ( 712) hydrogen bonds : angle 4.05687 ( 2031) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3066 Ramachandran restraints generated. 1533 Oldfield, 0 Emsley, 1533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3066 Ramachandran restraints generated. 1533 Oldfield, 0 Emsley, 1533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 209 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 565 SER cc_start: 0.8591 (t) cc_final: 0.8015 (p) REVERT: C 575 MET cc_start: 0.8036 (mtp) cc_final: 0.7795 (mmt) REVERT: D 564 LEU cc_start: 0.6729 (OUTLIER) cc_final: 0.6404 (mm) REVERT: D 577 MET cc_start: 0.6066 (ttp) cc_final: 0.4669 (tmt) REVERT: E 553 ILE cc_start: 0.5177 (OUTLIER) cc_final: 0.4858 (tt) REVERT: H 1554 TRP cc_start: 0.7359 (m-90) cc_final: 0.7092 (m-90) REVERT: H 1637 MET cc_start: 0.7250 (mtp) cc_final: 0.6271 (mmp) REVERT: H 1659 LEU cc_start: 0.7088 (OUTLIER) cc_final: 0.6629 (pt) REVERT: H 1692 GLU cc_start: 0.6105 (OUTLIER) cc_final: 0.5888 (tm-30) REVERT: A 58 ARG cc_start: 0.6013 (OUTLIER) cc_final: 0.5555 (mtp-110) REVERT: A 101 GLN cc_start: 0.8821 (mt0) cc_final: 0.8277 (mp10) REVERT: A 103 MET cc_start: 0.8618 (OUTLIER) cc_final: 0.8180 (mtt) REVERT: A 221 ASP cc_start: 0.6932 (m-30) cc_final: 0.6402 (p0) REVERT: A 332 LYS cc_start: 0.6850 (tppt) cc_final: 0.6546 (mptt) REVERT: A 471 MET cc_start: 0.7674 (OUTLIER) cc_final: 0.7392 (mmm) REVERT: A 503 ARG cc_start: 0.7248 (mtt180) cc_final: 0.6850 (mtm180) REVERT: A 725 LYS cc_start: 0.8299 (mttm) cc_final: 0.8051 (mtmt) REVERT: A 780 GLU cc_start: 0.6984 (tp30) cc_final: 0.6452 (mp0) REVERT: A 876 ASN cc_start: 0.8378 (t0) cc_final: 0.8127 (t0) REVERT: A 893 LYS cc_start: 0.8465 (mtpt) cc_final: 0.8171 (mtmt) REVERT: A 972 THR cc_start: 0.7375 (OUTLIER) cc_final: 0.7052 (p) REVERT: A 1011 ASN cc_start: 0.8077 (t0) cc_final: 0.7201 (p0) REVERT: A 1066 GLN cc_start: 0.7184 (pp30) cc_final: 0.6917 (pp30) REVERT: A 1189 ASN cc_start: 0.7571 (m-40) cc_final: 0.6829 (t0) REVERT: A 1206 GLU cc_start: 0.8389 (tm-30) cc_final: 0.8033 (tm-30) REVERT: A 1292 LYS cc_start: 0.6762 (OUTLIER) cc_final: 0.5404 (pptt) REVERT: A 1299 ARG cc_start: 0.7230 (tpt170) cc_final: 0.6957 (tpt170) REVERT: A 1306 TRP cc_start: 0.7233 (m-10) cc_final: 0.6757 (m100) REVERT: A 1308 TYR cc_start: 0.6950 (m-80) cc_final: 0.6351 (m-80) REVERT: A 1432 GLU cc_start: 0.5401 (OUTLIER) cc_final: 0.4349 (pm20) outliers start: 83 outliers final: 29 residues processed: 264 average time/residue: 0.5305 time to fit residues: 153.4499 Evaluate side-chains 229 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 190 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 546 ILE Chi-restraints excluded: chain C residue 556 VAL Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 575 MET Chi-restraints excluded: chain E residue 553 ILE Chi-restraints excluded: chain E residue 572 VAL Chi-restraints excluded: chain E residue 573 SER Chi-restraints excluded: chain G residue 660 SER Chi-restraints excluded: chain G residue 695 GLN Chi-restraints excluded: chain H residue 1634 ILE Chi-restraints excluded: chain H residue 1659 LEU Chi-restraints excluded: chain H residue 1692 GLU Chi-restraints excluded: chain H residue 1709 THR Chi-restraints excluded: chain H residue 1712 ARG Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 58 ARG Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 471 MET Chi-restraints excluded: chain A residue 853 GLU Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 972 THR Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1033 THR Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1062 LEU Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1109 MET Chi-restraints excluded: chain A residue 1188 SER Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1292 LYS Chi-restraints excluded: chain A residue 1328 ILE Chi-restraints excluded: chain A residue 1432 GLU Chi-restraints excluded: chain A residue 1436 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 44 optimal weight: 0.8980 chunk 96 optimal weight: 0.6980 chunk 103 optimal weight: 0.9980 chunk 128 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 chunk 123 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 54 optimal weight: 0.8980 chunk 21 optimal weight: 6.9990 chunk 154 optimal weight: 0.4980 chunk 57 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 HIS ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.170511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.138400 restraints weight = 17060.313| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 2.11 r_work: 0.3609 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3478 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12868 Z= 0.122 Angle : 0.524 6.717 17365 Z= 0.268 Chirality : 0.041 0.147 1996 Planarity : 0.004 0.050 2183 Dihedral : 3.842 24.102 1690 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.33 % Favored : 96.61 % Rotamer: Outliers : 6.46 % Allowed : 30.62 % Favored : 62.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.79 (0.22), residues: 1533 helix: 2.05 (0.18), residues: 891 sheet: 0.07 (0.57), residues: 83 loop : 0.02 (0.27), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 74 TYR 0.016 0.001 TYR A 284 PHE 0.013 0.001 PHE A 357 TRP 0.013 0.001 TRP A1248 HIS 0.007 0.001 HIS A 55 Details of bonding type rmsd covalent geometry : bond 0.00285 (12868) covalent geometry : angle 0.52437 (17365) hydrogen bonds : bond 0.03493 ( 712) hydrogen bonds : angle 4.00188 ( 2031) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3066 Ramachandran restraints generated. 1533 Oldfield, 0 Emsley, 1533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3066 Ramachandran restraints generated. 