Starting phenix.real_space_refine on Sat Sep 12 06:54:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8d97_27257/09_2026/8d97_27257.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d97_27257/09_2026/8d97_27257.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8d97_27257/09_2026/8d97_27257.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d97_27257/09_2026/8d97_27257.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8d97_27257/09_2026/8d97_27257.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8d97_27257/09_2026/8d97_27257.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8d97_27257/09_2026/8d97_27257.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d97_27257/09_2026/8d97_27257.map" } resolution = 3.8 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= 0.031 sd= 1.128 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 P 42 5.49 5 S 41 5.16 5 C 8625 2.51 5 N 2445 2.21 5 O 2717 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 88 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13874 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 12990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1600, 12990 Classifications: {'peptide': 1600} Link IDs: {'PTRANS': 70, 'TRANS': 1529} Chain breaks: 8 Chain: "C" Number of atoms: 880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 880 Classifications: {'RNAv2': 42} Modifications used: {'rna2p_pur': 11, 'rna2p_pyr': 11, 'rna3p_pur': 5, 'rna3p_pyr': 15} Link IDs: {'rna2p': 21, 'rna3p': 20} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 668 SG CYS A 83 42.188 58.213 17.775 1.00112.54 S ATOM 939 SG CYS A 116 42.722 55.946 14.103 1.00121.93 S ATOM 985 SG CYS A 122 44.991 56.202 17.287 1.00100.15 S ATOM 1009 SG CYS A 125 41.791 54.844 17.275 1.00 97.33 S ATOM 3703 SG CYS A 486 34.125 74.468 46.993 1.00 79.62 S ATOM 3771 SG CYS A 496 35.438 72.708 43.943 1.00 73.06 S ATOM 3785 SG CYS A 498 37.071 75.312 45.520 1.00 71.64 S ATOM 3807 SG CYS A 501 38.009 71.893 46.011 1.00 70.88 S ATOM 5778 SG CYS A 745 25.020 80.291 78.130 1.00140.63 S ATOM 5791 SG CYS A 747 28.461 81.408 78.582 1.00121.80 S ATOM 5813 SG CYS A 750 29.191 78.549 76.694 1.00105.45 S ATOM 7764 SG CYS A1013 31.267 68.320 113.568 1.00118.39 S ATOM 10846 SG CYS A1401 28.623 68.577 111.063 1.00125.65 S ATOM 10897 SG CYS A1409 30.301 71.505 112.762 1.00106.08 S ATOM 10914 SG CYS A1412 32.758 70.068 110.750 1.00102.04 S Time building chain proxies: 3.17, per 1000 atoms: 0.23 Number of scatterers: 13874 At special positions: 0 Unit cell: (88.596, 110.424, 186.18, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 S 41 16.00 P 42 15.00 O 2717 8.00 N 2445 7.00 C 8625 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A1160 " - pdb=" SG CYS A1166 " distance=2.03 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: 1.19 Conformation dependent library (CDL) restraints added in 674.0 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1701 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 116 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 122 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 83 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 125 " pdb=" ZN A1702 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 498 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 486 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 501 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 496 " pdb=" ZN A1703 " pdb="ZN ZN A1703 " - pdb=" SG CYS A 745 " pdb="ZN ZN A1703 " - pdb=" SG CYS A 747 " pdb="ZN ZN A1703 " - pdb=" SG CYS A 750 " pdb="ZN ZN A1703 " - pdb=" ND1 HIS A 742 " pdb=" ZN A1704 " pdb="ZN ZN A1704 " - pdb=" SG CYS A1013 " pdb="ZN ZN A1704 " - pdb=" SG CYS A1401 " pdb="ZN ZN A1704 " - pdb=" SG CYS A1412 " pdb="ZN ZN A1704 " - pdb=" SG CYS A1409 " Number of angles added : 21 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2946 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 20 sheets defined 32.6% alpha, 22.5% beta 0 base pairs and 5 stacking pairs defined. Time for finding SS restraints: 1.77 Creating SS restraints... Processing helix chain 'A' and resid 22 through 26 Processing helix chain 'A' and resid 27 through 33 Processing helix chain 'A' and resid 54 through 73 removed outlier: 3.935A pdb=" N VAL A 58 " --> pdb=" O THR A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 129 Processing helix chain 'A' and resid 163 through 168 removed outlier: 3.645A pdb=" N ILE A 167 " --> pdb=" O ARG A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 211 through 220 Processing helix chain 'A' and resid 262 through 282 removed outlier: 3.524A pdb=" N ASP A 266 " --> pdb=" O GLU A 262 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASN A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 298 removed outlier: 4.216A pdb=" N ARG A 289 " --> pdb=" O LEU A 285 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ILE A 290 " --> pdb=" O GLU A 286 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASP A 293 " --> pdb=" O ARG A 289 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ARG A 296 " --> pdb=" O ALA A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 302 removed outlier: 4.489A pdb=" N GLY A 302 " --> pdb=" O ARG A 299 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 299 through 302' Processing helix chain 'A' and resid 303 through 308 removed outlier: 3.899A pdb=" N GLU A 307 " --> pdb=" O GLU A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 345 Processing helix chain 'A' and resid 349 through 369 Processing helix chain 'A' and resid 466 through 483 removed outlier: 3.559A pdb=" N LEU A 470 " --> pdb=" O PRO A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 505 Processing helix chain 'A' and resid 564 through 575 Processing helix chain 'A' and resid 589 through 593 removed outlier: 3.625A pdb=" N THR A 592 " --> pdb=" O LEU A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 620 Processing helix chain 'A' and resid 621 through 623 No H-bonds generated for 'chain 'A' and resid 621 through 623' Processing helix chain 'A' and resid 625 through 632 removed outlier: 3.503A pdb=" N LEU A 629 " --> pdb=" O LYS A 625 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLU A 631 " --> pdb=" O LYS A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 637 Processing helix chain 'A' and resid 653 through 659 Processing helix chain 'A' and resid 681 through 688 Processing helix chain 'A' and resid 718 through 735 removed outlier: 3.560A pdb=" N PHE A 726 " --> pdb=" O HIS A 722 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ARG A 733 " --> pdb=" O ALA A 729 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 775 removed outlier: 3.611A