Starting phenix.real_space_refine on Wed Mar 4 14:49:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d97_27257/03_2026/8d97_27257.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d97_27257/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8d97_27257/03_2026/8d97_27257.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d97_27257/03_2026/8d97_27257.map" model { file = "/net/cci-nas-00/data/ceres_data/8d97_27257/03_2026/8d97_27257.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d97_27257/03_2026/8d97_27257.cif" } 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-dev-5986/lib/python3.9/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: {'RNA': 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: 2.97, per 1000 atoms: 0.21 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: 1.20 Conformation dependent library (CDL) restraints added in 536.1 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: 1.62 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: 3.02 Time building geometry restraints manager: 1.51 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=" C3' G C 45 " pdb=" C2' G C 45 " ideal model delta sigma weight residual 1.523 1.541 -0.018 1.50e-02 4.44e+03 1.43e+00 bond pdb=" C4' G C 45 " pdb=" O4' G C 45 " ideal model delta sigma weight residual 1.451 1.434 0.017 1.50e-02 4.44e+03 1.27e+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 ... (remaining 14253 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.31: 18333 1.31 - 2.61: 905 2.61 - 3.92: 134 3.92 - 5.22: 19 5.22 - 6.53: 6 Bond angle restraints: 19397 Sorted by residual: angle pdb=" C2' G C 45 " pdb=" C1' G C 45 " pdb=" N9 G C 45 " ideal model delta sigma weight residual 112.00 118.53 -6.53 1.50e+00 4.44e-01 1.89e+01 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 ... (remaining 19392 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.82: 8347 34.82 - 69.64: 281 69.64 - 104.46: 41 104.46 - 139.28: 1 139.28 - 174.10: 3 Dihedral angle restraints: 8673 sinusoidal: 4078 harmonic: 4595 Sorted by residual: dihedral pdb=" C4' G C 26 " pdb=" C3' G C 26 " pdb=" C2' G C 26 " pdb=" C1' G C 26 " ideal model delta sinusoidal sigma weight residual -35.00 31.58 -66.58 1 8.00e+00 1.56e-02 9.04e+01 dihedral pdb=" C5' G C 26 " pdb=" C4' G C 26 " pdb=" C3' G C 26 " pdb=" O3' G C 26 " ideal model delta sinusoidal sigma weight residual 147.00 83.00 64.00 1 8.00e+00 1.56e-02 8.43e+01 dihedral pdb=" O4' C C 22 " pdb=" C1' C C 22 " pdb=" N1 C C 22 " pdb=" C2 C C 22 " ideal model delta sinusoidal sigma weight residual 200.00 55.93 144.07 1 1.50e+01 4.44e-03 7.72e+01 ... (remaining 8670 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1764 0.056 - 0.113: 271 0.113 - 0.169: 42 0.169 - 0.226: 1 0.226 - 0.282: 2 Chirality restraints: 2080 Sorted by residual: chirality pdb=" C3' G C 26 " pdb=" C4' G C 26 " pdb=" O3' G C 26 " pdb=" C2' G C 26 " both_signs ideal model delta sigma weight residual False -2.74 -2.46 -0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" C1' G C 45 " pdb=" O4' G C 45 " pdb=" C2' G C 45 " pdb=" N9 G C 45 " both_signs ideal model delta sigma weight residual False 2.46 2.19 0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" C2' G C 26 " pdb=" C3' G C 26 " pdb=" O2' G C 26 " pdb=" C1' G C 26 " both_signs ideal model delta sigma weight residual False -2.52 -2.73 0.21 2.00e-01 2.50e+01 1.14e+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: 1.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 15.490 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 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= 0.255 Angle : 0.973 58.763 19420 Z= 0.421 Chirality : 0.043 0.282 2080 Planarity : 0.004 0.044 2367 Dihedral : 17.275 174.102 5724 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 covalent geometry : bond 0.00417 (14258) covalent geometry : angle 0.64286 (19397) SS BOND : bond 0.00095 ( 1) SS BOND : angle 0.34035 ( 2) hydrogen bonds : bond 0.17093 ( 447) hydrogen bonds : angle 6.34465 ( 1368) metal coordination : bond 0.18743 ( 16) metal coordination : angle 22.23980 ( 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 : 0.495 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: 0.1442 time to fit residues: 10.2659 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 : 0.414 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3807 r_free = 0.3807 target = 0.122901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.073142 restraints weight = 37132.