1533 Oldfield, 0 Emsley, 1533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 205 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 562 THR cc_start: 0.7262 (OUTLIER) cc_final: 0.6822 (t) REVERT: B 565 SER cc_start: 0.8596 (t) cc_final: 0.8015 (p) REVERT: C 551 GLU cc_start: 0.6304 (OUTLIER) cc_final: 0.5514 (tm-30) REVERT: C 575 MET cc_start: 0.8012 (mtp) cc_final: 0.7769 (mmt) REVERT: D 564 LEU cc_start: 0.6641 (OUTLIER) cc_final: 0.6396 (mm) REVERT: D 577 MET cc_start: 0.6111 (ttp) cc_final: 0.4893 (tmt) REVERT: E 553 ILE cc_start: 0.5276 (OUTLIER) cc_final: 0.4953 (tt) REVERT: G 682 ILE cc_start: 0.7151 (OUTLIER) cc_final: 0.6939 (mt) REVERT: H 1554 TRP cc_start: 0.7482 (m-90) cc_final: 0.7177 (m-90) REVERT: H 1637 MET cc_start: 0.7304 (mtp) cc_final: 0.6305 (mmp) REVERT: H 1659 LEU cc_start: 0.7101 (OUTLIER) cc_final: 0.6647 (pt) REVERT: H 1692 GLU cc_start: 0.6017 (OUTLIER) cc_final: 0.5809 (tm-30) REVERT: A 58 ARG cc_start: 0.6077 (OUTLIER) cc_final: 0.5615 (mtp-110) REVERT: A 101 GLN cc_start: 0.8830 (mt0) cc_final: 0.8280 (mp10) REVERT: A 103 MET cc_start: 0.8619 (OUTLIER) cc_final: 0.8213 (mtt) REVERT: A 189 LYS cc_start: 0.6151 (OUTLIER) cc_final: 0.5784 (mtmt) REVERT: A 221 ASP cc_start: 0.6934 (m-30) cc_final: 0.6419 (p0) REVERT: A 332 LYS cc_start: 0.6756 (tppt) cc_final: 0.6485 (mptt) REVERT: A 441 ASP cc_start: 0.7475 (t0) cc_final: 0.7270 (t0) REVERT: A 471 MET cc_start: 0.7844 (OUTLIER) cc_final: 0.7549 (mmm) REVERT: A 503 ARG cc_start: 0.7298 (mtt180) cc_final: 0.6890 (mtm180) REVERT: A 504 ARG cc_start: 0.7638 (mtm180) cc_final: 0.7112 (mtt180) REVERT: A 551 ARG cc_start: 0.4891 (OUTLIER) cc_final: 0.4149 (mtp180) REVERT: A 725 LYS cc_start: 0.8308 (mttm) cc_final: 0.8015 (mtmt) REVERT: A 780 GLU cc_start: 0.6959 (tp30) cc_final: 0.6446 (mp0) REVERT: A 876 ASN cc_start: 0.8351 (t0) cc_final: 0.8109 (t0) REVERT: A 893 LYS cc_start: 0.8457 (mtpt) cc_final: 0.8170 (mtmt) REVERT: A 972 THR cc_start: 0.7440 (OUTLIER) cc_final: 0.7231 (p) REVERT: A 1066 GLN cc_start: 0.7232 (pp30) cc_final: 0.6934 (pp30) REVERT: A 1189 ASN cc_start: 0.7590 (m-40) cc_final: 0.6861 (t0) REVERT: A 1206 GLU cc_start: 0.8378 (tm-30) cc_final: 0.7985 (tm-30) REVERT: A 1292 LYS cc_start: 0.6797 (OUTLIER) cc_final: 0.5369 (pptt) REVERT: A 1299 ARG cc_start: 0.7223 (tpt170) cc_final: 0.6933 (tpt170) REVERT: A 1308 TYR cc_start: 0.7005 (m-80) cc_final: 0.6544 (m-80) REVERT: A 1432 GLU cc_start: 0.5340 (OUTLIER) cc_final: 0.4389 (pm20) outliers start: 92 outliers final: 39 residues processed: 270 average time/residue: 0.5538 time to fit residues: 164.2893 Evaluate side-chains 247 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 193 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 546 ILE Chi-restraints excluded: chain B residue 562 THR Chi-restraints excluded: chain C residue 551 GLU Chi-restraints excluded: chain C residue 556 VAL Chi-restraints excluded: chain C residue 557 LEU Chi-restraints excluded: chain C residue 562 THR Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 575 MET Chi-restraints excluded: chain E residue 553 ILE Chi-restraints excluded: chain E residue 572 VAL Chi-restraints excluded: chain E residue 573 SER Chi-restraints excluded: chain G residue 660 SER Chi-restraints excluded: chain G residue 682 ILE Chi-restraints excluded: chain G residue 704 ILE Chi-restraints excluded: chain H residue 1659 LEU Chi-restraints excluded: chain H residue 1665 THR Chi-restraints excluded: chain H residue 1692 GLU Chi-restraints excluded: chain H residue 1709 THR Chi-restraints excluded: chain H residue 1712 ARG Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 58 ARG Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 189 LYS Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 459 MET Chi-restraints excluded: chain A residue 471 MET Chi-restraints excluded: chain A residue 551 ARG Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 764 ILE Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 853 GLU Chi-restraints excluded: chain A residue 972 THR Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1033 THR Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1062 LEU Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1109 MET Chi-restraints excluded: chain A residue 1166 ASP Chi-restraints excluded: chain A residue 1188 SER Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1292 LYS Chi-restraints excluded: chain A residue 1328 ILE Chi-restraints excluded: chain A residue 1432 GLU Chi-restraints excluded: chain A residue 1436 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 149 optimal weight: 5.9990 chunk 72 optimal weight: 0.5980 chunk 139 optimal weight: 2.9990 chunk 27 optimal weight: 7.9990 chunk 22 optimal weight: 6.9990 chunk 99 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 29 optimal weight: 9.9990 chunk 142 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 722 GLN ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1423 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.166722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.133462 restraints weight = 17230.018| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 2.21 r_work: 0.3559 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3428 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12868 Z= 0.172 Angle : 0.568 6.954 17365 Z= 0.291 Chirality : 0.043 0.177 1996 Planarity : 0.004 0.051 2183 Dihedral : 4.089 23.444 1690 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.98 % Favored : 95.96 % Rotamer: Outliers : 6.81 % Allowed : 30.13 % Favored : 63.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.49 (0.22), residues: 1533 helix: 1.84 (0.18), residues: 890 sheet: -0.06 (0.56), residues: 83 loop : -0.17 (0.27), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 74 TYR 0.019 0.002 TYR A 284 PHE 0.017 0.001 PHE A 399 TRP 0.011 0.001 TRP A1248 HIS 0.004 0.001 HIS A 314 Details of bonding type rmsd covalent geometry : bond 0.00418 (12868) covalent geometry : angle 0.56829 (17365) hydrogen bonds : bond 0.04065 ( 712) hydrogen bonds : angle 4.16239 ( 2031) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3066 Ramachandran restraints generated. 