pdb=" N GLU A 774 " --> pdb=" O ASN A 771 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE A 775 " --> pdb=" O GLY A 772 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 771 through 775' Processing helix chain 'A' and resid 795 through 799 removed outlier: 3.811A pdb=" N LYS A 799 " --> pdb=" O ASP A 796 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 843 Processing helix chain 'A' and resid 868 through 877 Processing helix chain 'A' and resid 994 through 1011 removed outlier: 3.944A pdb=" N LEU A 998 " --> pdb=" O PRO A 994 " (cutoff:3.500A) Processing helix chain 'A' and resid 1034 through 1039 removed outlier: 3.740A pdb=" N LYS A1037 " --> pdb=" O ALA A1034 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N TYR A1039 " --> pdb=" O GLU A1036 " (cutoff:3.500A) Processing helix chain 'A' and resid 1042 through 1052 Processing helix chain 'A' and resid 1054 through 1058 removed outlier: 3.651A pdb=" N ARG A1058 " --> pdb=" O PRO A1055 " (cutoff:3.500A) Processing helix chain 'A' and resid 1060 through 1069 Processing helix chain 'A' and resid 1083 through 1090 removed outlier: 3.991A pdb=" N SER A1087 " --> pdb=" O ARG A1083 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASP A1088 " --> pdb=" O ARG A1084 " (cutoff:3.500A) Processing helix chain 'A' and resid 1096 through 1107 Processing helix chain 'A' and resid 1144 through 1148 Processing helix chain 'A' and resid 1152 through 1157 Processing helix chain 'A' and resid 1163 through 1201 removed outlier: 4.015A pdb=" N ARG A1167 " --> pdb=" O SER A1163 " (cutoff:3.500A) Processing helix chain 'A' and resid 1201 through 1210 Processing helix chain 'A' and resid 1228 through 1230 No H-bonds generated for 'chain 'A' and resid 1228 through 1230' Processing helix chain 'A' and resid 1327 through 1341 Processing helix chain 'A' and resid 1346 through 1354 Processing helix chain 'A' and resid 1395 through 1399 Processing helix chain 'A' and resid 1409 through 1415 Processing helix chain 'A' and resid 1458 through 1463 removed outlier: 4.457A pdb=" N SER A1462 " --> pdb=" O ARG A1458 " (cutoff:3.500A) Processing helix chain 'A' and resid 1481 through 1486 removed outlier: 3.888A pdb=" N ILE A1485 " --> pdb=" O GLY A1481 " (cutoff:3.500A) Processing helix chain 'A' and resid 1488 through 1496 removed outlier: 3.515A pdb=" N ARG A1493 " --> pdb=" O GLN A1489 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU A1494 " --> pdb=" O LEU A1490 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL A1496 " --> pdb=" O ILE A1492 " (cutoff:3.500A) Processing helix chain 'A' and resid 1523 through 1535 Processing helix chain 'A' and resid 1581 through 1596 Processing helix chain 'A' and resid 1610 through 1613 removed outlier: 3.757A pdb=" N VAL A1613 " --> pdb=" O GLN A1610 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1610 through 1613' Processing helix chain 'A' and resid 1614 through 1624 Processing helix chain 'A' and resid 1668 through 1678 Processing sheet with id=AA1, first strand: chain 'A' and resid 146 through 148 removed outlier: 3.890A pdb=" N LEU A 153 " --> pdb=" O SER A 51 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N SER A 51 " --> pdb=" O LEU A 153 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA A 37 " --> pdb=" O ARG A 14 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N TRP A 190 " --> pdb=" O LEU A 15 " (cutoff:3.500A) removed outlier: 9.376A pdb=" N GLU A 17 " --> pdb=" O ARG A 188 " (cutoff:3.500A) removed outlier: 13.243A pdb=" N ARG A 188 " --> pdb=" O GLU A 17 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 183 through 191 current: chain 'A' and resid 230 through 235 Processing sheet with id=AA2, first strand: chain 'A' and resid 169 through 176 removed outlier: 6.181A pdb=" N SER A 169 " --> pdb=" O TRP A 190 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N TRP A 190 " --> pdb=" O SER A 169 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ARG A 171 " --> pdb=" O ARG A 188 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ARG A 188 " --> pdb=" O ARG A 171 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N LEU A 173 " --> pdb=" O TYR A 186 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N TYR A 186 " --> pdb=" O LEU A 173 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ARG A 175 " --> pdb=" O LYS A 184 " (cutoff:3.500A) removed outlier: 13.243A pdb=" N ARG A 188 " --> pdb=" O GLU A 17 " (cutoff:3.500A) removed outlier: 9.376A pdb=" N GLU A 17 " --> pdb=" O ARG A 188 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N TRP A 190 " --> pdb=" O LEU A 15 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA A 37 " --> pdb=" O ARG A 14 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N SER A 51 " --> pdb=" O LEU A 153 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU A 153 " --> pdb=" O SER A 51 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 76 through 77 Processing sheet with id=AA4, first strand: chain 'A' and resid 105 through 106 removed outlier: 6.229A pdb=" N THR A 105 " --> pdb=" O VAL A 400 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 507 through 508 removed outlier: 6.673A pdb=" N GLU A 410 " --> pdb=" O GLU A 606 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N GLU A 606 " --> pdb=" O GLU A 410 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ILE A 412 " --> pdb=" O ILE A 604 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ILE A 604 " --> pdb=" O ILE A 412 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL A 414 " --> pdb=" O ILE A 602 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ILE A 602 " --> pdb=" O VAL A 414 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 507 through 508 removed outlier: 6.673A pdb=" N GLU A 410 " --> pdb=" O GLU A 606 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N GLU A 606 " --> pdb=" O GLU A 410 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ILE A 412 " --> pdb=" O ILE A 604 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ILE A 604 " --> pdb=" O ILE A 412 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL A 414 " --> pdb=" O ILE A 602 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ILE A 602 " --> pdb=" O VAL A 414 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 521 through 525 Processing sheet with id=AA8, first strand: chain 'A' and resid 698 through 699 removed outlier: 6.234A pdb=" N PHE A 715 " --> pdb=" O LEU A 769 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N ARG A 818 " --> pdb=" O GLU A 765 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N LEU A 767 " --> pdb=" O LYS A 816 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N LYS A 816 " --> pdb=" O LEU A 767 