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.075027 restraints weight = 19377.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.076065 restraints weight = 13864.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.076577 restraints weight = 11678.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.076990 restraints weight = 10759.428| |-----------------------------------------------------------------------------| r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.0953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 14275 Z= 0.166 Angle : 0.568 12.929 19420 Z= 0.288 Chirality : 0.042 0.161 2080 Planarity : 0.004 0.043 2367 Dihedral : 15.756 170.303 2409 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 0.99 % Allowed : 8.42 % 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: -1.36 (0.20), residues: 1582 helix: 0.27 (0.24), residues: 452 sheet: -1.14 (0.29), residues: 271 loop : -1.48 (0.20), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 377 TYR 0.012 0.001 TYR A 644 PHE 0.017 0.001 PHE A1353 TRP 0.012 0.001 TRP A1030 HIS 0.005 0.001 HIS A 781 Details of bonding type rmsd covalent geometry : bond 0.00375 (14258) covalent geometry : angle 0.54133 (19397) SS BOND : bond 0.00100 ( 1) SS BOND : angle 0.47996 ( 2) hydrogen bonds : bond 0.04193 ( 447) hydrogen bonds : angle 5.01593 ( 1368) metal coordination : bond 0.02384 ( 16) metal coordination : angle 5.28604 ( 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 50 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 36 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.9240 (tpp) cc_final: 0.8937 (tpp) REVERT: A 583 MET cc_start: 0.8741 (mmm) cc_final: 0.7502 (mmm) REVERT: A 825 PHE cc_start: 0.8982 (OUTLIER) cc_final: 0.8453 (m-10) REVERT: A 874 MET cc_start: 0.9022 (mtm) cc_final: 0.8327 (mtp) outliers start: 14 outliers final: 3 residues processed: 46 average time/residue: 0.1229 time to fit residues: 8.8322 Evaluate side-chains 34 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 30 time to evaluate : 0.487 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 17 optimal weight: 2.9990 chunk 113 optimal weight: 30.0000 chunk 99 optimal weight: 5.9990 chunk 120 optimal weight: 20.0000 chunk 131 optimal weight: 8.9990 chunk 77 optimal weight: 4.9990 chunk 156 optimal weight: 10.0000 chunk 76 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1252 ASN ** A1320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.120441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.071008 restraints weight = 37851.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.072788 restraints weight = 20042.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.073790 restraints weight = 14340.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.074295 restraints weight = 12147.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.074613 restraints weight = 11187.285| |-----------------------------------------------------------------------------| r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 14275 Z= 0.316 Angle : 0.671 12.964 19420 Z= 0.339 Chirality : 0.046 0.195 2080 Planarity : 0.004 0.049 2367 Dihedral : 15.640 174.590 2409 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 1.20 % Allowed : 12.17 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 442 sheet: -1.20 (0.29), residues: 275 loop : -1.41 (0.20), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 464 TYR 0.010 0.002 TYR A 644 PHE 0.022 0.002 PHE A1353 TRP 0.016 0.002 TRP A1030 HIS 0.008 0.001 HIS A 138 Details of bonding type rmsd covalent geometry : bond 0.00717 (14258) covalent geometry : angle 0.64739 (19397) SS BOND : bond 0.00152 ( 1) SS BOND : angle 0.62295 ( 2) hydrogen bonds : bond 0.05028 ( 447) hydrogen bonds : angle 5.23632 ( 1368) metal coordination : bond 0.01982 ( 16) metal coordination : angle 5.43034 ( 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 : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 825 PHE cc_start: 0.9091 (OUTLIER) cc_final: 0.8623 (m-10) REVERT: A 874 MET cc_start: 0.9102 (mtm) cc_final: 0.8430 (mtp) REVERT: A 1436 GLU cc_start: 0.8773 (OUTLIER) cc_final: 0.8410 (tm-30) REVERT: A 1458 ARG cc_start: 0.7856 (mmt180) cc_final: 0.6939 (mmm-85) REVERT: A 1507 MET cc_start: 