1533 Oldfield, 0 Emsley, 1533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3066 Ramachandran restraints generated. 1533 Oldfield, 0 Emsley, 1533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 206 time to evaluate : 0.511 Fit side-chains revert: symmetry clash REVERT: B 562 THR cc_start: 0.7313 (OUTLIER) cc_final: 0.6870 (t) REVERT: B 565 SER cc_start: 0.8625 (t) cc_final: 0.8044 (p) REVERT: B 574 MET cc_start: 0.7978 (tmt) cc_final: 0.7626 (tmt) REVERT: C 575 MET cc_start: 0.8103 (mtp) cc_final: 0.7892 (mmt) REVERT: D 577 MET cc_start: 0.6390 (ttp) cc_final: 0.4939 (tmt) REVERT: E 722 GLN cc_start: 0.6924 (mm110) cc_final: 0.6714 (mm-40) REVERT: H 1554 TRP cc_start: 0.7533 (m-90) cc_final: 0.7239 (m-90) REVERT: H 1637 MET cc_start: 0.7115 (mtp) cc_final: 0.6432 (mmp) REVERT: H 1659 LEU cc_start: 0.7111 (OUTLIER) cc_final: 0.6622 (pt) REVERT: A 101 GLN cc_start: 0.8851 (mt0) cc_final: 0.8319 (mp10) REVERT: A 103 MET cc_start: 0.8687 (OUTLIER) cc_final: 0.8476 (mtt) REVERT: A 221 ASP cc_start: 0.7008 (m-30) cc_final: 0.6555 (p0) REVERT: A 332 LYS cc_start: 0.6925 (tppt) cc_final: 0.6568 (mptt) REVERT: A 471 MET cc_start: 0.7824 (OUTLIER) cc_final: 0.7540 (mmm) REVERT: A 504 ARG cc_start: 0.7761 (mtm180) cc_final: 0.7240 (mtt180) REVERT: A 725 LYS cc_start: 0.8362 (mttm) cc_final: 0.8097 (mtmt) REVERT: A 780 GLU cc_start: 0.7096 (tp30) cc_final: 0.6661 (mp0) REVERT: A 838 ILE cc_start: 0.8490 (OUTLIER) cc_final: 0.7892 (mp) REVERT: A 876 ASN cc_start: 0.8418 (t0) cc_final: 0.8181 (t0) REVERT: A 973 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8164 (mm) REVERT: A 1066 GLN cc_start: 0.7291 (pp30) cc_final: 0.6953 (pp30) REVERT: A 1128 THR cc_start: 0.6209 (m) cc_final: 0.5831 (p) REVERT: A 1189 ASN cc_start: 0.7590 (m-40) cc_final: 0.6868 (t0) REVERT: A 1206 GLU cc_start: 0.8430 (tm-30) cc_final: 0.8043 (tm-30) REVERT: A 1292 LYS cc_start: 0.6915 (OUTLIER) cc_final: 0.5408 (pptt) REVERT: A 1299 ARG cc_start: 0.7298 (tpt170) cc_final: 0.7090 (tpt170) REVERT: A 1306 TRP cc_start: 0.7344 (m-10) cc_final: 0.6855 (m100) REVERT: A 1308 TYR cc_start: 0.7050 (m-80) cc_final: 0.6573 (m-80) REVERT: A 1394 GLN cc_start: 0.6176 (OUTLIER) cc_final: 0.5828 (mm110) REVERT: A 1432 GLU cc_start: 0.5442 (OUTLIER) cc_final: 0.4563 (pm20) outliers start: 97 outliers final: 51 residues processed: 273 average time/residue: 0.5211 time to fit residues: 156.3056 Evaluate side-chains 251 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 191 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 546 ILE Chi-restraints excluded: chain B residue 562 THR Chi-restraints excluded: chain C residue 556 VAL Chi-restraints excluded: chain C residue 562 THR Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain D residue 575 MET Chi-restraints excluded: chain E residue 572 VAL Chi-restraints excluded: chain E residue 573 SER Chi-restraints excluded: chain G residue 660 SER Chi-restraints excluded: chain G residue 704 ILE Chi-restraints excluded: chain H residue 1659 LEU Chi-restraints excluded: chain H residue 1665 THR Chi-restraints excluded: chain H residue 1688 LEU Chi-restraints excluded: chain H residue 1709 THR Chi-restraints excluded: chain H residue 1712 ARG Chi-restraints excluded: chain H residue 1713 SER Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 357 PHE Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 440 ILE Chi-restraints excluded: chain A residue 459 MET Chi-restraints excluded: chain A residue 471 MET Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 764 ILE Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 838 ILE Chi-restraints excluded: chain A residue 853 GLU Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 885 SER Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 970 THR Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1033 THR Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1041 MET Chi-restraints excluded: chain A residue 1062 LEU Chi-restraints excluded: chain A residue 1109 MET Chi-restraints excluded: chain A residue 1166 ASP Chi-restraints excluded: chain A residue 1188 SER Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1292 LYS Chi-restraints excluded: chain A residue 1328 ILE Chi-restraints excluded: chain A residue 1394 GLN Chi-restraints excluded: chain A residue 1432 GLU Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain A residue 1443 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 102 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 11 optimal weight: 0.2980 chunk 149 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 141 optimal weight: 0.7980 chunk 97 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 8 optimal weight: 0.0470 chunk 113 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 overall best weight: 0.5680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 HIS A 957 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.169572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.136545 restraints weight = 17012.968| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 2.22 r_work: 0.3597 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3464 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12868 Z= 0.115 Angle : 0.530 6.773 17365 Z= 0.271 Chirality : 0.041 0.148 1996 Planarity : 0.004 0.052 2183 Dihedral : 3.927 23.133 1690 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.52 % Favored : 96.41 % Rotamer: Outliers : 5.90 % Allowed : 31.25 % Favored : 62.