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N LEU A 769 " --> pdb=" O LYS A 814 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N LYS A 814 " --> pdb=" O LEU A 769 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 702 through 703 removed outlier: 3.551A pdb=" N ALA A 708 " --> pdb=" O ASN A 703 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 782 through 784 Processing sheet with id=AB2, first strand: chain 'A' and resid 915 through 916 Processing sheet with id=AB3, first strand: chain 'A' and resid 919 through 922 Processing sheet with id=AB4, first strand: chain 'A' and resid 986 through 987 removed outlier: 7.460A pdb=" N LEU A 991 " --> pdb=" O TYR A1431 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TYR A1431 " --> pdb=" O LEU A 991 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N VAL A1512 " --> pdb=" O GLU A1432 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N LEU A 945 " --> pdb=" O ASN A1521 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N LYS A 952 " --> pdb=" O ILE A1559 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N ILE A1559 " --> pdb=" O LYS A 952 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLU A 954 " --> pdb=" O ILE A1557 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N ILE A1557 " --> pdb=" O GLU A 954 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL A1555 " --> pdb=" O HIS A1542 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1424 through 1426 removed outlier: 6.060A pdb=" N LEU A 945 " --> pdb=" O ASN A1521 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N LYS A 952 " --> pdb=" O ILE A1559 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N ILE A1559 " --> pdb=" O LYS A 952 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLU A 954 " --> pdb=" O ILE A1557 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N ILE A1557 " --> pdb=" O GLU A 954 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR A1564 " --> pdb=" O LYS A1575 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 981 through 982 removed outlier: 7.279A pdb=" N TYR A 982 " --> pdb=" O GLU A1505 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1323 through 1326 removed outlier: 4.546A pdb=" N LEU A1125 " --> pdb=" O VAL A1326 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER A1380 " --> pdb=" O HIS A1371 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1131 through 1136 removed outlier: 8.876A pdb=" N VAL A1132 " --> pdb=" O VAL A1232 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N ALA A1234 " --> pdb=" O VAL A1132 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ARG A1134 " --> pdb=" O ALA A1234 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1255 through 1258 Processing sheet with id=AC1, first strand: chain 'A' and resid 1255 through 1258 removed outlier: 3.836A pdb=" N ARG A1292 " --> pdb=" O GLU A1282 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1416 through 1417 497 hydrogen bonds defined for protein. 1368 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 5 stacking parallelities Total time for adding SS restraints: 3.29 Time building geometry restraints manager: 1.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3223 1.33 - 1.45: 3177 1.45 - 1.57: 7719 1.57 - 1.69: 83 1.69 - 1.81: 56 Bond restraints: 14258 Sorted by residual: bond pdb=" C ASP A 933 " pdb=" N ILE A 934 " ideal model delta sigma weight residual 1.335 1.317 0.018 1.41e-02 5.03e+03 1.55e+00 bond pdb=" C GLY A1115 " pdb=" O GLY A1115 " ideal model delta sigma weight residual 1.237 1.225 0.012 9.70e-03 1.06e+04 1.44e+00 bond pdb=" C LYS A 976 " pdb=" O LYS A 976 " ideal model delta sigma weight residual 1.249 1.240 0.009 8.50e-03 1.38e+04 1.06e+00 bond pdb=" CA PHE A 131 " pdb=" CB PHE A 131 " ideal model delta sigma weight residual 1.531 1.500 0.031 3.28e-02 9.30e+02 8.84e-01 bond pdb=" CA ILE A1470 " pdb=" CB ILE A1470 " ideal model delta sigma weight residual 1.537 1.525 0.012 1.29e-02 6.01e+03 8.81e-01 ... (remaining 14253 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.23: 17961 1.23 - 2.45: 1097 2.45 - 3.68: 250 3.68 - 4.90: 73 4.90 - 6.13: 16 Bond angle restraints: 19397 Sorted by residual: angle pdb=" N GLY A1472 " pdb=" CA GLY A1472 " pdb=" C GLY A1472 " ideal model delta sigma weight residual 110.29 115.52 -5.23 1.28e+00 6.10e-01 1.67e+01 angle pdb=" N LYS A 911 " pdb=" CA LYS A 911 " pdb=" C LYS A 911 " ideal model delta sigma weight residual 114.56 109.74 4.82 1.27e+00 6.20e-01 1.44e+01 angle pdb=" N ASN A1252 " pdb=" CA ASN A1252 " pdb=" C ASN A1252 " ideal model delta sigma weight residual 110.91 115.25 -4.34 1.17e+00 7.31e-01 1.38e+01 angle pdb=" C PRO A1435 " pdb=" N GLU A1436 " pdb=" CA GLU A1436 " ideal model delta sigma weight residual 121.54 127.58 -6.04 1.91e+00 2.74e-01 1.00e+01 angle pdb=" C2' G C 45 " pdb=" C1' G C 45 " pdb=" N9 G C 45 " ideal model delta sigma weight residual 112.40 118.53 -6.13 2.00e+00 2.50e-01 9.38e+00 ... (remaining 19392 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.20: 8041 29.20 - 58.41: 399 58.41 - 87.61: 75 87.61 - 116.82: 5 116.82 - 146.02: 1 Dihedral angle restraints: 8521 sinusoidal: 3926 harmonic: 4595 Sorted by residual: dihedral pdb=" C4' U C 49 " pdb=" C3' U C 49 " pdb=" C2' U C 49 " pdb=" C1' U C 49 " ideal model delta sinusoidal sigma weight residual 36.35 -38.11 74.46 1 3.10e+00 1.04e-01 7.31e+02 dihedral pdb=" C4' A C 17 " pdb=" C3' A C 17 " pdb=" C2' A C 17 " pdb=" C1' A C 17 " ideal model delta sinusoidal sigma weight residual 36.34 -38.00 74.35 1 3.10e+00 1.04e-01 7.29e+02 dihedral pdb=" C4' A C 33 " pdb=" C3' A C 33 " pdb=" C2' A C 33 " pdb=" C1' A C 33 " ideal model delta sinusoidal sigma weight residual 36.34 -37.89 74.23 1 3.10e+00 1.04e-01 7.28e+02 ... (remaining 8518 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1730 0.061 - 0.122: 238 0.122 - 0.183: 28 0.183 - 0.244: 40 0.244 - 0.305: 44 Chirality restraints: 2080 Sorted by residual: chirality pdb=" C2' U C 49 " pdb=" C3' U C 49 " pdb=" O2' U C 49 " pdb=" C1' U C 49 " both_signs ideal model delta sigma weight residual False -2.79 -2.48 -0.30 2.00e-01 2.50e+01 2.32e+00 chirality pdb=" P U C 27 " pdb=" OP1 U C 27 " pdb=" OP2 U C 27 " pdb=" O5' U C 27 " both_signs ideal model delta sigma weight residual True 2.17 -2.48 -0.30 2.00e-01 2.50e+01 2.31e+00 chirality pdb=" C3' A C 28 " pdb=" C4' A C 28 " pdb=" O3' A C 28 " pdb=" C2' A C 28 " both_signs ideal model delta sigma weight residual False -2.50 -2.80 0.30 2.00e-01 2.50e+01 2.23e+00 ... (remaining 2077 not shown) Planarity restraints: 2367 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G C 45 " 0.047 2.00e-02 2.50e+03 2.11e-02 1.34e+01 pdb=" N9 G C 45 " -0.053 2.00e-02 