Starting phenix.real_space_refine on Thu Feb 5 00:32:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nfu_49373/02_2026/9nfu_49373_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nfu_49373/02_2026/9nfu_49373.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9nfu_49373/02_2026/9nfu_49373_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nfu_49373/02_2026/9nfu_49373_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9nfu_49373/02_2026/9nfu_49373.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nfu_49373/02_2026/9nfu_49373.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 39 5.16 5 C 8642 2.51 5 N 2330 2.21 5 O 2459 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13470 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 12355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1794, 12355 Classifications: {'peptide': 1794} Incomplete info: {'truncation_to_alanine': 654} Link IDs: {'PTRANS': 43, 'TRANS': 1750} Chain breaks: 13 Unresolved non-hydrogen bonds: 2044 Unresolved non-hydrogen angles: 2578 Unresolved non-hydrogen dihedrals: 1588 Unresolved non-hydrogen chiralities: 178 Planarities with less than four sites: {'ARG:plan': 8, 'ASP:plan': 93, 'GLU:plan': 119, 'ASN:plan1': 46, 'GLN:plan1': 12, 'TYR:plan': 14, 'PHE:plan': 15, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 1181 Chain: "C" Number of atoms: 1115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1115 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 87} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 167} Chain breaks: 7 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 271 Unresolved non-hydrogen angles: 339 Unresolved non-hydrogen dihedrals: 212 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'GLN:plan1': 9, 'GLU:plan': 3, 'ARG:plan': 5, 'PHE:plan': 4, 'ASN:plan1': 5, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 130 Time building chain proxies: 2.94, per 1000 atoms: 0.22 Number of scatterers: 13470 At special positions: 0 Unit cell: (112.395, 109.74, 193.815, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 39 16.00 O 2459 8.00 N 2330 7.00 C 8642 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 163 " - pdb=" SG CYS C 225 " 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: 1.14 Conformation dependent library (CDL) restraints added in 725.2 milliseconds 3850 Ramachandran restraints generated. 1925 Oldfield, 0 Emsley, 1925 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3742 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 29 sheets defined 37.0% alpha, 22.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'A' and resid 5 through 14 removed outlier: 3.579A pdb=" N ASN A 14 " --> pdb=" O GLU A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 37 removed outlier: 4.064A pdb=" N ALA A 26 " --> pdb=" O ASP A 22 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N ILE A 27 " --> pdb=" O GLU A 23 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU A 28 " --> pdb=" O TYR A 24 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU A 32 " --> pdb=" O LEU A 28 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU A 33 " --> pdb=" O ASP A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 63 Processing helix chain 'A' and resid 68 through 90 removed outlier: 4.662A pdb=" N LYS A 74 " --> pdb=" O LYS A 70 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASN A 88 " --> pdb=" O LEU A 84 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ASN A 90 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 122 removed outlier: 3.723A pdb=" N ILE A 112 " --> pdb=" O ASN A 108 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASN A 113 " --> pdb=" O ASP A 109 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN A 117 " --> pdb=" O ASN A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 155 Processing helix chain 'A' and resid 156 through 158 No H-bonds generated for 'chain 'A' and resid 156 through 158' Processing helix chain 'A' and resid 167 through 197 removed outlier: 4.147A pdb=" N ARG A 173 " --> pdb=" O ASN A 169 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ASP A 181 " --> pdb=" O GLU A 177 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE A 186 " --> pdb=" O LYS A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 215 removed outlier: 3.739A pdb=" N SER A 215 " --> pdb=" O SER A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 234 removed outlier: 3.526A pdb=" N LEU A 221 " --> pdb=" O GLU A 217 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLN A 234 " --> pdb=" O ASN A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 248 Processing helix chain 'A' and resid 251 through 261 Processing helix chain 'A' and resid 264 through 280 removed outlier: 3.788A pdb=" N ILE A 274 " --> pdb=" O ASP A 270 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU A 277 " --> pdb=" O ARG A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 324 removed outlier: 3.671A pdb=" N MET A 314 " --> pdb=" O ASP A 310 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LYS A 316 " --> pdb=" O TRP A 312 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N LEU A 317 " --> pdb=" O GLU A 313 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU A 318 " --> pdb=" O MET A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 338 Processing helix chain 'A' and resid 339 through 353 removed outlier: 3.838A pdb=" N SER A 352 " --> pdb=" O SER A 348 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS A 353 " --> pdb=" O VAL A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 360 Processing helix chain 'A' and resid 393 through 419 Proline residue: A 416 - end of helix Processing helix chain 'A' and resid 423 through 439 Processing helix chain 'A' and resid 443 through 450 removed outlier: 4.030A pdb=" N GLU A 449 " --> pdb=" O ARG A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 456 removed outlier: 5.167A pdb=" N LEU A 454 " --> pdb=" O GLY A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 469 removed outlier: 4.368A pdb=" N THR A 464 " --> pdb=" O ASP A 461 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LEU A 468 " --> pdb=" O THR A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 483 removed outlier: 3.704A pdb=" N TYR A 474 " --> pdb=" O GLY A 470 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA A 475 " --> pdb=" O PRO A 471 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA A 476 " --> pdb=" O GLU A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 499 Processing helix chain 'A' and resid 500 through 502 No H-bonds generated for 'chain 'A' and resid 500 through 502' Processing helix chain 'A' and resid 523 through 539 removed outlier: 3.865A pdb=" N ALA A 529 " --> pdb=" O ALA A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 555 Processing helix chain 'A' and resid 561 through 569 removed outlier: 3.822A pdb=" N LEU A 569 " --> pdb=" O LYS A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 601 removed outlier: 4.128A pdb=" N THR A 601 " --> pdb=" O LEU A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 613 Processing helix chain 'A' and resid 667 through 683 removed outlier: 4.016A pdb=" N LEU A 681 " --> pdb=" O ALA A 677 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N LYS A 683 " --> pdb=" O ILE A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 727 removed outlier: 4.589A pdb=" N