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.67 (0.22), residues: 1533 helix: 2.00 (0.18), residues: 887 sheet: 0.03 (0.56), residues: 83 loop : -0.10 (0.27), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 58 TYR 0.022 0.001 TYR A1001 PHE 0.013 0.001 PHE A 399 TRP 0.013 0.001 TRP A1248 HIS 0.002 0.001 HIS A 778 Details of bonding type rmsd covalent geometry : bond 0.00264 (12868) covalent geometry : angle 0.53025 (17365) hydrogen bonds : bond 0.03503 ( 712) hydrogen bonds : angle 4.02397 ( 2031) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3066 Ramachandran restraints generated. 1533 Oldfield, 0 Emsley, 1533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3066 Ramachandran restraints generated. 1533 Oldfield, 0 Emsley, 1533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 205 time to evaluate : 0.513 Fit side-chains revert: symmetry clash REVERT: B 565 SER cc_start: 0.8603 (t) cc_final: 0.8019 (p) REVERT: C 551 GLU cc_start: 0.6321 (OUTLIER) cc_final: 0.5054 (tm-30) REVERT: D 577 MET cc_start: 0.6349 (ttp) cc_final: 0.4858 (tmt) REVERT: H 1554 TRP cc_start: 0.7553 (m-90) cc_final: 0.7274 (m-90) REVERT: H 1637 MET cc_start: 0.7256 (mtp) cc_final: 0.6350 (mmp) REVERT: H 1659 LEU cc_start: 0.7135 (OUTLIER) cc_final: 0.6659 (pt) REVERT: A 101 GLN cc_start: 0.8814 (mt0) cc_final: 0.8304 (mp10) REVERT: A 103 MET cc_start: 0.8603 (OUTLIER) cc_final: 0.8230 (mtt) REVERT: A 221 ASP cc_start: 0.7037 (m-30) cc_final: 0.6476 (p0) REVERT: A 332 LYS cc_start: 0.6811 (tppt) cc_final: 0.6477 (mptt) REVERT: A 471 MET cc_start: 0.7971 (OUTLIER) cc_final: 0.7679 (mmm) REVERT: A 504 ARG cc_start: 0.7706 (mtm180) cc_final: 0.7180 (mtt180) REVERT: A 725 LYS cc_start: 0.8302 (mttm) cc_final: 0.8046 (mtmt) REVERT: A 780 GLU cc_start: 0.7092 (tp30) cc_final: 0.6580 (mp0) REVERT: A 876 ASN cc_start: 0.8384 (t0) cc_final: 0.8181 (t0) REVERT: A 1066 GLN cc_start: 0.7263 (pp30) cc_final: 0.6955 (pp30) REVERT: A 1109 MET cc_start: 0.8985 (OUTLIER) cc_final: 0.8680 (mpt) REVERT: A 1128 THR cc_start: 0.6337 (m) cc_final: 0.5984 (p) REVERT: A 1161 ARG cc_start: 0.6021 (OUTLIER) cc_final: 0.5799 (tpt170) REVERT: A 1189 ASN cc_start: 0.7548 (m-40) cc_final: 0.6897 (t0) REVERT: A 1206 GLU cc_start: 0.8387 (tm-30) cc_final: 0.7981 (tm-30) REVERT: A 1292 LYS cc_start: 0.6832 (OUTLIER) cc_final: 0.5325 (pptt) REVERT: A 1299 ARG cc_start: 0.7282 (tpt170) cc_final: 0.7060 (tpt170) REVERT: A 1308 TYR cc_start: 0.7001 (m-80) cc_final: 0.6566 (m-80) REVERT: A 1394 GLN cc_start: 0.5919 (OUTLIER) cc_final: 0.5583 (mm110) REVERT: A 1432 GLU cc_start: 0.5473 (OUTLIER) cc_final: 0.4533 (pm20) outliers start: 84 outliers final: 33 residues processed: 262 average time/residue: 0.5469 time to fit residues: 157.2056 Evaluate side-chains 231 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 189 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 546 ILE Chi-restraints excluded: chain C residue 551 GLU Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain E residue 572 VAL Chi-restraints excluded: chain G residue 704 ILE Chi-restraints excluded: chain H residue 1659 LEU Chi-restraints excluded: chain H residue 1665 THR Chi-restraints excluded: chain H residue 1712 ARG Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 165 LYS Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 357 PHE Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 459 MET Chi-restraints excluded: chain A residue 471 MET Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 853 GLU Chi-restraints excluded: chain A residue 908 SER Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1033 THR Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1062 LEU Chi-restraints excluded: chain A residue 1109 MET Chi-restraints excluded: chain A residue 1161 ARG Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain A residue 1166 ASP Chi-restraints excluded: chain A residue 1188 SER Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1292 LYS Chi-restraints excluded: chain A residue 1328 ILE Chi-restraints excluded: chain A residue 1394 GLN Chi-restraints excluded: chain A residue 1432 GLU Chi-restraints excluded: chain A residue 1436 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 30 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 chunk 101 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 72 optimal weight: 0.7980 chunk 51 optimal weight: 0.0980 chunk 35 optimal weight: 0.0970 chunk 57 optimal weight: 0.9990 chunk 85 optimal weight: 0.6980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.170287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.137284 restraints weight = 17106.702| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 2.26 r_work: 0.3607 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3475 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12868 Z= 0.110 Angle : 0.530 6.933 17365 Z= 0.270 Chirality : 0.040 0.155 1996 Planarity : 0.004 0.053 2183 Dihedral : 3.847 22.449 1690 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.52 % Favored : 96.41 % Rotamer: Outliers : 5.06 % Allowed : 31.95 % Favored : 62.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.76 (0.22), residues: 1533 helix: 2.06 (0.18), residues: 885 sheet: 0.09 (0.57), residues: 83 loop : -0.04 (0.27), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 361 TYR 0.020 0.001 TYR A1001 PHE 0.013 0.001 PHE A 399 TRP 0.013 0.001 TRP A1248 HIS 0.002 0.001 HIS A 778 Details of bonding type rmsd covalent geometry : bond 0.00254 (12868) covalent geometry : angle 0.53002 (17365) hydrogen bonds : bond 0.03370 ( 712) hydrogen bonds : angle 3.97430 ( 2031) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3066 Ramachandran restraints generated. 1533 Oldfield, 0 Emsley, 1533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3066 Ramachandran restraints generated. 