2.50e+03 pdb=" C8 G C 45 " -0.003 2.00e-02 2.50e+03 pdb=" N7 G C 45 " 0.002 2.00e-02 2.50e+03 pdb=" C5 G C 45 " 0.002 2.00e-02 2.50e+03 pdb=" C6 G C 45 " 0.006 2.00e-02 2.50e+03 pdb=" O6 G C 45 " 0.012 2.00e-02 2.50e+03 pdb=" N1 G C 45 " 0.002 2.00e-02 2.50e+03 pdb=" C2 G C 45 " -0.003 2.00e-02 2.50e+03 pdb=" N2 G C 45 " -0.001 2.00e-02 2.50e+03 pdb=" N3 G C 45 " -0.005 2.00e-02 2.50e+03 pdb=" C4 G C 45 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 957 " 0.029 5.00e-02 4.00e+02 4.39e-02 3.08e+00 pdb=" N PRO A 958 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 958 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 958 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A1684 " 0.029 5.00e-02 4.00e+02 4.33e-02 3.00e+00 pdb=" N PRO A1685 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO A1685 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A1685 " 0.024 5.00e-02 4.00e+02 ... (remaining 2364 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 303 2.67 - 3.23: 13187 3.23 - 3.79: 20312 3.79 - 4.34: 27173 4.34 - 4.90: 44303 Nonbonded interactions: 105278 Sorted by model distance: nonbonded pdb=" O CYS A 745 " pdb="ZN ZN A1703 " model vdw 2.113 2.230 nonbonded pdb=" NH1 ARG A 723 " pdb=" OP1 A C 32 " model vdw 2.189 3.120 nonbonded pdb=" O GLU A1455 " pdb=" O2' C C 42 " model vdw 2.190 3.040 nonbonded pdb=" O PRO A1668 " pdb=" OG1 THR A1671 " model vdw 2.192 3.040 nonbonded pdb=" O GLN A 904 " pdb=" NZ LYS A1622 " model vdw 2.195 3.120 ... (remaining 105273 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.620 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: 0.020 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 17.690 Find NCS groups from input model: 0.080 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:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 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 : 0.008 0.609 14275 Z= 0.258 Angle : 1.033 58.763 19420 Z= 0.438 Chirality : 0.065 0.305 2080 Planarity : 0.004 0.044 2367 Dihedral : 17.360 146.019 5572 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % 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 are not related in a simple way. whole: -2.43 (0.18), residues: 1582 helix: -1.05 (0.21), residues: 453 sheet: -1.35 (0.29), residues: 262 loop : -2.03 (0.19), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 464 TYR 0.014 0.001 TYR A 644 PHE 0.022 0.001 PHE A1085 TRP 0.017 0.001 TRP A1030 HIS 0.005 0.001 HIS A 781 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.20 (14258) covalent geometry : angle 0.72998 / 0.41 (19397) SS BOND : bond 0.00095 / 0.05 ( 1) SS BOND : angle 0.34035 / 0.19 ( 2) hydrogen bonds : bond 0.17093 / 10.49 ( 447) hydrogen bonds : angle 6.34465 / 4.36 ( 1368) metal coordination : bond 0.18743 / 13.78 ( 16) metal coordination : angle 22.23980 / 13.47 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.601 Fit side-chains revert: symmetry clash REVERT: A 874 MET cc_start: 0.9169 (mtm) cc_final: 0.8432 (mtp) outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.1471 time to fit residues: 10.6055 Evaluate side-chains 28 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.0270 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.5242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 28 HIS A 264 HIS A 282 ASN A 323 HIS A 610 ASN A 866 ASN A1033 ASN A1076 ASN A1140 ASN A1207 GLN ** A1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1252 ASN A1487 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.124057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.074716 restraints weight = 37397.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.076683 restraints weight = 19412.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.077865 restraints weight = 13736.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.078416 restraints weight = 11411.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 58)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.078836 restraints weight = 10443.660| |-----------------------------------------------------------------------------| r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.1181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 14275 Z= 0.194 Angle : 1.034 27.350 19420 Z= 0.430 Chirality : 0.105 1.516 2080 Planarity : 0.004 0.043 2367 Dihedral : 13.417 146.827 2257 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.92 % Allowed : 8.49 % Favored : 90.59 % 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 are not related in a simple way. whole: -1.38 (0.20), residues: 1582 helix: 0.25 (0.24), residues: 452 sheet: -1.14 (0.29), residues: 273 loop : -1.49 (0.20), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 471 TYR 0.012 0.001 TYR A 644 PHE 0.017 0.001 PHE A1353 TRP 0.012 0.001 TRP A1030 HIS 0.006 0.001 HIS A 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.19 (14258) covalent geometry : angle 1.02122 / 0.43 (19397) SS BOND : bond 0.00097 / 0.05 ( 1) SS BOND : angle 0.44361 / 0.24 ( 2) hydrogen bonds : bond 0.04199 / 2.72 ( 447) hydrogen bonds : angle 5.03612 / 3.46 ( 1368) metal coordination : bond 0.02340 / 1.68 ( 16) metal coordination : angle 5.11106 / 3.20 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 36 time to evaluate : 0.506 Fit side-chains revert: symmetry clash REVERT: A 31 MET cc_start: 0.9253 (tpp) cc_final: 0.8969 (tpp) REVERT: A 583 MET cc_start: 0.8731 (mmm) cc_final: 0.7510 (mmm) REVERT: A 825 PHE cc_start: 0.8974 (OUTLIER) cc_final: 0.8468 (m-10) REVERT: A 874 MET cc_start: 0.9011 (mtm) cc_final: 0.8322 (mtp) REVERT: A 1054 ASN cc_start: 0.2327 (OUTLIER) cc_final: 0.2123 (p0) REVERT: A 1458 ARG cc_start: 0.8331 (mmm160) cc_final: 0.8031 (mmm-85) outliers start: 13 outliers final: 3 residues processed: 45 average time/residue: 0.1257 time to fit residues: 8.8691 Evaluate side-chains 34 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 29 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 652 CYS Chi-restraints excluded: chain A residue 825 PHE Chi-restraints excluded: chain A residue 871 PHE Chi-restraints excluded: chain A residue 1039 TYR Chi-restraints excluded: chain A residue 1054 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 17 optimal weight: 3.9990 chunk 113 optimal weight: 30.0000 chunk 99 optimal weight: 5.9990 chunk 120 optimal weight: 20.0000 chunk 131 optimal weight: 6.9990 chunk 77 optimal weight: 4.9990 chunk 156 optimal weight: 7.9990 chunk 76 optimal weight: 5.9990 chunk 45 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.121699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.072680 restraints weight = 37826.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.074441 restraints weight = 19995.