ASP A 721 " --> pdb=" O LEU A 717 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N LYS A 722 " --> pdb=" O LYS A 718 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N SER A 724 " --> pdb=" O LYS A 720 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLU A 725 " --> pdb=" O ASP A 721 " (cutoff:3.500A) Processing helix chain 'A' and resid 731 through 733 No H-bonds generated for 'chain 'A' and resid 731 through 733' Processing helix chain 'A' and resid 764 through 775 Processing helix chain 'A' and resid 793 through 809 removed outlier: 3.530A pdb=" N LEU A 797 " --> pdb=" O ASN A 793 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N THR A 799 " --> pdb=" O PRO A 795 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLN A 802 " --> pdb=" O SER A 798 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 838 removed outlier: 3.796A pdb=" N MET A 820 " --> pdb=" O GLU A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 877 Processing helix chain 'A' and resid 916 through 934 removed outlier: 3.962A pdb=" N GLU A 927 " --> pdb=" O ASN A 923 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER A 930 " --> pdb=" O THR A 926 " (cutoff:3.500A) Processing helix chain 'A' and resid 961 through 970 Processing helix chain 'A' and resid 979 through 995 removed outlier: 4.254A pdb=" N VAL A 983 " --> pdb=" O SER A 979 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN A 988 " --> pdb=" O ALA A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 1003 through 1016 removed outlier: 3.625A pdb=" N ASP A1016 " --> pdb=" O SER A1012 " (cutoff:3.500A) Processing helix chain 'A' and resid 1041 through 1051 Processing helix chain 'A' and resid 1053 through 1065 Processing helix chain 'A' and resid 1073 through 1081 removed outlier: 4.157A pdb=" N ILE A1078 " --> pdb=" O ALA A1074 " (cutoff:3.500A) Processing helix chain 'A' and resid 1083 through 1092 removed outlier: 4.473A pdb=" N GLY A1088 " --> pdb=" O GLY A1084 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N PHE A1089 " --> pdb=" O ILE A1085 " (cutoff:3.500A) Processing helix chain 'A' and resid 1119 through 1126 Processing helix chain 'A' and resid 1127 through 1132 removed outlier: 3.785A pdb=" N GLU A1132 " --> pdb=" O VAL A1129 " (cutoff:3.500A) Processing helix chain 'A' and resid 1156 through 1159 Processing helix chain 'A' and resid 1304 through 1310 removed outlier: 4.172A pdb=" N LYS A1310 " --> pdb=" O TYR A1306 " (cutoff:3.500A) Processing helix chain 'A' and resid 1347 through 1352 Processing helix chain 'A' and resid 1367 through 1372 Processing helix chain 'A' and resid 1431 through 1438 Processing helix chain 'A' and resid 1438 through 1450 Processing helix chain 'A' and resid 1557 through 1572 removed outlier: 4.454A pdb=" N ALA A1562 " --> pdb=" O GLU A1558 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLU A1563 " --> pdb=" O SER A1559 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE A1564 " --> pdb=" O GLY A1560 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLY A1572 " --> pdb=" O MET A1568 " (cutoff:3.500A) Processing helix chain 'A' and resid 1580 through 1585 Processing helix chain 'A' and resid 1587 through 1592 removed outlier: 4.333A pdb=" N SER A1591 " --> pdb=" O MET A1587 " (cutoff:3.500A) Processing helix chain 'A' and resid 1649 through 1651 No H-bonds generated for 'chain 'A' and resid 1649 through 1651' Processing helix chain 'A' and resid 1678 through 1681 Processing helix chain 'A' and resid 1682 through 1686 removed outlier: 4.092A pdb=" N SER A1685 " --> pdb=" O GLY A1682 " (cutoff:3.500A) Processing helix chain 'A' and resid 1772 through 1777 removed outlier: 4.183A pdb=" N ASN A1777 " --> pdb=" O LYS A1773 " (cutoff:3.500A) Processing helix chain 'A' and resid 1790 through 1794 Processing helix chain 'A' and resid 1866 through 1870 Processing sheet with id=AA1, first strand: chain 'A' and resid 92 through 93 removed outlier: 3.688A pdb=" N THR A 92 " --> pdb=" O ALA A 368 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 237 through 239 removed outlier: 6.218A pdb=" N ASN A 97 " --> pdb=" O MET A 283 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N LEU A 285 " --> pdb=" O ASN A 97 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N HIS A 99 " --> pdb=" O LEU A 285 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ALA A 376 " --> pdb=" O ILE A 383 " (cutoff:3.500A) removed outlier: 8.427A pdb=" N GLN A 385 " --> pdb=" O LYS A 374 " (cutoff:3.500A) removed outlier: 11.415A pdb=" N LYS A 374 " --> pdb=" O GLN A 385 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 290 through 291 removed outlier: 3.655A pdb=" N LEU A 290 " --> pdb=" O SER A 509 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 627 through 632 removed outlier: 3.777A pdb=" N GLU A 627 " --> pdb=" O ASN A 622 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N TYR A 621 " --> pdb=" O SER A 605 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N SER A 605 " --> pdb=" O TYR A 621 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ILE A 578 " --> pdb=" O LYS A 647 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N THR A 649 " --> pdb=" O ILE A 578 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N TYR A 580 " --> pdb=" O THR A 649 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N ILE A 651 " --> pdb=" O TYR A 580 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N VAL A 582 " --> pdb=" O ILE A 651 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N ILE A 646 " --> pdb=" O GLU A 692 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N ASN A 694 " --> pdb=" O ILE A 646 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LEU A 648 " --> pdb=" O ASN A 694 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N LEU A 696 " --> pdb=" O LEU A 648 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N PHE A 650 " --> pdb=" O LEU A 696 " (cutoff:3.500A) removed outlier: 8.446A pdb=" N ASN A 740 " --> pdb=" O ILE A 693 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N LEU A 695 " --> pdb=" O ASN A 740 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 627 through 632 removed outlier: 3.777A pdb=" N GLU A 627 " --> pdb=" O ASN A 622 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N TYR A 621 " --> pdb=" O SER A 605 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N SER A 605 " --> pdb=" O TYR A 621 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ILE A 578 " --> pdb=" O LYS A 647 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N THR A 649 " --> pdb=" O ILE A 578 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N TYR A 580 " --> pdb=" O THR A 649 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N ILE A 651 " --> pdb=" O TYR A 580 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N VAL A 582 " --> pdb=" O ILE A 651 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N ILE A 646 " --> pdb=" O GLU A 692 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N ASN A 694 " --> pdb=" O ILE A 646 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LEU A 648 " --> pdb=" O ASN A 694 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N LEU A 696 " --> pdb=" O LEU A 648 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N PHE A 650 " --> pdb=" O LEU A 696 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ILE A 691 " --> pdb=" O ILE A 736 