0.8610 (mmm) cc_final: 0.8389 (mmm) outliers start: 17 outliers final: 8 residues processed: 47 average time/residue: 0.1101 time to fit residues: 8.2030 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 : 0.517 ------------------------------------------------------------------------------- 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 770 ILE 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 1039 TYR Chi-restraints excluded: chain A residue 1257 SER 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: 8.9990 chunk 58 optimal weight: 0.7980 chunk 75 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 141 optimal weight: 4.9990 chunk 43 optimal weight: 0.5980 chunk 130 optimal weight: 6.9990 chunk 101 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 chunk 63 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1242 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 = 0.3824 r_free = 0.3824 target = 0.123764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.074143 restraints weight = 37321.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.076092 restraints weight = 19079.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.077120 restraints weight = 13382.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.077839 restraints weight = 11251.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.078123 restraints weight = 10254.743| |-----------------------------------------------------------------------------| r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14275 Z= 0.109 Angle : 0.496 9.870 19420 Z= 0.255 Chirality : 0.041 0.146 2080 Planarity : 0.004 0.047 2367 Dihedral : 15.380 173.603 2409 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.71 % Allowed : 13.59 % 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: -0.78 (0.21), residues: 1582 helix: 0.92 (0.25), residues: 455 sheet: -0.94 (0.30), residues: 274 loop : -1.16 (0.21), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1423 TYR 0.011 0.001 TYR A 644 PHE 0.018 0.001 PHE A1353 TRP 0.012 0.001 TRP A1030 HIS 0.004 0.001 HIS A 781 Details of bonding type rmsd covalent geometry : bond 0.00247 (14258) covalent geometry : angle 0.47791 (19397) SS BOND : bond 0.00076 ( 1) SS BOND : angle 0.36774 ( 2) hydrogen bonds : bond 0.03317 ( 447) hydrogen bonds : angle 4.60760 ( 1368) metal coordination : bond 0.01273 ( 16) metal coordination : angle 4.02785 ( 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 44 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 34 time to evaluate : 0.449 Fit side-chains revert: symmetry clash REVERT: A 210 HIS cc_start: 0.8972 (OUTLIER) cc_final: 0.8761 (t70) REVERT: A 583 MET cc_start: 0.8800 (mmm) cc_final: 0.7729 (mmm) REVERT: A 825 PHE cc_start: 0.9035 (OUTLIER) cc_final: 0.8535 (m-10) REVERT: A 874 MET cc_start: 0.9105 (mtm) cc_final: 0.8434 (mtp) REVERT: A 1436 GLU cc_start: 0.8782 (OUTLIER) cc_final: 0.8373 (tm-30) REVERT: A 1458 ARG cc_start: 0.7969 (mmt180) cc_final: 0.7107 (mmm-85) REVERT: A 1507 MET cc_start: 0.8564 (mmm) cc_final: 0.8317 (mmm) outliers start: 10 outliers final: 5 residues processed: 41 average time/residue: 0.1156 time to fit residues: 7.4353 Evaluate side-chains 36 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 28 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 HIS 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 951 CYS Chi-restraints excluded: chain A residue 1039 TYR 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: 5.9990 chunk 76 optimal weight: 6.9990 chunk 140 optimal weight: 7.9990 chunk 14 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 134 optimal weight: 0.9980 chunk 85 optimal weight: 0.6980 chunk 88 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 150 optimal weight: 4.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 908 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.122737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.073005 restraints weight = 37428.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.074853 restraints weight = 19382.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.075809 restraints weight = 13823.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.076492 restraints weight = 11678.