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.075539 restraints weight = 14303.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.076061 restraints weight = 11993.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.076446 restraints weight = 11003.602| |-----------------------------------------------------------------------------| r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 14275 Z= 0.305 Angle : 0.910 15.321 19420 Z= 0.403 Chirality : 0.083 0.945 2080 Planarity : 0.004 0.050 2367 Dihedral : 14.248 152.193 2257 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 1.20 % Allowed : 11.32 % Favored : 87.47 % 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 are not related in a simple way. whole: -1.20 (0.20), residues: 1582 helix: 0.58 (0.24), residues: 441 sheet: -1.19 (0.30), residues: 277 loop : -1.40 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 471 TYR 0.010 0.002 TYR A 644 PHE 0.021 0.002 PHE A1353 TRP 0.015 0.002 TRP A1030 HIS 0.010 0.001 HIS A 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00694 / 0.30 (14258) covalent geometry : angle 0.89477 / 0.40 (19397) SS BOND : bond 0.00148 / 0.08 ( 1) SS BOND : angle 0.57803 / 0.32 ( 2) hydrogen bonds : bond 0.04799 / 3.04 ( 447) hydrogen bonds : angle 5.16604 / 3.55 ( 1368) metal coordination : bond 0.01856 / 0.97 ( 16) metal coordination : angle 5.19952 / 3.17 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 32 time to evaluate : 0.551 Fit side-chains revert: symmetry clash REVERT: A 825 PHE cc_start: 0.9065 (OUTLIER) cc_final: 0.8604 (m-10) REVERT: A 874 MET cc_start: 0.9113 (mtm) cc_final: 0.8428 (mtp) REVERT: A 1054 ASN cc_start: 0.2129 (OUTLIER) cc_final: 0.1922 (p0) REVERT: A 1436 GLU cc_start: 0.8756 (OUTLIER) cc_final: 0.8395 (tm-30) REVERT: A 1507 MET cc_start: 0.8574 (mmm) cc_final: 0.8360 (mmm) outliers start: 17 outliers final: 7 residues processed: 47 average time/residue: 0.1206 time to fit residues: 9.0788 Evaluate side-chains 38 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 28 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 HIS Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 652 CYS Chi-restraints excluded: chain A residue 825 PHE Chi-restraints excluded: chain A residue 871 PHE Chi-restraints excluded: chain A residue 913 LYS Chi-restraints excluded: chain A residue 951 CYS Chi-restraints excluded: chain A residue 1039 TYR Chi-restraints excluded: chain A residue 1054 ASN Chi-restraints excluded: chain A residue 1436 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 117 optimal weight: 0.0030 chunk 58 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 141 optimal weight: 0.9990 chunk 43 optimal weight: 0.4980 chunk 130 optimal weight: 3.9990 chunk 101 optimal weight: 0.0980 chunk 87 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.126009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.076765 restraints weight = 37291.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.078843 restraints weight = 18893.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.080055 restraints weight = 13179.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.080621 restraints weight = 10871.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.081009 restraints weight = 9921.556| |-----------------------------------------------------------------------------| r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 14275 Z= 0.112 Angle : 0.680 10.895 19420 Z= 0.304 Chirality : 0.061 0.553 2080 Planarity : 0.004 0.047 2367 Dihedral : 13.751 162.195 2257 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.92 % Allowed : 12.38 % Favored : 86.69 % 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 are not related in a simple way. whole: -0.74 (0.21), residues: 1582 helix: 0.90 (0.25), residues: 461 sheet: -0.85 (0.30), residues: 277 loop : -1.15 (0.21), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 101 TYR 0.011 0.001 TYR A 644 PHE 0.018 0.001 PHE A1353 TRP 0.011 0.001 TRP A1030 HIS 0.005 0.001 HIS A 781 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (14258) covalent geometry : angle 0.66882 / 0.30 (19397) SS BOND : bond 0.00044 / 0.02 ( 1) SS BOND : angle 0.30729 / 0.17 ( 2) hydrogen bonds : bond 0.03035 / 2.01 ( 447) hydrogen bonds : angle 4.51527 / 3.12 ( 1368) metal coordination : bond 0.02130 / 1.20 ( 16) metal coordination : angle 3.73276 / 2.40 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 34 time to evaluate : 0.518 Fit side-chains revert: symmetry clash REVERT: A 223 ASP cc_start: 0.8429 (p0) cc_final: 0.8226 (p0) REVERT: A 825 PHE cc_start: 0.8961 (OUTLIER) cc_final: 0.8478 (m-10) REVERT: A 874 MET cc_start: 0.9062 (mtm) cc_final: 0.8410 (mtp) REVERT: A 1054 ASN cc_start: 0.2159 (OUTLIER) cc_final: 0.1954 (p0) REVERT: A 1436 GLU cc_start: 0.8758 (OUTLIER) cc_final: 0.8359 (tm-30) REVERT: A 1458 ARG cc_start: 0.7757 (mmm-85) cc_final: 0.7297 (mtt180) REVERT: A 1507 MET cc_start: 0.8562 (mmm) cc_final: 0.8321 (mmm) outliers start: 13 outliers final: 6 residues processed: 45 average time/residue: 0.1199 time to fit residues: 8.7160 Evaluate side-chains 37 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 28 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 652 CYS Chi-restraints excluded: chain A residue 749 MET Chi-restraints excluded: chain A residue 825 PHE Chi-restraints excluded: chain A residue 871 PHE Chi-restraints excluded: chain A residue 1039 TYR Chi-restraints excluded: chain A residue 1054 ASN Chi-restraints excluded: chain A residue 1257 SER Chi-restraints excluded: chain A residue 1436 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 2 optimal weight: 7.9990 chunk 141 optimal weight: 6.9990 chunk 76 optimal weight: 2.9990 chunk 140 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 134 optimal weight: 0.0570 chunk 85 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 150 optimal weight: 5.9990 overall best weight: 1.4104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 908 GLN ** A1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.124459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.075546 restraints weight = 37442.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.077496 restraints weight = 19147.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.078740 restraints weight = 13391.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.079306 restraints weight = 11055.