1533 Oldfield, 0 Emsley, 1533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 202 time to evaluate : 0.593 Fit side-chains revert: symmetry clash REVERT: B 565 SER cc_start: 0.8608 (t) cc_final: 0.8027 (p) REVERT: D 577 MET cc_start: 0.6203 (ttp) cc_final: 0.4942 (tmt) REVERT: H 1554 TRP cc_start: 0.7583 (m-90) cc_final: 0.7323 (m-90) REVERT: H 1625 GLN cc_start: 0.3392 (OUTLIER) cc_final: 0.1274 (pm20) REVERT: H 1637 MET cc_start: 0.7021 (mtp) cc_final: 0.6348 (mmp) REVERT: H 1659 LEU cc_start: 0.7117 (OUTLIER) cc_final: 0.6648 (pt) REVERT: A 101 GLN cc_start: 0.8818 (mt0) cc_final: 0.8282 (mp10) REVERT: A 103 MET cc_start: 0.8589 (OUTLIER) cc_final: 0.8216 (mtt) REVERT: A 221 ASP cc_start: 0.7075 (m-30) cc_final: 0.6479 (p0) REVERT: A 332 LYS cc_start: 0.6817 (tppt) cc_final: 0.6510 (mptt) REVERT: A 471 MET cc_start: 0.7994 (OUTLIER) cc_final: 0.7680 (mmm) REVERT: A 504 ARG cc_start: 0.7728 (mtm180) cc_final: 0.7210 (mtt180) REVERT: A 568 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7890 (mp0) REVERT: A 725 LYS cc_start: 0.8318 (mttm) cc_final: 0.8096 (mtmt) REVERT: A 780 GLU cc_start: 0.7058 (tp30) cc_final: 0.6586 (mp0) REVERT: A 838 ILE cc_start: 0.8446 (OUTLIER) cc_final: 0.7894 (mp) REVERT: A 1066 GLN cc_start: 0.7216 (pp30) cc_final: 0.6951 (pp30) REVERT: A 1109 MET cc_start: 0.8962 (OUTLIER) cc_final: 0.8680 (mpt) REVERT: A 1128 THR cc_start: 0.6414 (m) cc_final: 0.6075 (p) REVERT: A 1161 ARG cc_start: 0.5984 (OUTLIER) cc_final: 0.5762 (tpt170) REVERT: A 1189 ASN cc_start: 0.7675 (m-40) cc_final: 0.6978 (t0) REVERT: A 1235 GLU cc_start: 0.8087 (mm-30) cc_final: 0.7320 (pp20) REVERT: A 1292 LYS cc_start: 0.6897 (OUTLIER) cc_final: 0.5431 (pptt) REVERT: A 1299 ARG cc_start: 0.7278 (tpt170) cc_final: 0.7057 (tpt170) REVERT: A 1306 TRP cc_start: 0.7333 (m-10) cc_final: 0.6861 (m100) REVERT: A 1308 TYR cc_start: 0.6941 (m-80) cc_final: 0.6397 (m-80) REVERT: A 1394 GLN cc_start: 0.5879 (OUTLIER) cc_final: 0.5492 (mm-40) REVERT: A 1432 GLU cc_start: 0.5453 (OUTLIER) cc_final: 0.4530 (pm20) outliers start: 72 outliers final: 36 residues processed: 256 average time/residue: 0.5517 time to fit residues: 154.5429 Evaluate side-chains 238 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 191 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 556 VAL Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain E residue 572 VAL Chi-restraints excluded: chain G residue 704 ILE Chi-restraints excluded: chain H residue 1625 GLN Chi-restraints excluded: chain H residue 1630 THR Chi-restraints excluded: chain H residue 1659 LEU Chi-restraints excluded: chain H residue 1665 THR Chi-restraints excluded: chain H residue 1688 LEU Chi-restraints excluded: chain H residue 1712 ARG Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 165 LYS Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 357 PHE Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 459 MET Chi-restraints excluded: chain A residue 471 MET Chi-restraints excluded: chain A residue 568 GLU Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 764 ILE Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 838 ILE Chi-restraints excluded: chain A residue 853 GLU Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1033 THR Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1062 LEU Chi-restraints excluded: chain A residue 1109 MET Chi-restraints excluded: chain A residue 1161 ARG Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain A residue 1166 ASP Chi-restraints excluded: chain A residue 1188 SER Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1292 LYS Chi-restraints excluded: chain A residue 1328 ILE Chi-restraints excluded: chain A residue 1394 GLN Chi-restraints excluded: chain A residue 1432 GLU Chi-restraints excluded: chain A residue 1436 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 2 optimal weight: 0.8980 chunk 84 optimal weight: 0.0980 chunk 126 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 52 optimal weight: 4.9990 chunk 122 optimal weight: 5.9990 chunk 117 optimal weight: 0.0370 chunk 26 optimal weight: 6.9990 chunk 98 optimal weight: 0.4980 chunk 106 optimal weight: 0.8980 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 HIS A 427 HIS A 876 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.170765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.137854 restraints weight = 16975.276| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 2.22 r_work: 0.3619 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3488 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.2938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12868 Z= 0.113 Angle : 0.537 8.619 17365 Z= 0.274 Chirality : 0.040 0.149 1996 Planarity : 0.004 0.053 2183 Dihedral : 3.815 22.587 1690 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.59 % Favored : 96.35 % Rotamer: Outliers : 4.78 % Allowed : 32.44 % Favored : 62.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.79 (0.22), residues: 1533 helix: 2.07 (0.18), residues: 887 sheet: 0.15 (0.58), residues: 83 loop : -0.03 (0.27), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 430 TYR 0.020 0.001 TYR A1001 PHE 0.013 0.001 PHE A 399 TRP 0.013 0.001 TRP A1248 HIS 0.003 0.001 HIS A 778 Details of bonding type rmsd covalent geometry : bond 0.00259 (12868) covalent geometry : angle 0.53684 (17365) hydrogen bonds : bond 0.03323 ( 712) hydrogen bonds : angle 3.94742 ( 2031) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3066 Ramachandran restraints generated. 1533 Oldfield, 0 Emsley, 1533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3066 Ramachandran restraints generated. 