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.076785 restraints weight = 10659.610| |-----------------------------------------------------------------------------| r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14275 Z= 0.146 Angle : 0.501 9.181 19420 Z= 0.257 Chirality : 0.041 0.154 2080 Planarity : 0.004 0.049 2367 Dihedral : 15.298 173.894 2409 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.20 % Allowed : 14.30 % 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: -0.58 (0.21), residues: 1582 helix: 1.15 (0.25), residues: 455 sheet: -0.82 (0.31), residues: 274 loop : -1.09 (0.21), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 467 TYR 0.010 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 covalent geometry : bond 0.00331 (14258) covalent geometry : angle 0.48424 (19397) SS BOND : bond 0.00085 ( 1) SS BOND : angle 0.40420 ( 2) hydrogen bonds : bond 0.03514 ( 447) hydrogen bonds : angle 4.56515 ( 1368) metal coordination : bond 0.01297 ( 16) metal coordination : angle 3.90903 ( 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 46 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 29 time to evaluate : 0.455 Fit side-chains revert: symmetry clash REVERT: A 825 PHE cc_start: 0.9019 (OUTLIER) cc_final: 0.8542 (m-10) REVERT: A 874 MET cc_start: 0.9105 (mtm) cc_final: 0.8430 (mtp) REVERT: A 1436 GLU cc_start: 0.8773 (OUTLIER) cc_final: 0.8338 (tm-30) REVERT: A 1458 ARG cc_start: 0.8026 (mmt180) cc_final: 0.7159 (mmm-85) REVERT: A 1507 MET cc_start: 0.8450 (mmm) cc_final: 0.8170 (mmm) outliers start: 17 outliers final: 7 residues processed: 43 average time/residue: 0.1069 time to fit residues: 7.3764 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 : 0.426 ------------------------------------------------------------------------------- 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 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 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: 3.9990 chunk 77 optimal weight: 0.0170 chunk 96 optimal weight: 3.9990 chunk 137 optimal weight: 2.9990 chunk 36 optimal weight: 0.0970 chunk 59 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 151 optimal weight: 6.9990 chunk 118 optimal weight: 8.9990 chunk 76 optimal weight: 5.9990 chunk 92 optimal weight: 6.9990 overall best weight: 1.8222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3803 r_free = 0.3803 target = 0.122533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.073224 restraints weight = 37359.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.074952 restraints weight = 19540.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.076026 restraints weight = 13950.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.076517 restraints weight = 11724.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.076884 restraints weight = 10800.748| |-----------------------------------------------------------------------------| r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14275 Z= 0.185 Angle : 0.527 9.850 19420 Z= 0.271 Chirality : 0.042 0.163 2080 Planarity : 0.004 0.050 2367 Dihedral : 15.292 173.540 2409 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 0.78 % Allowed : 15.36 % Favored : 83.86 % 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: -0.49 (0.21), residues: 1582 helix: 1.33 (0.25), residues: 443 sheet: -0.85 (0.31), residues: 275 loop : -1.03 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 467 TYR 0.009 0.001 TYR A 644 PHE 0.018 0.001 PHE A1353 TRP 0.013 0.001 TRP A1030 HIS 0.005 0.001 HIS A 781 Details of bonding type rmsd covalent geometry : bond 0.00422 (14258) covalent geometry : angle 0.51159 (19397) SS BOND : bond 0.00085 ( 1) SS BOND : angle 0.39926 ( 2) hydrogen bonds : bond 0.03685 ( 447) hydrogen bonds : angle 4.61615 ( 1368) metal coordination : bond 0.01374 ( 16) metal coordination : angle 3.94454 ( 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 38 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 27 time to evaluate : 0.500 Fit side-chains revert: symmetry clash REVERT: A 825 PHE cc_start: 0.9074 (OUTLIER) cc_final: 0.8615 (m-10) REVERT: A 874 MET cc_start: 0.9102 (mtm) cc_final: 0.8435 (mtp) REVERT: A 1436 GLU cc_start: 0.8785 (OUTLIER) cc_final: 0.8333 (tm-30) REVERT: A 1458 ARG cc_start: 0.7876 (mmt180) cc_final: 0.7009 (mmm-85) REVERT: A 1507 MET cc_start: 0.8452 (mmm) cc_final: 0.8158 (mmm) outliers start: 11 outliers final: 7 residues processed: 36 average time/residue: 0.0986 time to fit residues: 