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ILE A 735 " --> pdb=" O PHE A 780 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N PHE A 780 " --> pdb=" O ILE A 735 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS A 786 " --> pdb=" O ASN A 781 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 744 through 746 Processing sheet with id=AA7, first strand: chain 'A' and resid 882 through 889 removed outlier: 6.583A pdb=" N SER A 885 " --> pdb=" O ILE A 901 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N ILE A 901 " --> pdb=" O SER A 885 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N GLU A 887 " --> pdb=" O ARG A 899 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1067 through 1068 removed outlier: 7.444A pdb=" N ASN A1524 " --> pdb=" O LEU A1543 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N LEU A1543 " --> pdb=" O ASN A1524 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N LYS A1536 " --> pdb=" O LEU A1556 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N LEU A1556 " --> pdb=" O LYS A1536 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N SER A1538 " --> pdb=" O VAL A1554 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N VAL A1554 " --> pdb=" O SER A1538 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N SER A1540 " --> pdb=" O ASN A1552 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N THR A1548 " --> pdb=" O GLN A1544 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE A1549 " --> pdb=" O ILE A1604 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1530 through 1532 removed outlier: 7.015A pdb=" N LYS A1536 " --> pdb=" O LEU A1556 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N LEU A1556 " --> pdb=" O LYS A1536 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N SER A1538 " --> pdb=" O VAL A1554 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N VAL A1554 " --> pdb=" O SER A1538 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N SER A1540 " --> pdb=" O ASN A1552 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N THR A1548 " --> pdb=" O GLN A1544 " (cutoff:3.500A) removed outlier: 8.740A pdb=" N SER A1612 " --> pdb=" O ASN A1552 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N VAL A1554 " --> pdb=" O SER A1612 " (cutoff:3.500A) removed outlier: 8.452A pdb=" N THR A1614 " --> pdb=" O VAL A1554 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N LEU A1556 " --> pdb=" O THR A1614 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N PHE A1634 " --> pdb=" O GLU A1621 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N ILE A1623 " --> pdb=" O PRO A1632 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE A1637 " --> pdb=" O TYR A1644 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N MET A1654 " --> pdb=" O VAL A1691 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N VAL A1716 " --> pdb=" O ARG A1765 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1151 through 1155 removed outlier: 3.931A pdb=" N GLU A1153 " --> pdb=" O VAL A1162 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1227 through 1228 Processing sheet with id=AB3, first strand: chain 'A' and resid 1312 through 1313 Processing sheet with id=AB4, first strand: chain 'A' and resid 1316 through 1318 Processing sheet with id=AB5, first strand: chain 'A' and resid 1322 through 1325 removed outlier: 4.529A pdb=" N TRP A1343 " --> pdb=" O PHE A1400 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ILE A1411 " --> pdb=" O ILE A1407 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1322 through 1325 removed outlier: 4.529A pdb=" N TRP A1343 " --> pdb=" O PHE A1400 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ILE A1411 " --> pdb=" O ILE A1407 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1353 through 1357 Processing sheet with id=AB8, first strand: chain 'A' and resid 1374 through 1376 Processing sheet with id=AB9, first strand: chain 'A' and resid 1458 through 1464 removed outlier: 3.682A pdb=" N GLY A1472 " --> pdb=" O TYR A1461 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N PHE A1463 " --> pdb=" O GLU A1470 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1672 through 1676 removed outlier: 6.186A pdb=" N ILE A1673 " --> pdb=" O ASN A1702 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N THR A1704 " --> pdb=" O ILE A1673 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N PHE A1675 " --> pdb=" O THR A1704 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1813 through 1817 removed outlier: 3.517A pdb=" N GLY A1813 " --> pdb=" O ILE A1824 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 1833 through 1837 Processing sheet with id=AC4, first strand: chain 'A' and resid 1854 through 1858 Processing sheet with id=AC5, first strand: chain 'A' and resid 1876 through 1880 Processing sheet with id=AC6, first strand: chain 'A' and resid 1896 through 1897 removed outlier: 3.567A pdb=" N LYS A1905 " --> pdb=" O VAL A1897 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid -1 through 7 removed outlier: 3.612A pdb=" N THR C 78 " --> pdb=" O ASP C 73 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 57 through 60 removed outlier: 6.346A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ARG C 50 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ILE C 34 " --> pdb=" O ARG C 50 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N CYS C 96 " --> pdb=" O TRP C 111 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N TRP C 111 " --> pdb=" O CYS C 96 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ARG C 98 " --> pdb=" O ASP C 109 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 144 through 147 Processing sheet with id=AD1, first strand: chain 'C' and resid 181 through 183 Processing sheet with id=AD2, first strand: chain 'C' and resid 181 through 183 695 hydrogen bonds defined for protein. 1896 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.10 Time building geometry restraints manager: 1.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 4472 1.35 - 1.47: 3334 1.47 - 1.59: 5828 1.59 - 1.71: 0 1.71 - 1.83: 66 Bond restraints: 13700 Sorted by residual: bond pdb=" N LEU A 3 " pdb=" CA LEU A 3 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.92e+00 bond pdb=" CA GLY A1745 " pdb=" C GLY A1745 " ideal model delta sigma weight residual 1.530 1.513 0.018 1.04e-02 9.25e+03 2.91e+00 bond pdb=" N VAL C -2 " pdb=" CA VAL C -2 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.65e+00 bond pdb=" N GLY A1745 " pdb=" CA GLY A1745 " ideal model delta sigma weight residual 1.464 1.448 0.017 1.12e-02 7.97e+03 2.21e+00 bond pdb=" CG GLN A 583 " pdb=" CD GLN A 583 " ideal model delta sigma weight residual 1.516 1.482 0.034 2.50e-02 1.60e+03 1.80e+00 ... (remaining 13695 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.20: 18660 3.20 - 6.41: 59 6.41 - 9.61: 0 9.61 - 12.81: 1 12.81 - 16.01: 1 Bond angle restraints: 18721 Sorted by residual: angle pdb=" CG1 ILE A1064 " pdb=" CB ILE A1064 " pdb=" CG2 ILE A1064 " ideal model delta sigma weight residual 110.70 126.71 -16.01 3.00e+00 1.11e-01 2.85e+01 angle pdb=" C ASP A1348 " pdb=" CA ASP A1348 " pdb=" CB ASP A1348 " ideal model delta sigma weight residual 116.54 110.59 5.95 1.15e+00 7.56e-01 2.67e+01 angle pdb=" N ASN A 949 " pdb=" CA ASN A 949 " pdb=" CB ASN A 949 " ideal model delta sigma weight residual 114.17 110.03 4.14 1.14e+00 7.69e-01 