1533 Oldfield, 0 Emsley, 1533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 193 time to evaluate : 0.440 Fit side-chains revert: symmetry clash REVERT: B 565 SER cc_start: 0.8653 (t) cc_final: 0.8058 (p) REVERT: C 551 GLU cc_start: 0.5700 (OUTLIER) cc_final: 0.5079 (tm-30) REVERT: D 577 MET cc_start: 0.6295 (ttp) cc_final: 0.4948 (tmt) REVERT: H 1554 TRP cc_start: 0.7581 (m-90) cc_final: 0.7363 (m-90) REVERT: H 1625 GLN cc_start: 0.3437 (OUTLIER) cc_final: 0.1306 (pm20) REVERT: H 1637 MET cc_start: 0.7048 (mtp) cc_final: 0.6482 (mmp) REVERT: H 1659 LEU cc_start: 0.7122 (OUTLIER) cc_final: 0.6639 (pt) REVERT: A 101 GLN cc_start: 0.8776 (mt0) cc_final: 0.8250 (mp10) REVERT: A 103 MET cc_start: 0.8561 (OUTLIER) cc_final: 0.8182 (mtt) REVERT: A 221 ASP cc_start: 0.7085 (m-30) cc_final: 0.6484 (p0) REVERT: A 222 LYS cc_start: 0.7928 (pmmt) cc_final: 0.7469 (pptt) REVERT: A 332 LYS cc_start: 0.6807 (tppt) cc_final: 0.6517 (mptt) REVERT: A 471 MET cc_start: 0.7992 (OUTLIER) cc_final: 0.7688 (mmm) REVERT: A 568 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7882 (mp0) REVERT: A 725 LYS cc_start: 0.8315 (mttm) cc_final: 0.8086 (mtmt) REVERT: A 780 GLU cc_start: 0.7048 (tp30) cc_final: 0.6593 (mp0) REVERT: A 838 ILE cc_start: 0.8446 (OUTLIER) cc_final: 0.7895 (mp) REVERT: A 1066 GLN cc_start: 0.7206 (pp30) cc_final: 0.6919 (pp30) REVERT: A 1109 MET cc_start: 0.8965 (OUTLIER) cc_final: 0.8707 (mpt) REVERT: A 1128 THR cc_start: 0.6439 (m) cc_final: 0.6106 (p) REVERT: A 1161 ARG cc_start: 0.5979 (OUTLIER) cc_final: 0.5745 (tpt170) REVERT: A 1189 ASN cc_start: 0.7673 (m-40) cc_final: 0.6956 (t0) REVERT: A 1206 GLU cc_start: 0.8395 (tm-30) cc_final: 0.7974 (tm-30) REVERT: A 1235 GLU cc_start: 0.8049 (mm-30) cc_final: 0.7365 (pp20) REVERT: A 1292 LYS cc_start: 0.6853 (OUTLIER) cc_final: 0.5357 (pptt) REVERT: A 1299 ARG cc_start: 0.7270 (tpt170) cc_final: 0.7046 (tpt170) REVERT: A 1306 TRP cc_start: 0.7340 (m-10) cc_final: 0.6844 (m100) REVERT: A 1308 TYR cc_start: 0.6938 (m-80) cc_final: 0.6413 (m-80) REVERT: A 1394 GLN cc_start: 0.5862 (OUTLIER) cc_final: 0.5493 (mm-40) REVERT: A 1432 GLU cc_start: 0.5395 (OUTLIER) cc_final: 0.4564 (pm20) outliers start: 68 outliers final: 37 residues processed: 241 average time/residue: 0.5660 time to fit residues: 149.1536 Evaluate side-chains 238 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 189 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 551 GLU Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain E residue 572 VAL Chi-restraints excluded: chain E residue 573 SER Chi-restraints excluded: chain E residue 718 ILE Chi-restraints excluded: chain G residue 660 SER Chi-restraints excluded: chain G residue 695 GLN Chi-restraints excluded: chain G residue 704 ILE Chi-restraints excluded: chain H residue 1546 LEU Chi-restraints excluded: chain H residue 1625 GLN Chi-restraints excluded: chain H residue 1659 LEU Chi-restraints excluded: chain H residue 1665 THR Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 165 LYS Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 357 PHE Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 459 MET Chi-restraints excluded: chain A residue 471 MET Chi-restraints excluded: chain A residue 568 GLU Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 838 ILE Chi-restraints excluded: chain A residue 853 GLU Chi-restraints excluded: chain A residue 908 SER Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 979 ILE Chi-restraints excluded: chain A residue 1033 THR Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1062 LEU Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1109 MET Chi-restraints excluded: chain A residue 1161 ARG Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain A residue 1166 ASP Chi-restraints excluded: chain A residue 1188 SER Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1244 THR Chi-restraints excluded: chain A residue 1292 LYS Chi-restraints excluded: chain A residue 1394 GLN Chi-restraints excluded: chain A residue 1432 GLU Chi-restraints excluded: chain A residue 1436 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 14 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 138 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 109 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 30 optimal weight: 7.9990 chunk 91 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 150 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 427 HIS A1165 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.169490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.136305 restraints weight = 17185.647| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 2.25 r_work: 0.3594 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3461 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12868 Z= 0.127 Angle : 0.552 8.615 17365 Z= 0.281 Chirality : 0.041 0.148 1996 Planarity : 0.004 0.053 2183 Dihedral : 3.842 22.393 1688 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.46 % Favored : 96.48 % Rotamer: Outliers : 4.99 % Allowed : 32.23 % Favored : 62.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.72 (0.22), residues: 1533 helix: 2.06 (0.18), residues: 886 sheet: 0.12 (0.58), residues: 83 loop : -0.12 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 430 TYR 0.021 0.001 TYR A1001 PHE 0.015 0.001 PHE A 399 TRP 0.012 0.001 TRP A1248 HIS 0.004 0.001 HIS A 778 Details of bonding type rmsd covalent geometry : bond 0.00303 (12868) covalent geometry : angle 0.55193 (17365) hydrogen bonds : bond 0.03508 ( 712) hydrogen bonds : angle 3.99365 ( 2031) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3066 Ramachandran restraints generated. 1533 Oldfield, 0 Emsley, 1533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3066 Ramachandran restraints generated. 