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.079680 restraints weight = 10055.812| |-----------------------------------------------------------------------------| r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14275 Z= 0.158 Angle : 0.683 10.297 19420 Z= 0.306 Chirality : 0.062 0.569 2080 Planarity : 0.004 0.049 2367 Dihedral : 13.924 172.090 2257 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.13 % Allowed : 13.16 % Favored : 85.70 % 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 are not related in a simple way. whole: -0.62 (0.21), residues: 1582 helix: 1.08 (0.25), residues: 461 sheet: -0.80 (0.30), residues: 277 loop : -1.12 (0.21), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 471 TYR 0.009 0.001 TYR A 644 PHE 0.017 0.001 PHE A1353 TRP 0.011 0.001 TRP A1030 HIS 0.005 0.001 HIS A 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 (14258) covalent geometry : angle 0.67055 / 0.31 (19397) SS BOND : bond 0.00065 / 0.03 ( 1) SS BOND : angle 0.37592 / 0.21 ( 2) hydrogen bonds : bond 0.03454 / 2.23 ( 447) hydrogen bonds : angle 4.53282 / 3.12 ( 1368) metal coordination : bond 0.01345 / 0.82 ( 16) metal coordination : angle 3.98165 / 2.56 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 29 time to evaluate : 0.506 Fit side-chains revert: symmetry clash REVERT: A 31 MET cc_start: 0.9158 (tpp) cc_final: 0.8934 (tpp) REVERT: A 223 ASP cc_start: 0.8330 (p0) cc_final: 0.8081 (p0) REVERT: A 825 PHE cc_start: 0.8979 (OUTLIER) cc_final: 0.8575 (m-10) REVERT: A 874 MET cc_start: 0.9080 (mtm) cc_final: 0.8419 (mtp) REVERT: A 1054 ASN cc_start: 0.2034 (OUTLIER) cc_final: 0.1805 (p0) REVERT: A 1436 GLU cc_start: 0.8766 (OUTLIER) cc_final: 0.8335 (tm-30) REVERT: A 1458 ARG cc_start: 0.7708 (mmm-85) cc_final: 0.7178 (mtt180) REVERT: A 1507 MET cc_start: 0.8451 (mmm) cc_final: 0.8175 (mmm) outliers start: 16 outliers final: 6 residues processed: 42 average time/residue: 0.1193 time to fit residues: 8.0585 Evaluate side-chains 38 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 29 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 652 CYS Chi-restraints excluded: chain A residue 749 MET Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 825 PHE Chi-restraints excluded: chain A residue 871 PHE Chi-restraints excluded: chain A residue 1039 TYR Chi-restraints excluded: chain A residue 1054 ASN Chi-restraints excluded: chain A residue 1257 SER Chi-restraints excluded: chain A residue 1436 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 25 optimal weight: 0.0030 chunk 77 optimal weight: 0.4980 chunk 96 optimal weight: 0.9980 chunk 137 optimal weight: 0.6980 chunk 36 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 151 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 92 optimal weight: 7.9990 overall best weight: 0.8392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.125886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.076716 restraints weight = 37220.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.078826 restraints weight = 18684.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.079900 restraints weight = 12890.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.080680 restraints weight = 10712.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.080992 restraints weight = 9688.873| |-----------------------------------------------------------------------------| r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14275 Z= 0.113 Angle : 0.628 9.047 19420 Z= 0.285 Chirality : 0.058 0.542 2080 Planarity : 0.003 0.049 2367 Dihedral : 13.884 177.692 2257 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.92 % Allowed : 13.59 % Favored : 85.49 % 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 are not related in a simple way. whole: -0.41 (0.21), residues: 1582 helix: 1.26 (0.25), residues: 461 sheet: -0.65 (0.30), residues: 283 loop : -1.00 (0.21), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 471 TYR 0.009 0.001 TYR A 644 PHE 0.016 0.001 PHE A1353 TRP 0.010 0.001 TRP A1030 HIS 0.005 0.001 HIS A 781 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 (14258) covalent geometry : angle 0.61873 / 0.28 (19397) SS BOND : bond 0.00033 / 0.02 ( 1) SS BOND : angle 0.27783 / 0.15 ( 2) hydrogen bonds : bond 0.02981 / 1.95 ( 447) hydrogen bonds : angle 4.35385 / 3.01 ( 1368) metal coordination : bond 0.01152 / 0.83 ( 16) metal coordination : angle 3.25014 / 2.10 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 28 time to evaluate : 0.522 Fit side-chains revert: symmetry clash REVERT: A 223 ASP cc_start: 0.8327 (p0) cc_final: 0.8095 (p0) REVERT: A 583 MET cc_start: 0.8792 (mmm) cc_final: 0.8576 (mmm) REVERT: A 825 PHE cc_start: 0.8929 (OUTLIER) cc_final: 0.8546 (m-10) REVERT: A 874 MET cc_start: 0.9046 (mtm) cc_final: 0.8404 (mtp) REVERT: A 1032 MET cc_start: 0.6751 (mmp) cc_final: 0.6465 (mmp) REVERT: A 1436 GLU cc_start: 0.8689 (OUTLIER) cc_final: 0.8264 (tm-30) REVERT: A 1458 ARG cc_start: 0.7585 (mmm-85) cc_final: 0.7137 (mtt180) REVERT: A 1507 MET cc_start: 0.8522 (mmm) cc_final: 0.8263 (mmm) outliers start: 13 outliers final: 6 residues processed: 39 average time/residue: 0.1124 time to fit residues: 7.2154 Evaluate side-chains 35 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 27 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 749 MET Chi-restraints excluded: chain A residue 825 PHE Chi-restraints excluded: chain A residue 871 PHE Chi-restraints excluded: chain A residue 1039 TYR Chi-restraints excluded: chain A residue 1257 SER Chi-restraints excluded: chain A residue 1436 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 94 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 152 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 83 optimal weight: 0.0980 chunk 100 optimal weight: 6.9990 chunk 51 optimal weight: 4.9990 chunk 99 optimal weight: 9.9990 chunk 162 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 overall best weight: 3.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 668 GLN ** A1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.122464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.073523 restraints weight = 37810.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.075206 restraints weight = 19564.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.076221 restraints weight = 13842.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.076866 restraints weight = 11608.