1.32e+01 angle pdb=" CB MET A1143 " pdb=" CG MET A1143 " pdb=" SD MET A1143 " ideal model delta sigma weight residual 112.70 122.99 -10.29 3.00e+00 1.11e-01 1.18e+01 angle pdb=" OG1 THR A1080 " pdb=" CB THR A1080 " pdb=" CG2 THR A1080 " ideal model delta sigma weight residual 109.30 103.29 6.01 2.00e+00 2.50e-01 9.04e+00 ... (remaining 18716 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.98: 7493 16.98 - 33.96: 439 33.96 - 50.94: 96 50.94 - 67.92: 17 67.92 - 84.90: 11 Dihedral angle restraints: 8056 sinusoidal: 2281 harmonic: 5775 Sorted by residual: dihedral pdb=" CB CYS C 163 " pdb=" SG CYS C 163 " pdb=" SG CYS C 225 " pdb=" CB CYS C 225 " ideal model delta sinusoidal sigma weight residual 93.00 14.78 78.22 1 1.00e+01 1.00e-02 7.64e+01 dihedral pdb=" CA MET A1587 " pdb=" C MET A1587 " pdb=" N ASN A1588 " pdb=" CA ASN A1588 " ideal model delta harmonic sigma weight residual -180.00 -157.60 -22.40 0 5.00e+00 4.00e-02 2.01e+01 dihedral pdb=" CA THR A1704 " pdb=" C THR A1704 " pdb=" N PRO A1705 " pdb=" CA PRO A1705 " ideal model delta harmonic sigma weight residual 180.00 -160.55 -19.45 0 5.00e+00 4.00e-02 1.51e+01 ... (remaining 8053 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.329: 2244 0.329 - 0.658: 0 0.658 - 0.986: 0 0.986 - 1.315: 0 1.315 - 1.644: 1 Chirality restraints: 2245 Sorted by residual: chirality pdb=" CB ILE A1064 " pdb=" CA ILE A1064 " pdb=" CG1 ILE A1064 " pdb=" CG2 ILE A1064 " both_signs ideal model delta sigma weight residual False 2.64 1.00 1.64 2.00e-01 2.50e+01 6.75e+01 chirality pdb=" CG LEU A 584 " pdb=" CB LEU A 584 " pdb=" CD1 LEU A 584 " pdb=" CD2 LEU A 584 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 9.54e-01 chirality pdb=" CB THR A1080 " pdb=" CA THR A1080 " pdb=" OG1 THR A1080 " pdb=" CG2 THR A1080 " both_signs ideal model delta sigma weight residual False 2.55 2.72 -0.17 2.00e-01 2.50e+01 7.15e-01 ... (remaining 2242 not shown) Planarity restraints: 2436 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 643 " 0.022 5.00e-02 4.00e+02 3.39e-02 1.84e+00 pdb=" N PRO A 644 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 644 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 644 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 794 " 0.021 5.00e-02 4.00e+02 3.22e-02 1.66e+00 pdb=" N PRO A 795 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO A 795 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 795 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 303 " -0.019 5.00e-02 4.00e+02 2.91e-02 1.35e+00 pdb=" N PRO A 304 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO A 304 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 304 " -0.016 5.00e-02 4.00e+02 ... (remaining 2433 not shown) Histogram of nonbonded interaction distances: 2.41 - 2.91: 5775 2.91 - 3.41: 13449 3.41 - 3.90: 19743 3.90 - 4.40: 22012 4.40 - 4.90: 38101 Nonbonded interactions: 99080 Sorted by model distance: nonbonded pdb=" O PRO A 728 " pdb=" OG SER A 729 " model vdw 2.411 3.040 nonbonded pdb=" OG SER C 97 " pdb=" O VAL C 110 " model vdw 2.434 3.040 nonbonded pdb=" O THR A1704 " pdb=" OG1 THR A1704 " model vdw 2.455 3.040 nonbonded pdb=" O LEU A1071 " pdb=" OG1 THR A1076 " model vdw 2.510 3.040 nonbonded pdb=" O ARG A 445 " pdb=" NH1 ARG A 445 " model vdw 2.518 3.120 ... (remaining 99075 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: 9.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.620 Find NCS groups from input model: 0.060 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 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 : 0.003 0.037 13702 Z= 0.141 Angle : 0.589 16.014 18725 Z= 0.343 Chirality : 0.055 1.644 2245 Planarity : 0.003 0.034 2436 Dihedral : 12.513 84.905 4308 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.67 % Allowed : 8.54 % Favored : 90.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % 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: -0.85 (0.19), residues: 1925 helix: 0.81 (0.22), residues: 587 sheet: -1.42 (0.25), residues: 428 loop : -0.97 (0.20), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 445 TYR 0.011 0.001 TYR A 620 PHE 0.010 0.001 PHE A 172 TRP 0.008 0.001 TRP C 52 HIS 0.003 0.001 HIS A1555 Details of bonding type rmsd covalent geometry : bond 0.00273 (13700) covalent geometry : angle 0.58799 (18721) SS BOND : bond 0.00076 ( 2) SS BOND : angle 2.93494 ( 4) hydrogen bonds : bond 0.19740 ( 659) hydrogen bonds : angle 8.51757 ( 1896) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3850 Ramachandran restraints generated. 1925 Oldfield, 0 Emsley, 1925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3850 Ramachandran restraints generated. 1925 Oldfield, 0 Emsley, 1925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 100 time to evaluate : 0.551 Fit side-chains REVERT: A 137 LEU cc_start: 0.8598 (tp) cc_final: 0.8325 (tp) REVERT: A 412 ASN cc_start: 0.8461 (t0) cc_final: 0.8198 (t0) REVERT: A 447 MET cc_start: 0.8662 (tpp) cc_final: 0.8386 (mpp) REVERT: A 700 MET cc_start: 0.8936 (mmm) cc_final: 0.8613 (tpp) REVERT: A 732 GLN cc_start: 0.8168 (mt0) cc_final: 0.7878 (mm-40) REVERT: A 896 PHE cc_start: 0.6961 (p90) cc_final: 0.6680 (p90) REVERT: A 1297 PHE cc_start: 0.8083 (t80) cc_final: 0.7554 (t80) REVERT: A 1324 LEU cc_start: 0.9254 (tt) cc_final: 0.8839 (tp) outliers start: 7 outliers final: 5 residues processed: 104 average time/residue: 0.1092 time to fit residues: 17.6507 Evaluate side-chains 95 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 90 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 ASN Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 620 TYR Chi-restraints excluded: chain A residue 787 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 20.0000 chunk 194 optimal weight: 8.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 20.0000 chunk 91 optimal weight: 0.4980 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 583 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 = 0.3644 r_free = 0.3644 target = 0.101464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.070845 restraints weight = 34020.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.073077 restraints weight = 17598.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.074564 restraints weight = 11728.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.075560 restraints weight = 9072.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.076216 restraints weight = 7678.953| |-----------------------------------------------------------------------------| r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.1189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 13702 Z= 0.239 Angle : 0.613 7.668 18725 Z= 0.333 Chirality : 0.047 0.149 2245 Planarity : 0.004 0.036 2436 Dihedral : 5.539 57.856 2079 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.59 % Allowed : 9.88 % Favored : 87.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % 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: -0.90 (0.19), residues: 1925 helix: 0.78 (0.22), residues: 616 sheet: -1.29 (0.24), residues: 433 loop : -1.16 (0.20), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 445 TYR 0.022 0.002 TYR A 620 PHE 0.020 0.002 PHE A1748 TRP 0.007 0.001 TRP C 47 HIS 0.005 0.001 HIS A1555 Details of bonding type rmsd covalent geometry : bond 0.00556 (13700) covalent geometry : angle 0.61257 (18721) SS BOND : bond 0.00252 ( 2) SS BOND : angle 1.41663 ( 4) hydrogen bonds : bond 0.04900 ( 659) hydrogen bonds : angle 5.77475 ( 1896) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3850 Ramachandran restraints generated. 