1533 Oldfield, 0 Emsley, 1533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 189 time to evaluate : 0.540 Fit side-chains revert: symmetry clash REVERT: B 565 SER cc_start: 0.8629 (t) cc_final: 0.8042 (p) REVERT: C 551 GLU cc_start: 0.5779 (OUTLIER) cc_final: 0.5135 (tm-30) REVERT: D 577 MET cc_start: 0.6234 (ttp) cc_final: 0.4926 (tmt) REVERT: H 1554 TRP cc_start: 0.7517 (m-90) cc_final: 0.7296 (m-90) REVERT: H 1625 GLN cc_start: 0.3390 (OUTLIER) cc_final: 0.1276 (pm20) REVERT: H 1637 MET cc_start: 0.7063 (mtp) cc_final: 0.6474 (mmp) REVERT: H 1659 LEU cc_start: 0.7112 (OUTLIER) cc_final: 0.6639 (pt) REVERT: H 1712 ARG cc_start: 0.8483 (OUTLIER) cc_final: 0.7918 (ptp90) REVERT: A 43 ASP cc_start: 0.6709 (OUTLIER) cc_final: 0.6431 (t0) REVERT: A 101 GLN cc_start: 0.8785 (mt0) cc_final: 0.8240 (mp10) REVERT: A 103 MET cc_start: 0.8636 (OUTLIER) cc_final: 0.8255 (mtt) REVERT: A 221 ASP cc_start: 0.7080 (m-30) cc_final: 0.6517 (p0) REVERT: A 332 LYS cc_start: 0.6862 (tppt) cc_final: 0.6545 (mptt) REVERT: A 471 MET cc_start: 0.7982 (OUTLIER) cc_final: 0.7678 (mmm) REVERT: A 504 ARG cc_start: 0.7665 (mtm180) cc_final: 0.7292 (ttt-90) REVERT: A 568 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7903 (mp0) REVERT: A 725 LYS cc_start: 0.8355 (mttm) cc_final: 0.8101 (mtmt) REVERT: A 780 GLU cc_start: 0.7087 (tp30) cc_final: 0.6632 (mp0) REVERT: A 893 LYS cc_start: 0.8617 (OUTLIER) cc_final: 0.7873 (mmtp) REVERT: A 1066 GLN cc_start: 0.7235 (pp30) cc_final: 0.6967 (pp30) REVERT: A 1068 ILE cc_start: 0.7753 (OUTLIER) cc_final: 0.7368 (mt) REVERT: A 1109 MET cc_start: 0.8982 (OUTLIER) cc_final: 0.8697 (mpt) REVERT: A 1128 THR cc_start: 0.6462 (m) cc_final: 0.6130 (p) REVERT: A 1161 ARG cc_start: 0.5994 (OUTLIER) cc_final: 0.5777 (tpt170) REVERT: A 1189 ASN cc_start: 0.7654 (m-40) cc_final: 0.6990 (t0) REVERT: A 1206 GLU cc_start: 0.8416 (tm-30) cc_final: 0.7996 (tm-30) REVERT: A 1235 GLU cc_start: 0.8047 (mm-30) cc_final: 0.7392 (pp20) REVERT: A 1292 LYS cc_start: 0.6874 (OUTLIER) cc_final: 0.5425 (pptt) REVERT: A 1299 ARG cc_start: 0.7310 (tpt170) cc_final: 0.7092 (tpt170) REVERT: A 1308 TYR cc_start: 0.6996 (m-80) cc_final: 0.6480 (m-80) REVERT: A 1394 GLN cc_start: 0.5889 (OUTLIER) cc_final: 0.5503 (mm-40) REVERT: A 1432 GLU cc_start: 0.5448 (OUTLIER) cc_final: 0.4587 (pm20) outliers start: 71 outliers final: 43 residues processed: 241 average time/residue: 0.5739 time to fit residues: 151.3084 Evaluate side-chains 244 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 186 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 551 GLU Chi-restraints excluded: chain C residue 556 VAL Chi-restraints excluded: chain C residue 562 THR Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain E residue 572 VAL Chi-restraints excluded: chain E residue 573 SER Chi-restraints excluded: chain E residue 718 ILE Chi-restraints excluded: chain G residue 660 SER Chi-restraints excluded: chain G residue 704 ILE Chi-restraints excluded: chain H residue 1625 GLN Chi-restraints excluded: chain H residue 1630 THR Chi-restraints excluded: chain H residue 1659 LEU Chi-restraints excluded: chain H residue 1712 ARG Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 165 LYS Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 357 PHE Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 459 MET Chi-restraints excluded: chain A residue 471 MET Chi-restraints excluded: chain A residue 568 GLU Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 764 ILE Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 853 GLU Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 893 LYS Chi-restraints excluded: chain A residue 908 SER Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1033 THR Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1062 LEU Chi-restraints excluded: chain A residue 1068 ILE Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1109 MET Chi-restraints excluded: chain A residue 1161 ARG Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain A residue 1166 ASP Chi-restraints excluded: chain A residue 1188 SER Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1244 THR Chi-restraints excluded: chain A residue 1292 LYS Chi-restraints excluded: chain A residue 1328 ILE Chi-restraints excluded: chain A residue 1394 GLN Chi-restraints excluded: chain A residue 1432 GLU Chi-restraints excluded: chain A residue 1436 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 67 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 21 optimal weight: 6.9990 chunk 153 optimal weight: 9.9990 chunk 65 optimal weight: 0.6980 chunk 58 optimal weight: 0.8980 chunk 14 optimal weight: 0.0570 chunk 84 optimal weight: 0.0970 chunk 11 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 chunk 27 optimal weight: 5.9990 overall best weight: 0.4896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 HIS A 427 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.171072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.137939 restraints weight = 17171.365| |-----------------------------------------------------------------------------| r_work (start): 0.3728 rms_B_bonded: 2.25 r_work: 0.3618 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3487 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.3048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12868 Z= 0.112 Angle : 0.544 8.721 17365 Z= 0.277 Chirality : 0.040 0.152 1996 Planarity : 0.004 0.053 2183 Dihedral : 3.786 22.764 1688 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.39 % Favored : 96.54 % Rotamer: Outliers : 3.79 % Allowed : 33.43 % Favored : 62.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.82 (0.22), residues: 1533 helix: 2.11 (0.18), residues: 885 sheet: 0.23 (0.59), residues: 83 loop : -0.04 (0.28), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 430 TYR 0.020 0.001 TYR A1001 PHE 0.013 0.001 PHE A 399 TRP 0.013 0.001 TRP A 415 HIS 0.003 0.001 HIS A 778 Details of bonding type rmsd covalent geometry : bond 0.00258 (12868) covalent geometry : angle 0.54381 (17365) hydrogen bonds : bond 0.03307 ( 712) hydrogen bonds : angle 3.94028 ( 2031) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3066 Ramachandran restraints generated. 1533 Oldfield, 0 Emsley, 1533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3066 Ramachandran restraints generated. 