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.077010 restraints weight = 10559.837| |-----------------------------------------------------------------------------| r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 14275 Z= 0.300 Angle : 0.818 13.114 19420 Z= 0.369 Chirality : 0.069 0.698 2080 Planarity : 0.004 0.050 2367 Dihedral : 14.186 178.262 2257 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 0.99 % Allowed : 14.37 % Favored : 84.64 % 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 are not related in a simple way. whole: -0.55 (0.21), residues: 1582 helix: 1.25 (0.25), residues: 447 sheet: -0.78 (0.31), residues: 273 loop : -1.10 (0.21), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 471 TYR 0.013 0.002 TYR A 616 PHE 0.018 0.002 PHE A1353 TRP 0.016 0.002 TRP A1030 HIS 0.009 0.001 HIS A 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00685 / 0.30 (14258) covalent geometry : angle 0.80304 / 0.37 (19397) SS BOND : bond 0.00102 / 0.05 ( 1) SS BOND : angle 0.43635 / 0.24 ( 2) hydrogen bonds : bond 0.04412 / 2.80 ( 447) hydrogen bonds : angle 4.83446 / 3.33 ( 1368) metal coordination : bond 0.01786 / 0.92 ( 16) metal coordination : angle 4.75229 / 3.08 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 29 time to evaluate : 0.551 Fit side-chains revert: symmetry clash REVERT: A 223 ASP cc_start: 0.8282 (p0) cc_final: 0.8066 (p0) REVERT: A 825 PHE cc_start: 0.9069 (OUTLIER) cc_final: 0.8591 (m-10) REVERT: A 874 MET cc_start: 0.9087 (mtm) cc_final: 0.8407 (mtp) REVERT: A 1436 GLU cc_start: 0.8779 (OUTLIER) cc_final: 0.8475 (tm-30) REVERT: A 1458 ARG cc_start: 0.7585 (mmm-85) cc_final: 0.7006 (mtt180) outliers start: 14 outliers final: 9 residues processed: 41 average time/residue: 0.1125 time to fit residues: 7.5560 Evaluate side-chains 38 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 27 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 652 CYS Chi-restraints excluded: chain A residue 749 MET Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 825 PHE Chi-restraints excluded: chain A residue 871 PHE Chi-restraints excluded: chain A residue 1039 TYR Chi-restraints excluded: chain A residue 1257 SER Chi-restraints excluded: chain A residue 1436 GLU Chi-restraints excluded: chain A residue 1564 THR Chi-restraints excluded: chain A residue 1596 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 121 optimal weight: 20.0000 chunk 83 optimal weight: 3.9990 chunk 145 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 124 optimal weight: 7.9990 chunk 34 optimal weight: 0.0030 chunk 146 optimal weight: 0.8980 chunk 149 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 overall best weight: 0.7792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.125720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.076699 restraints weight = 37245.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.078624 restraints weight = 18818.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.079682 restraints weight = 13151.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.080423 restraints weight = 10968.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.080589 restraints weight = 9976.498| |-----------------------------------------------------------------------------| r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14275 Z= 0.113 Angle : 0.638 8.976 19420 Z= 0.290 Chirality : 0.059 0.557 2080 Planarity : 0.003 0.049 2367 Dihedral : 13.943 179.205 2257 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.57 % Allowed : 14.72 % Favored : 84.71 % 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 are not related in a simple way. whole: -0.41 (0.21), residues: 1582 helix: 1.33 (0.25), residues: 462 sheet: -0.68 (0.30), residues: 283 loop : -1.04 (0.21), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 471 TYR 0.009 0.001 TYR A 644 PHE 0.015 0.001 PHE A1353 TRP 0.012 0.001 TRP A1030 HIS 0.004 0.001 HIS A 781 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 (14258) covalent geometry : angle 0.62960 / 0.29 (19397) SS BOND : bond 0.00040 / 0.02 ( 1) SS BOND : angle 0.16977 / 0.09 ( 2) hydrogen bonds : bond 0.03092 / 2.02 ( 447) hydrogen bonds : angle 4.43684 / 3.07 ( 1368) metal coordination : bond 0.01079 / 0.77 ( 16) metal coordination : angle 3.23423 / 2.06 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 29 time to evaluate : 0.544 Fit side-chains revert: symmetry clash REVERT: A 31 MET cc_start: 0.9086 (tpp) cc_final: 0.8856 (tpp) REVERT: A 223 ASP cc_start: 0.8399 (p0) cc_final: 0.8125 (p0) REVERT: A 825 PHE cc_start: 0.8976 (OUTLIER) cc_final: 0.8461 (m-10) REVERT: A 874 MET cc_start: 0.9069 (mtm) cc_final: 0.8426 (mtp) REVERT: A 1032 MET cc_start: 0.6680 (mmp) cc_final: 0.5714 (mmm) REVERT: A 1436 GLU cc_start: 0.8758 (OUTLIER) cc_final: 0.8267 (tm-30) REVERT: A 1458 ARG cc_start: 0.7476 (mmm-85) cc_final: 0.6890 (mtt180) REVERT: A 1507 MET cc_start: 0.8583 (mmm) cc_final: 0.8304 (mmm) REVERT: A 1633 LYS cc_start: 0.8908 (mmmt) cc_final: 0.8705 (mmmt) outliers start: 8 outliers final: 4 residues processed: 35 average time/residue: 0.1403 time to fit residues: 7.7446 Evaluate side-chains 35 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 29 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 749 MET Chi-restraints excluded: chain A residue 825 PHE Chi-restraints excluded: chain A residue 871 PHE Chi-restraints excluded: chain A residue 1039 TYR Chi-restraints excluded: chain A residue 1257 SER Chi-restraints excluded: chain A residue 1436 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 132 optimal weight: 0.0170 chunk 159 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 65 optimal weight: 5.9990 chunk 100 optimal weight: 9.9990 chunk 3 optimal weight: 3.9990 chunk 15 optimal weight: 0.3980 chunk 79 optimal weight: 3.9990 chunk 39 optimal weight: 0.5980 chunk 148 optimal weight: 0.0770 chunk 126 optimal weight: 0.5980 overall best weight: 0.3376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 668 GLN ** A 742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1616 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.127779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.079026 restraints weight = 37137.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.081011 restraints weight = 18503.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.082198 restraints weight = 12774.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.082805 restraints weight = 10578.