6.0436 Evaluate side-chains 36 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 27 time to evaluate : 0.509 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A residue 1564 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 94 optimal weight: 4.9990 chunk 4 optimal weight: 0.0470 chunk 152 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 83 optimal weight: 6.9990 chunk 100 optimal weight: 9.9990 chunk 51 optimal weight: 3.9990 chunk 99 optimal weight: 0.0870 chunk 162 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 overall best weight: 0.7860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3829 r_free = 0.3829 target = 0.124103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.074358 restraints weight = 37328.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.076325 restraints weight = 19058.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.077407 restraints weight = 13408.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.077901 restraints weight = 11242.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.078277 restraints weight = 10360.474| |-----------------------------------------------------------------------------| r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 14275 Z= 0.102 Angle : 0.466 8.016 19420 Z= 0.241 Chirality : 0.040 0.146 2080 Planarity : 0.003 0.051 2367 Dihedral : 15.164 173.455 2409 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 0.99 % Allowed : 15.29 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.32 (0.21), residues: 1582 helix: 1.40 (0.25), residues: 449 sheet: -0.63 (0.31), residues: 272 loop : -0.94 (0.21), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1053 TYR 0.009 0.001 TYR A 644 PHE 0.015 0.001 PHE A1353 TRP 0.010 0.001 TRP A1030 HIS 0.004 0.001 HIS A 781 Details of bonding type rmsd covalent geometry : bond 0.00234 (14258) covalent geometry : angle 0.45528 (19397) SS BOND : bond 0.00038 ( 1) SS BOND : angle 0.26677 ( 2) hydrogen bonds : bond 0.03030 ( 447) hydrogen bonds : angle 4.39138 ( 1368) metal coordination : bond 0.01116 ( 16) metal coordination : angle 3.11228 ( 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 : 0.537 Fit side-chains revert: symmetry clash REVERT: A 223 ASP cc_start: 0.8355 (p0) cc_final: 0.7560 (t70) REVERT: A 825 PHE cc_start: 0.8972 (OUTLIER) cc_final: 0.8485 (m-10) REVERT: A 874 MET cc_start: 0.9067 (mtm) cc_final: 0.8420 (mtp) REVERT: A 1436 GLU cc_start: 0.8732 (OUTLIER) cc_final: 0.8261 (tm-30) REVERT: A 1458 ARG cc_start: 0.8050 (mmt180) cc_final: 0.7178 (mmm-85) REVERT: A 1507 MET cc_start: 0.8554 (mmm) cc_final: 0.8266 (mmm) outliers start: 14 outliers final: 7 residues processed: 41 average time/residue: 0.1124 time to fit residues: 7.6466 Evaluate side-chains 36 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 27 time to evaluate : 0.486 ------------------------------------------------------------------------------- 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 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 1436 GLU Chi-restraints excluded: chain A residue 1564 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 121 optimal weight: 7.9990 chunk 83 optimal weight: 0.0970 chunk 145 optimal weight: 2.9990 chunk 17 optimal weight: 0.1980 chunk 27 optimal weight: 5.9990 chunk 95 optimal weight: 2.9990 chunk 124 optimal weight: 20.0000 chunk 34 optimal weight: 0.0010 chunk 146 optimal weight: 0.9980 chunk 149 optimal weight: 2.9990 chunk 103 optimal weight: 0.0670 overall best weight: 0.2722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3853 r_free = 0.3853 target = 0.125713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.076027 restraints weight = 36839.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.077963 restraints weight = 18871.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.078958 restraints weight = 13303.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.079636 restraints weight = 11183.