1533 Oldfield, 0 Emsley, 1533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 190 time to evaluate : 0.524 Fit side-chains revert: symmetry clash REVERT: B 565 SER cc_start: 0.8655 (t) cc_final: 0.8073 (p) REVERT: B 573 SER cc_start: 0.7637 (m) cc_final: 0.7350 (m) REVERT: D 577 MET cc_start: 0.6281 (ttp) cc_final: 0.4964 (tmt) REVERT: E 722 GLN cc_start: 0.6867 (mm-40) cc_final: 0.6602 (mm110) REVERT: H 1554 TRP cc_start: 0.7481 (m-90) cc_final: 0.7258 (m-90) REVERT: H 1625 GLN cc_start: 0.3306 (OUTLIER) cc_final: 0.1279 (pm20) REVERT: H 1637 MET cc_start: 0.6999 (mtp) cc_final: 0.6439 (mmp) REVERT: H 1659 LEU cc_start: 0.7054 (OUTLIER) cc_final: 0.6579 (pt) REVERT: H 1712 ARG cc_start: 0.8476 (OUTLIER) cc_final: 0.7920 (ptp90) REVERT: A 43 ASP cc_start: 0.6705 (OUTLIER) cc_final: 0.6451 (t0) REVERT: A 101 GLN cc_start: 0.8779 (mt0) cc_final: 0.8232 (mp10) REVERT: A 103 MET cc_start: 0.8568 (OUTLIER) cc_final: 0.8192 (mtt) REVERT: A 221 ASP cc_start: 0.7069 (m-30) cc_final: 0.6453 (p0) REVERT: A 222 LYS cc_start: 0.7929 (pmmt) cc_final: 0.7445 (pptt) REVERT: A 332 LYS cc_start: 0.6791 (tppt) cc_final: 0.6448 (mptt) REVERT: A 471 MET cc_start: 0.7999 (OUTLIER) cc_final: 0.7716 (mmm) REVERT: A 504 ARG cc_start: 0.7668 (mtm180) cc_final: 0.7217 (ttt-90) REVERT: A 568 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7961 (mp0) REVERT: A 725 LYS cc_start: 0.8342 (mttm) cc_final: 0.8101 (mtmt) REVERT: A 780 GLU cc_start: 0.7080 (tp30) cc_final: 0.6589 (mp0) REVERT: A 893 LYS cc_start: 0.8628 (OUTLIER) cc_final: 0.7890 (mmtp) REVERT: A 1066 GLN cc_start: 0.7256 (pp30) cc_final: 0.6961 (pp30) REVERT: A 1068 ILE cc_start: 0.7708 (OUTLIER) cc_final: 0.7311 (OUTLIER) REVERT: A 1109 MET cc_start: 0.8977 (OUTLIER) cc_final: 0.8742 (mpt) REVERT: A 1128 THR cc_start: 0.6457 (m) cc_final: 0.6139 (p) REVERT: A 1161 ARG cc_start: 0.5985 (OUTLIER) cc_final: 0.5770 (tpt170) REVERT: A 1189 ASN cc_start: 0.7708 (m-40) cc_final: 0.7011 (t0) REVERT: A 1206 GLU cc_start: 0.8442 (tm-30) cc_final: 0.8013 (tm-30) REVERT: A 1235 GLU cc_start: 0.8001 (mm-30) cc_final: 0.7404 (pp20) REVERT: A 1292 LYS cc_start: 0.6807 (OUTLIER) cc_final: 0.5309 (pptt) REVERT: A 1308 TYR cc_start: 0.6995 (m-80) cc_final: 0.6549 (m-80) REVERT: A 1394 GLN cc_start: 0.5876 (OUTLIER) cc_final: 0.5496 (mm-40) REVERT: A 1432 GLU cc_start: 0.5405 (OUTLIER) cc_final: 0.4605 (pm20) outliers start: 54 outliers final: 34 residues processed: 230 average time/residue: 0.5600 time to fit residues: 141.4016 Evaluate side-chains 237 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 190 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain E residue 572 VAL Chi-restraints excluded: chain E residue 573 SER Chi-restraints excluded: chain E residue 718 ILE Chi-restraints excluded: chain H residue 1546 LEU Chi-restraints excluded: chain H residue 1625 GLN Chi-restraints excluded: chain H residue 1659 LEU Chi-restraints excluded: chain H residue 1712 ARG Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 165 LYS Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 357 PHE Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 459 MET Chi-restraints excluded: chain A residue 471 MET Chi-restraints excluded: chain A residue 568 GLU Chi-restraints excluded: chain A residue 853 GLU Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 893 LYS Chi-restraints excluded: chain A residue 908 SER Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1033 THR Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1062 LEU Chi-restraints excluded: chain A residue 1068 ILE Chi-restraints excluded: chain A residue 1109 MET Chi-restraints excluded: chain A residue 1161 ARG Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain A residue 1166 ASP Chi-restraints excluded: chain A residue 1188 SER Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1244 THR Chi-restraints excluded: chain A residue 1292 LYS Chi-restraints excluded: chain A residue 1328 ILE Chi-restraints excluded: chain A residue 1394 GLN Chi-restraints excluded: chain A residue 1432 GLU Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain A residue 1439 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 41 optimal weight: 0.0870 chunk 34 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 89 optimal weight: 0.3980 chunk 21 optimal weight: 7.9990 chunk 33 optimal weight: 0.9980 chunk 9 optimal weight: 5.9990 chunk 69 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 56 optimal weight: 0.6980 chunk 123 optimal weight: 1.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 427 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.170615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.137585 restraints weight = 17181.475| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 2.24 r_work: 0.3615 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3481 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12868 Z= 0.116 Angle : 0.549 8.807 17365 Z= 0.277 Chirality : 0.041 0.152 1996 Planarity : 0.004 0.053 2183 Dihedral : 3.773 22.779 1688 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.46 % Favored : 96.48 % Rotamer: Outliers : 4.14 % Allowed : 33.36 % Favored : 62.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.81 (0.22), residues: 1533 helix: 2.15 (0.18), residues: 880 sheet: 0.11 (0.59), residues: 83 loop : -0.10 (0.27), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 430 TYR 0.024 0.001 TYR A1001 PHE 0.014 0.001 PHE A 399 TRP 0.013 0.001 TRP A 415 HIS 0.003 0.000 HIS A 778 Details of bonding type rmsd covalent geometry : bond 0.00270 (12868) covalent geometry : angle 0.54910 (17365) hydrogen bonds : bond 0.03359 ( 712) hydrogen bonds : angle 3.94706 ( 2031) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5146.83 seconds wall clock time: 88 minutes 22.46 seconds (5302.46 seconds total)