1925 Oldfield, 0 Emsley, 1925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3850 Ramachandran restraints generated. 1925 Oldfield, 0 Emsley, 1925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 93 time to evaluate : 0.543 Fit side-chains REVERT: A 37 MET cc_start: 0.7871 (ttm) cc_final: 0.7619 (ttm) REVERT: A 256 GLU cc_start: 0.8751 (OUTLIER) cc_final: 0.8425 (mm-30) REVERT: A 412 ASN cc_start: 0.8450 (t0) cc_final: 0.8208 (t0) REVERT: A 539 PHE cc_start: 0.8295 (OUTLIER) cc_final: 0.8070 (t80) REVERT: A 732 GLN cc_start: 0.8242 (mt0) cc_final: 0.7968 (mm-40) REVERT: A 1297 PHE cc_start: 0.8413 (t80) cc_final: 0.7772 (t80) REVERT: A 1324 LEU cc_start: 0.9288 (tt) cc_final: 0.8956 (tp) REVERT: A 1814 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.8126 (mp) outliers start: 27 outliers final: 19 residues processed: 111 average time/residue: 0.1007 time to fit residues: 17.8570 Evaluate side-chains 108 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 86 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 256 GLU Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 448 MET Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 539 PHE Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 620 TYR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 787 ILE Chi-restraints excluded: chain A residue 988 GLN Chi-restraints excluded: chain A residue 1459 ILE Chi-restraints excluded: chain A residue 1527 THR Chi-restraints excluded: chain A residue 1587 MET Chi-restraints excluded: chain A residue 1814 LEU Chi-restraints excluded: chain A residue 1852 ILE Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 212 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 128 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 131 optimal weight: 20.0000 chunk 44 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 100 optimal weight: 3.9990 chunk 186 optimal weight: 6.9990 chunk 53 optimal weight: 0.0980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 583 GLN A 853 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.105154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.074526 restraints weight = 33759.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.076906 restraints weight = 17227.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.078501 restraints weight = 11349.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.079539 restraints weight = 8691.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.080150 restraints weight = 7311.500| |-----------------------------------------------------------------------------| r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 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 : 0.002 0.028 13702 Z= 0.099 Angle : 0.492 8.823 18725 Z= 0.265 Chirality : 0.043 0.149 2245 Planarity : 0.003 0.037 2436 Dihedral : 4.685 51.865 2077 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.59 % Allowed : 10.56 % Favored : 86.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % 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: -0.42 (0.19), residues: 1925 helix: 1.23 (0.22), residues: 630 sheet: -0.96 (0.24), residues: 436 loop : -0.99 (0.20), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 165 TYR 0.011 0.001 TYR A 620 PHE 0.010 0.001 PHE A 446 TRP 0.007 0.001 TRP C 47 HIS 0.002 0.000 HIS A1555 Details of bonding type rmsd covalent geometry : bond 0.00211 (13700) covalent geometry : angle 0.49167 (18721) SS BOND : bond 0.00141 ( 2) SS BOND : angle 0.77524 ( 4) hydrogen bonds : bond 0.03251 ( 659) hydrogen bonds : angle 4.89430 ( 1896) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3850 Ramachandran restraints generated. 1925 Oldfield, 0 Emsley, 1925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3850 Ramachandran restraints generated. 1925 Oldfield, 0 Emsley, 1925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 109 time to evaluate : 0.603 Fit side-chains revert: symmetry clash REVERT: A 256 GLU cc_start: 0.8652 (OUTLIER) cc_final: 0.8435 (mm-30) REVERT: A 399 ILE cc_start: 0.8418 (OUTLIER) cc_final: 0.8164 (mt) REVERT: A 539 PHE cc_start: 0.8183 (OUTLIER) cc_final: 0.7981 (t80) REVERT: A 617 ILE cc_start: 0.8259 (mm) cc_final: 0.7949 (mm) REVERT: A 732 GLN cc_start: 0.8144 (mt0) cc_final: 0.7837 (mm-40) REVERT: A 1297 PHE cc_start: 0.8389 (t80) cc_final: 0.7774 (t80) REVERT: A 1331 MET cc_start: 0.6331 (ttm) cc_final: 0.5493 (tmm) outliers start: 27 outliers final: 14 residues processed: 129 average time/residue: 0.1007 time to fit residues: 20.4757 Evaluate side-chains 109 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 92 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 256 GLU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 448 MET Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 539 PHE Chi-restraints excluded: chain A residue 620 TYR Chi-restraints excluded: chain A residue 646 ILE Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 988 GLN Chi-restraints excluded: chain A residue 1459 ILE Chi-restraints excluded: chain A residue 1644 TYR Chi-restraints excluded: chain C residue 212 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 123 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 62 optimal weight: 10.0000 chunk 137 optimal weight: 5.9990 chunk 125 optimal weight: 9.9990 chunk 26 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 chunk 141 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 121 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN A 402 GLN A 583 GLN A 802 GLN A1652 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.099756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.069449 restraints weight = 34423.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.071649 restraints weight = 17607.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.073124 restraints weight = 11653.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.074080 restraints weight = 8976.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.074569 restraints weight = 7595.488| |-----------------------------------------------------------------------------| r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.060 13702 Z= 0.358 Angle : 0.708 10.361 18725 Z= 0.379 Chirality : 0.050 0.166 2245 Planarity : 0.004 0.038 2436 Dihedral : 5.555 59.252 2073 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 4.51 % Allowed : 12.28 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % 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: -1.14 (0.19), residues: 1925 helix: 0.66 (0.22), residues: 619 sheet: -1.38 (0.24), residues: 421 loop : -1.41 (0.19), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 273 TYR 0.026 0.002 TYR A 620 PHE 0.025 0.002 PHE A1748 TRP 0.007 0.001 TRP C 52 HIS 0.006 0.001 HIS A1555 Details of bonding type rmsd covalent geometry : bond 0.00838 (13700) covalent geometry : angle 0.70771 (18721) SS BOND : bond 0.00294 ( 2) SS BOND : angle 0.66528 ( 4) hydrogen bonds : bond 0.05351 ( 659) hydrogen bonds : angle 5.52188 ( 1896) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3850 Ramachandran restraints generated. 