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.080015 restraints weight = 10198.659| |-----------------------------------------------------------------------------| r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 14275 Z= 0.080 Angle : 0.445 6.368 19420 Z= 0.229 Chirality : 0.039 0.204 2080 Planarity : 0.003 0.051 2367 Dihedral : 15.020 174.099 2409 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 0.71 % Allowed : 15.57 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.12 (0.21), residues: 1582 helix: 1.52 (0.25), residues: 456 sheet: -0.45 (0.31), residues: 276 loop : -0.83 (0.21), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 505 TYR 0.010 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 covalent geometry : bond 0.00178 (14258) covalent geometry : angle 0.43589 (19397) SS BOND : bond 0.00019 ( 1) SS BOND : angle 0.15855 ( 2) hydrogen bonds : bond 0.02517 ( 447) hydrogen bonds : angle 4.19964 ( 1368) metal coordination : bond 0.01065 ( 16) metal coordination : angle 2.69546 ( 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 45 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 35 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 825 PHE cc_start: 0.8804 (OUTLIER) cc_final: 0.8544 (m-10) REVERT: A 874 MET cc_start: 0.8942 (mtm) cc_final: 0.8281 (mtp) REVERT: A 1458 ARG cc_start: 0.8048 (mmt180) cc_final: 0.7157 (mmm-85) outliers start: 10 outliers final: 5 residues processed: 43 average time/residue: 0.1530 time to fit residues: 9.8470 Evaluate side-chains 36 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 30 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 825 PHE Chi-restraints excluded: chain A residue 871 PHE Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1039 TYR 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: 6.9990 chunk 159 optimal weight: 0.9980 chunk 19 optimal weight: 0.0980 chunk 65 optimal weight: 5.9990 chunk 100 optimal weight: 10.0000 chunk 3 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 79 optimal weight: 3.9990 chunk 39 optimal weight: 0.5980 chunk 148 optimal weight: 0.2980 chunk 126 optimal weight: 5.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3855 r_free = 0.3855 target = 0.125479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.075609 restraints weight = 37304.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.077614 restraints weight = 19101.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.078611 restraints weight = 13423.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.079261 restraints weight = 11275.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.079652 restraints weight = 10278.157| |-----------------------------------------------------------------------------| r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 14275 Z= 0.091 Angle : 0.460 8.507 19420 Z= 0.234 Chirality : 0.039 0.141 2080 Planarity : 0.003 0.053 2367 Dihedral : 14.972 174.735 2409 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.71 % Allowed : 15.50 % Favored : 83.79 % 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: -0.03 (0.21), residues: 1582 helix: 1.58 (0.25), residues: 456 sheet: -0.32 (0.31), residues: 271 loop : -0.80 (0.21), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 476 TYR 0.008 0.001 TYR A1431 PHE 0.012 0.001 PHE A1353 TRP 0.006 0.001 TRP A1030 HIS 0.004 0.000 HIS A 781 Details of bonding type rmsd covalent geometry : bond 0.00208 (14258) covalent geometry : angle 0.44915 (19397) SS BOND : bond 0.00012 ( 1) SS BOND : angle 0.14274 ( 2) hydrogen bonds : bond 0.02745 ( 447) hydrogen bonds : angle 4.17341 ( 1368) metal coordination : bond 0.01040 ( 16) metal coordination : angle 3.09125 ( 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 43 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 33 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 825 PHE cc_start: 0.8810 (OUTLIER) cc_final: 0.8568 (m-10) REVERT: A 874 MET cc_start: 0.9012 (mtm) cc_final: 0.8417 (mtp) REVERT: A 1458 ARG cc_start: 0.8130 (mmt180) cc_final: 0.7265 (mmm-85) outliers start: 10 outliers final: 7 residues processed: 42 average time/residue: 0.1183 time to fit residues: 7.6466 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 : 0.475 ------------------------------------------------------------------------------- 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 825 PHE Chi-restraints excluded: chain A residue 871 PHE Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1039 TYR 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: 0.0370 chunk 46 optimal weight: 3.9990 chunk 148 optimal weight: 0.9980 chunk 91 optimal weight: 0.0020 chunk 69 optimal weight: 2.9990 chunk 130 optimal weight: 0.0270 chunk 79 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 overall best weight: 0.3924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3867 r_free = 0.3867 target = 0.126155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.076694 restraints weight = 37140.