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.083197 restraints weight = 9616.534| |-----------------------------------------------------------------------------| r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 14275 Z= 0.090 Angle : 0.579 9.135 19420 Z= 0.266 Chirality : 0.053 0.542 2080 Planarity : 0.003 0.052 2367 Dihedral : 13.608 177.954 2257 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.71 % Allowed : 14.79 % Favored : 84.50 % 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 are not related in a simple way. whole: -0.14 (0.21), residues: 1582 helix: 1.55 (0.25), residues: 462 sheet: -0.48 (0.31), residues: 281 loop : -0.89 (0.21), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 471 TYR 0.009 0.001 TYR A1431 PHE 0.012 0.001 PHE A1353 TRP 0.008 0.001 TRP A1030 HIS 0.005 0.000 HIS A 781 Details of bonding type rmsd/Z covalent geometry : bond 0.00199 / 0.09 (14258) covalent geometry : angle 0.57271 / 0.27 (19397) SS BOND : bond 0.00008 / 0.00 ( 1) SS BOND : angle 0.09576 / 0.05 ( 2) hydrogen bonds : bond 0.02541 / 1.69 ( 447) hydrogen bonds : angle 4.21434 / 2.91 ( 1368) metal coordination : bond 0.01109 / 0.85 ( 16) metal coordination : angle 2.66146 / 1.76 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 36 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.9080 (tpp) cc_final: 0.8818 (tpp) REVERT: A 223 ASP cc_start: 0.8458 (p0) cc_final: 0.8142 (p0) REVERT: A 749 MET cc_start: 0.8899 (OUTLIER) cc_final: 0.8460 (tmm) REVERT: A 825 PHE cc_start: 0.8794 (OUTLIER) cc_final: 0.8531 (m-10) REVERT: A 874 MET cc_start: 0.8928 (mtm) cc_final: 0.8284 (mtp) REVERT: A 1032 MET cc_start: 0.6612 (mmp) cc_final: 0.5665 (mmm) outliers start: 10 outliers final: 6 residues processed: 44 average time/residue: 0.1252 time to fit residues: 8.5623 Evaluate side-chains 38 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 30 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 749 MET Chi-restraints excluded: chain A residue 825 PHE Chi-restraints excluded: chain A residue 871 PHE Chi-restraints excluded: chain A residue 1039 TYR Chi-restraints excluded: chain A residue 1257 SER Chi-restraints excluded: chain A residue 1436 GLU Chi-restraints excluded: chain A residue 1596 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 109 optimal weight: 10.0000 chunk 46 optimal weight: 4.9990 chunk 148 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 130 optimal weight: 10.0000 chunk 79 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 49 optimal weight: 0.4980 chunk 53 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 876 ASN ** A1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.125416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.076318 restraints weight = 37280.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.078330 restraints weight = 18886.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.079410 restraints weight = 13150.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.080119 restraints weight = 10976.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.080437 restraints weight = 9979.910| |-----------------------------------------------------------------------------| r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14275 Z= 0.147 Angle : 0.641 9.654 19420 Z= 0.292 Chirality : 0.057 0.523 2080 Planarity : 0.004 0.052 2367 Dihedral : 13.701 177.640 2257 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.64 % Allowed : 14.93 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.21), residues: 1582 helix: 1.53 (0.25), residues: 467 sheet: -0.46 (0.31), residues: 276 loop : -0.93 (0.21), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 471 TYR 0.008 0.001 TYR A 644 PHE 0.014 0.001 PHE A1353 TRP 0.010 0.001 TRP A1030 HIS 0.006 0.001 HIS A 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (14258) covalent geometry : angle 0.63232 / 0.29 (19397) SS BOND : bond 0.00035 / 0.02 ( 1) SS BOND : angle 0.18180 / 0.10 ( 2) hydrogen bonds : bond 0.03170 / 2.04 ( 447) hydrogen bonds : angle 4.30165 / 2.96 ( 1368) metal coordination : bond 0.01154 / 0.74 ( 16) metal coordination : angle 3.30199 / 2.17 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 32 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.9196 (tpp) cc_final: 0.8936 (tpp) REVERT: A 210 HIS cc_start: 0.8940 (OUTLIER) cc_final: 0.8732 (t70) REVERT: A 223 ASP cc_start: 0.8471 (p0) cc_final: 0.8194 (p0) REVERT: A 825 PHE cc_start: 0.8922 (OUTLIER) cc_final: 0.8574 (m-10) REVERT: A 874 MET cc_start: 0.9049 (mtm) cc_final: 0.8434 (mtp) REVERT: A 1032 MET cc_start: 0.6660 (mmp) cc_final: 0.5651 (mmm) REVERT: A 1436 GLU cc_start: 0.8699 (OUTLIER) cc_final: 0.8312 (tm-30) outliers start: 9 outliers final: 6 residues processed: 39 average time/residue: 0.1274 time to fit residues: 7.8758 Evaluate side-chains 38 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 29 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 210 HIS Chi-restraints excluded: chain A residue 749 MET Chi-restraints excluded: chain A residue 825 PHE Chi-restraints excluded: chain A residue 871 PHE Chi-restraints excluded: chain A residue 1039 TYR Chi-restraints excluded: chain A residue 1257 SER Chi-restraints excluded: chain A residue 1436 GLU Chi-restraints excluded: chain A residue 1596 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 80 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 143 optimal weight: 0.6980 chunk 126 optimal weight: 0.0870 chunk 17 optimal weight: 0.5980 chunk 1 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 137 optimal weight: 0.8980 chunk 142 optimal weight: 0.8980 chunk 157 optimal weight: 10.0000 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.126656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.077633 restraints weight = 37133.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.079701 restraints weight = 18657.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.080910 restraints weight = 12925.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.081481 restraints weight = 10674.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.081875 restraints weight = 9728.089| |-----------------------------------------------------------------------------| r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 14275 Z= 0.099 Angle : 0.604 9.035 19420 Z= 0.275 Chirality : 0.055 0.534 2080 Planarity : 0.003 0.051 2367 Dihedral : 13.644 177.170 2257 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.78 % Allowed : 14.72 % Favored : 84.50 % 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 are not related in a simple way. whole: -0.07 (0.21), residues: 1582 helix: 1.64 (0.25), residues: 460 sheet: -0.42 (0.31), residues: 276 loop : -0.87 (0.21), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 471 TYR 0.009 0.001 TYR A1431 PHE 0.012 0.001 PHE A1353 TRP 0.009 0.001 TRP A1030 HIS 0.004 0.001 HIS A 781 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 (14258) covalent geometry : angle 0.59758 / 0.27 (19397) SS BOND : bond 0.00009 / 0.00 ( 1) SS BOND : angle 0.11333 / 0.06 ( 2) hydrogen bonds : bond 0.02795 / 1.83 ( 447) hydrogen bonds : angle 4.21717 / 2.91 ( 1368) metal coordination : bond 0.01014 / 0.74 ( 16) metal coordination : angle 2.80494 / 1.82 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2913.84 seconds wall clock time: 50 minutes 56.93 seconds (3056.93 seconds total)