1925 Oldfield, 0 Emsley, 1925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3850 Ramachandran restraints generated. 1925 Oldfield, 0 Emsley, 1925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 88 time to evaluate : 0.552 Fit side-chains REVERT: A 256 GLU cc_start: 0.8756 (OUTLIER) cc_final: 0.8187 (mm-30) REVERT: A 447 MET cc_start: 0.8952 (tpp) cc_final: 0.8752 (tpp) REVERT: A 732 GLN cc_start: 0.8331 (mt0) cc_final: 0.7930 (mm-40) REVERT: A 1297 PHE cc_start: 0.8381 (t80) cc_final: 0.8112 (t80) REVERT: A 1331 MET cc_start: 0.6563 (ttm) cc_final: 0.5642 (tmm) REVERT: A 1644 TYR cc_start: 0.8792 (OUTLIER) cc_final: 0.8516 (m-80) REVERT: C 80 TYR cc_start: 0.7907 (OUTLIER) cc_final: 0.7695 (p90) outliers start: 47 outliers final: 33 residues processed: 126 average time/residue: 0.0995 time to fit residues: 20.0916 Evaluate side-chains 120 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 84 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 256 GLU Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 337 MET Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 448 MET Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 583 GLN Chi-restraints excluded: chain A residue 596 ASN Chi-restraints excluded: chain A residue 620 TYR Chi-restraints excluded: chain A residue 646 ILE Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 787 ILE Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 988 GLN Chi-restraints excluded: chain A residue 1032 ILE Chi-restraints excluded: chain A residue 1056 LEU Chi-restraints excluded: chain A residue 1459 ILE Chi-restraints excluded: chain A residue 1527 THR Chi-restraints excluded: chain A residue 1638 ASN Chi-restraints excluded: chain A residue 1644 TYR Chi-restraints excluded: chain A residue 1841 LEU Chi-restraints excluded: chain A residue 1852 ILE Chi-restraints excluded: chain C residue 80 TYR Chi-restraints excluded: chain C residue 212 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 161 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 96 optimal weight: 0.8980 chunk 98 optimal weight: 6.9990 chunk 135 optimal weight: 0.9990 chunk 100 optimal weight: 0.7980 chunk 131 optimal weight: 0.1980 chunk 143 optimal weight: 0.3980 chunk 64 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 192 optimal weight: 10.0000 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 583 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.107582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.077603 restraints weight = 32437.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.079946 restraints weight = 17197.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.081495 restraints weight = 11634.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.082500 restraints weight = 9063.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.083079 restraints weight = 7698.159| |-----------------------------------------------------------------------------| r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13702 Z= 0.103 Angle : 0.503 11.342 18725 Z= 0.268 Chirality : 0.044 0.257 2245 Planarity : 0.003 0.037 2436 Dihedral : 4.609 55.391 2073 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.88 % Allowed : 14.01 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % 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: -0.51 (0.19), residues: 1925 helix: 1.27 (0.22), residues: 626 sheet: -0.97 (0.24), residues: 437 loop : -1.17 (0.20), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 173 TYR 0.013 0.001 TYR A 478 PHE 0.010 0.001 PHE A1400 TRP 0.010 0.001 TRP C 52 HIS 0.002 0.000 HIS A1555 Details of bonding type rmsd covalent geometry : bond 0.00226 (13700) covalent geometry : angle 0.50338 (18721) SS BOND : bond 0.00135 ( 2) SS BOND : angle 0.44705 ( 4) hydrogen bonds : bond 0.03125 ( 659) hydrogen bonds : angle 4.64366 ( 1896) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3850 Ramachandran restraints generated. 1925 Oldfield, 0 Emsley, 1925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3850 Ramachandran restraints generated. 1925 Oldfield, 0 Emsley, 1925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 99 time to evaluate : 0.568 Fit side-chains REVERT: A 373 VAL cc_start: 0.8425 (OUTLIER) cc_final: 0.8116 (p) REVERT: A 617 ILE cc_start: 0.8303 (mm) cc_final: 0.7990 (mm) REVERT: A 1297 PHE cc_start: 0.8231 (t80) cc_final: 0.7648 (t80) REVERT: A 1331 MET cc_start: 0.6660 (ttm) cc_final: 0.5742 (tmm) REVERT: A 1507 TYR cc_start: 0.8573 (m-80) cc_final: 0.8218 (m-10) REVERT: C 80 TYR cc_start: 0.7817 (OUTLIER) cc_final: 0.7544 (p90) outliers start: 30 outliers final: 17 residues processed: 122 average time/residue: 0.1013 time to fit residues: 19.6808 Evaluate side-chains 113 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 94 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 337 MET Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 448 MET Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 539 PHE Chi-restraints excluded: chain A residue 583 GLN Chi-restraints excluded: chain A residue 620 TYR Chi-restraints excluded: chain A residue 646 ILE Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 988 GLN Chi-restraints excluded: chain A residue 1459 ILE Chi-restraints excluded: chain A residue 1542 THR Chi-restraints excluded: chain C residue 80 TYR Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 212 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 33 optimal weight: 0.8980 chunk 191 optimal weight: 0.9990 chunk 170 optimal weight: 0.4980 chunk 82 optimal weight: 0.1980 chunk 139 optimal weight: 0.2980 chunk 123 optimal weight: 0.9980 chunk 173 optimal weight: 9.9990 chunk 30 optimal weight: 0.6980 chunk 58 optimal weight: 4.9990 chunk 88 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 583 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.108331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.079068 restraints weight = 32260.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.081406 restraints weight = 20544.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.082275 restraints weight = 13749.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.082961 restraints weight = 10940.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.083126 restraints weight = 10177.584| |-----------------------------------------------------------------------------| r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 13702 Z= 0.093 Angle : 0.488 10.581 18725 Z= 0.257 Chirality : 0.043 0.249 2245 Planarity : 0.003 0.038 2436 Dihedral : 4.309 54.501 2073 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.59 % Allowed : 14.68 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % 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: -0.26 (0.19), residues: 1925 helix: 1.39 (0.22), residues: 630 sheet: -0.73 (0.25), residues: 426 loop : -1.00 (0.20), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 575 TYR 0.010 0.001 TYR A 620 PHE 0.013 0.001 PHE A 446 TRP 0.005 0.001 TRP C 52 HIS 0.002 0.000 HIS A 579 Details of bonding type rmsd covalent geometry : bond 0.00200 (13700) covalent geometry : angle 0.48758 (18721) SS BOND : bond 0.00099 ( 2) SS BOND : angle 0.34486 ( 4) hydrogen bonds : bond 0.02934 ( 659) hydrogen bonds : angle 4.45921 ( 1896) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3850 Ramachandran restraints generated. 