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.078619 restraints weight = 18659.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.079715 restraints weight = 13055.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.080444 restraints weight = 10839.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.080743 restraints weight = 9860.005| |-----------------------------------------------------------------------------| r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 14275 Z= 0.080 Angle : 0.451 6.421 19420 Z= 0.230 Chirality : 0.039 0.139 2080 Planarity : 0.003 0.053 2367 Dihedral : 14.907 174.645 2409 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.57 % Allowed : 15.57 % Favored : 83.86 % 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: 0.04 (0.21), residues: 1582 helix: 1.63 (0.25), residues: 455 sheet: -0.35 (0.31), residues: 276 loop : -0.72 (0.21), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 505 TYR 0.009 0.001 TYR A1431 PHE 0.012 0.001 PHE A1353 TRP 0.006 0.001 TRP A1030 HIS 0.004 0.000 HIS A 781 Details of bonding type rmsd covalent geometry : bond 0.00182 (14258) covalent geometry : angle 0.44220 (19397) SS BOND : bond 0.00009 ( 1) SS BOND : angle 0.14545 ( 2) hydrogen bonds : bond 0.02546 ( 447) hydrogen bonds : angle 4.09362 ( 1368) metal coordination : bond 0.01037 ( 16) metal coordination : angle 2.74906 ( 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 42 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 34 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 874 MET cc_start: 0.8959 (mtm) cc_final: 0.8285 (mtp) REVERT: A 1458 ARG cc_start: 0.8097 (mmt180) cc_final: 0.7325 (mmm-85) outliers start: 8 outliers final: 7 residues processed: 41 average time/residue: 0.1072 time to fit residues: 6.9993 Evaluate side-chains 38 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 31 time to evaluate : 0.340 ------------------------------------------------------------------------------- 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 871 PHE Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1039 TYR 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: 0.9990 chunk 23 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 143 optimal weight: 2.9990 chunk 126 optimal weight: 7.9990 chunk 17 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 68 optimal weight: 0.3980 chunk 137 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 chunk 157 optimal weight: 0.9980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3838 r_free = 0.3838 target = 0.124409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.074879 restraints weight = 37231.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.076831 restraints weight = 19041.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.077911 restraints weight = 13356.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.078436 restraints weight = 11183.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.078849 restraints weight = 10265.463| |-----------------------------------------------------------------------------| r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14275 Z= 0.121 Angle : 0.482 8.792 19420 Z= 0.244 Chirality : 0.040 0.141 2080 Planarity : 0.004 0.053 2367 Dihedral : 14.921 174.848 2409 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.78 % Allowed : 15.71 % Favored : 83.51 % 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: 0.04 (0.22), residues: 1582 helix: 1.71 (0.26), residues: 454 sheet: -0.37 (0.31), residues: 271 loop : -0.75 (0.21), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 467 TYR 0.008 0.001 TYR A 644 PHE 0.012 0.001 PHE A1353 TRP 0.007 0.001 TRP A1030 HIS 0.005 0.001 HIS A 781 Details of bonding type rmsd covalent geometry : bond 0.00277 (14258) covalent geometry : angle 0.46944 (19397) SS BOND : bond 0.00046 ( 1) SS BOND : angle 0.23729 ( 2) hydrogen bonds : bond 0.03143 ( 447) hydrogen bonds : angle 4.20856 ( 1368) metal coordination : bond 0.01066 ( 16) metal coordination : angle 3.37883 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2845.82 seconds wall clock time: 49 minutes 35.67 seconds (2975.67 seconds total)