1925 Oldfield, 0 Emsley, 1925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3850 Ramachandran restraints generated. 1925 Oldfield, 0 Emsley, 1925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 104 time to evaluate : 0.537 Fit side-chains revert: symmetry clash REVERT: A 116 ASN cc_start: 0.8182 (m110) cc_final: 0.7793 (m-40) REVERT: A 373 VAL cc_start: 0.8341 (OUTLIER) cc_final: 0.8113 (p) REVERT: A 617 ILE cc_start: 0.8305 (mm) cc_final: 0.8039 (mm) REVERT: A 1297 PHE cc_start: 0.8114 (t80) cc_final: 0.7540 (t80) REVERT: A 1331 MET cc_start: 0.6751 (ttm) cc_final: 0.5856 (tmm) REVERT: A 1507 TYR cc_start: 0.8563 (m-80) cc_final: 0.8194 (m-10) outliers start: 27 outliers final: 17 residues processed: 126 average time/residue: 0.0971 time to fit residues: 19.2818 Evaluate side-chains 113 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 95 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 337 MET Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 448 MET Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 539 PHE Chi-restraints excluded: chain A residue 583 GLN Chi-restraints excluded: chain A residue 596 ASN Chi-restraints excluded: chain A residue 620 TYR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 988 GLN Chi-restraints excluded: chain A residue 1459 ILE Chi-restraints excluded: chain A residue 1542 THR Chi-restraints excluded: chain C residue 80 TYR Chi-restraints excluded: chain C residue 212 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 25 optimal weight: 2.9990 chunk 180 optimal weight: 0.0470 chunk 139 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 142 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 chunk 137 optimal weight: 3.9990 chunk 110 optimal weight: 30.0000 chunk 154 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 103 optimal weight: 0.5980 overall best weight: 1.3282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 402 GLN A 583 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.106790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.076594 restraints weight = 32479.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.078985 restraints weight = 17174.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.080579 restraints weight = 11467.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.081610 restraints weight = 8873.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.082197 restraints weight = 7524.014| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13702 Z= 0.148 Angle : 0.520 8.633 18725 Z= 0.277 Chirality : 0.044 0.264 2245 Planarity : 0.003 0.039 2436 Dihedral : 4.447 56.545 2073 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.17 % Allowed : 14.49 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % 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: -0.27 (0.19), residues: 1925 helix: 1.39 (0.22), residues: 625 sheet: -0.78 (0.25), residues: 416 loop : -0.98 (0.20), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 499 TYR 0.013 0.001 TYR A 620 PHE 0.014 0.001 PHE A1748 TRP 0.008 0.001 TRP A 118 HIS 0.003 0.001 HIS A1555 Details of bonding type rmsd covalent geometry : bond 0.00343 (13700) covalent geometry : angle 0.52017 (18721) SS BOND : bond 0.00125 ( 2) SS BOND : angle 0.35006 ( 4) hydrogen bonds : bond 0.03396 ( 659) hydrogen bonds : angle 4.52591 ( 1896) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3850 Ramachandran restraints generated. 1925 Oldfield, 0 Emsley, 1925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3850 Ramachandran restraints generated. 1925 Oldfield, 0 Emsley, 1925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 95 time to evaluate : 0.575 Fit side-chains revert: symmetry clash REVERT: A 116 ASN cc_start: 0.8379 (m110) cc_final: 0.7919 (m110) REVERT: A 373 VAL cc_start: 0.8234 (OUTLIER) cc_final: 0.8006 (p) REVERT: A 583 GLN cc_start: 0.8208 (OUTLIER) cc_final: 0.7905 (mm110) REVERT: A 617 ILE cc_start: 0.8313 (mm) cc_final: 0.8027 (mm) REVERT: A 896 PHE cc_start: 0.7170 (OUTLIER) cc_final: 0.6636 (p90) REVERT: A 1297 PHE cc_start: 0.8288 (t80) cc_final: 0.7667 (t80) REVERT: A 1331 MET cc_start: 0.6833 (ttm) cc_final: 0.5903 (tmm) outliers start: 33 outliers final: 23 residues processed: 119 average time/residue: 0.0974 time to fit residues: 18.4205 Evaluate side-chains 117 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 91 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 322 LYS Chi-restraints excluded: chain A residue 337 MET Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 448 MET Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 583 GLN Chi-restraints excluded: chain A residue 596 ASN Chi-restraints excluded: chain A residue 620 TYR Chi-restraints excluded: chain A residue 646 ILE Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 787 ILE Chi-restraints excluded: chain A residue 896 PHE Chi-restraints excluded: chain A residue 988 GLN Chi-restraints excluded: chain A residue 1032 ILE Chi-restraints excluded: chain A residue 1459 ILE Chi-restraints excluded: chain A residue 1542 THR Chi-restraints excluded: chain C residue 80 TYR Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 212 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 13 optimal weight: 2.9990 chunk 180 optimal weight: 0.0270 chunk 121 optimal weight: 6.9990 chunk 85 optimal weight: 0.9990 chunk 123 optimal weight: 0.9980 chunk 164 optimal weight: 0.1980 chunk 32 optimal weight: 3.9990 chunk 172 optimal weight: 5.9990 chunk 165 optimal weight: 2.9990 chunk 184 optimal weight: 40.0000 chunk 40 optimal weight: 0.8980 overall best weight: 0.6240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 583 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.108890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.077940 restraints weight = 32628.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.080404 restraints weight = 17338.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.082029 restraints weight = 11629.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.083024 restraints weight = 9043.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.083763 restraints weight = 7743.586| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 13702 Z= 0.097 Angle : 0.483 9.780 18725 Z= 0.257 Chirality : 0.043 0.270 2245 Planarity : 0.003 0.039 2436 Dihedral : 4.227 55.838 2073 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.17 % Allowed : 14.97 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % 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: -0.09 (0.20), residues: 1925 helix: 1.53 (0.22), residues: 625 sheet: -0.62 (0.25), residues: 430 loop : -0.90 (0.20), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 499 TYR 0.011 0.001 TYR A 478 PHE 0.011 0.001 PHE A 446 TRP 0.007 0.001 TRP C 52 HIS 0.002 0.000 HIS A 579 Details of bonding type rmsd covalent geometry : bond 0.00216 (13700) covalent geometry : angle 0.48349 (18721) SS BOND : bond 0.00090 ( 2) SS BOND : angle 0.30099 ( 4) hydrogen bonds : bond 0.02915 ( 659) hydrogen bonds : angle 4.33579 ( 1896) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3850 Ramachandran restraints generated. 1925 Oldfield, 0 Emsley, 1925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3850 Ramachandran restraints generated. 1925 Oldfield, 0 Emsley, 1925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 98 time to evaluate : 0.549 Fit side-chains revert: symmetry clash REVERT: A 820 MET cc_start: 0.7186 (tpp) cc_final: 0.6970 (tpp) REVERT: A 896 PHE cc_start: 0.7222 (OUTLIER) cc_final: 0.6637 (p90) REVERT: A 1297 PHE cc_start: 0.8294 (t80) cc_final: 0.7686 (t80) REVERT: A 1331 MET cc_start: 0.6830 (ttm) cc_final: 0.5904 (tmm) REVERT: A 1507 TYR cc_start: 0.8564 (m-80) cc_final: 0.8145 (m-10) outliers start: 33 outliers final: 20 residues processed: 124 average time/residue: 0.0975 time to fit residues: 19.1602 Evaluate side-chains 118 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 97 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 337 MET Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 448 MET Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 539 PHE Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 596 ASN Chi-restraints excluded: chain A residue 620 TYR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 896 PHE Chi-restraints excluded: chain A residue 988 GLN Chi-restraints excluded: chain A residue 1459 ILE Chi-restraints excluded: chain A residue 1542 THR Chi-restraints excluded: chain C residue 80 TYR Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 212 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 161 optimal weight: 7.9990 chunk 122 optimal weight: 30.0000 chunk 97 optimal weight: 4.9990 chunk 87 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 128 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 41 optimal weight: 0.3980 chunk 52 optimal weight: 3.9990 chunk 165 optimal weight: 3.9990 chunk 137 optimal weight: 3.9990 overall best weight: 2.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 802 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 = 0.3665 r_free = 0.3665 target = 0.103984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.076364 restraints weight = 33626.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.076079 restraints weight = 17471.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.076706 restraints weight = 14817.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.077284 restraints weight = 12989.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.077463 restraints weight = 11531.261| |-----------------------------------------------------------------------------| r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 13702 Z= 0.272 Angle : 0.615 8.846 18725 Z= 0.329 Chirality : 0.047 0.285 2245 Planarity : 0.004 0.042 2436 Dihedral : 4.912 59.587 2073 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.88 % Allowed : 14.97 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % 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: -0.56 (0.19), residues: 1925 helix: 1.13 (0.22), residues: 623 sheet: -0.94 (0.24), residues: 422 loop : -1.13 (0.20), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 499 TYR 0.019 0.002 TYR A 620 PHE 0.022 0.002 PHE A1748 TRP 0.009 0.001 TRP A 118 HIS 0.006 0.001 HIS A1555 Details of bonding type rmsd covalent geometry : bond 0.00638 (13700) covalent geometry : angle 0.61469 (18721) SS BOND : bond 0.00197 ( 2) SS BOND : angle 0.43323 ( 4) hydrogen bonds : bond 0.04314 ( 659) hydrogen bonds : angle 4.84019 ( 1896) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3850 Ramachandran restraints generated. 1925 Oldfield, 0 Emsley, 1925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3850 Ramachandran restraints generated. 1925 Oldfield, 0 Emsley, 1925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 88 time to evaluate : 0.538 Fit side-chains REVERT: A 68 ARG cc_start: 0.8025 (OUTLIER) cc_final: 0.7588 (mtt180) REVERT: A 617 ILE cc_start: 0.8428 (mm) cc_final: 0.7995 (mm) REVERT: A 896 PHE cc_start: 0.7216 (OUTLIER) cc_final: 0.6708 (p90) REVERT: A 1297 PHE cc_start: 0.8292 (t80) cc_final: 0.7646 (t80) REVERT: A 1331 MET cc_start: 0.6993 (ttm) cc_final: 0.5976 (tmm) outliers start: 30 outliers final: 24 residues processed: 109 average time/residue: 0.1065 time to fit residues: 18.1777 Evaluate side-chains 112 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 86 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 68 ARG Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 337 MET Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 448 MET Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 596 ASN Chi-restraints excluded: chain A residue 620 TYR Chi-restraints excluded: chain A residue 646 ILE Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 787 ILE Chi-restraints excluded: chain A residue 896 PHE Chi-restraints excluded: chain A residue 988 GLN Chi-restraints excluded: chain A residue 1032 ILE Chi-restraints excluded: chain A residue 1459 ILE Chi-restraints excluded: chain A residue 1542 THR Chi-restraints excluded: chain A residue 1611 ILE Chi-restraints excluded: chain C residue 80 TYR Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 212 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 148 optimal weight: 0.5980 chunk 184 optimal weight: 0.0370 chunk 125 optimal weight: 5.9990 chunk 43 optimal weight: 0.9980 chunk 181 optimal weight: 6.9990 chunk 75 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 186 optimal weight: 2.9990 chunk 178 optimal weight: 30.0000 chunk 158 optimal weight: 0.3980 chunk 50 optimal weight: 2.9990 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.107967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.077827 restraints weight = 32436.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.080213 restraints weight = 17236.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.081820 restraints weight = 11599.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.082896 restraints weight = 8965.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.083477 restraints weight = 7606.491| |-----------------------------------------------------------------------------| r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 13702 Z= 0.097 Angle : 0.496 9.737 18725 Z= 0.262 Chirality : 0.044 0.294 2245 Planarity : 0.003 0.039 2436 Dihedral : 4.334 57.998 2073 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.02 % Allowed : 15.83 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % 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: -0.19 (0.19), residues: 1925 helix: 1.48 (0.22), residues: 631 sheet: -0.72 (0.25), residues: 424 loop : -0.98 (0.20), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 499 TYR 0.011 0.001 TYR A 478 PHE 0.013 0.001 PHE A 446 TRP 0.008 0.001 TRP C 52 HIS 0.002 0.000 HIS A1555 Details of bonding type rmsd covalent geometry : bond 0.00211 (13700) covalent geometry : angle 0.49590 (18721) SS BOND : bond 0.00104 ( 2) SS BOND : angle 0.31313 ( 4) hydrogen bonds : bond 0.02941 ( 659) hydrogen bonds : angle 4.34992 ( 1896) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3850 Ramachandran restraints generated. 1925 Oldfield, 0 Emsley, 1925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3850 Ramachandran restraints generated. 1925 Oldfield, 0 Emsley, 1925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 101 time to evaluate : 0.533 Fit side-chains revert: symmetry clash REVERT: A 596 ASN cc_start: 0.8342 (OUTLIER) cc_final: 0.8049 (t0) REVERT: A 617 ILE cc_start: 0.8359 (mm) cc_final: 0.7976 (mm) REVERT: A 896 PHE cc_start: 0.7136 (OUTLIER) cc_final: 0.6622 (p90) REVERT: A 1297 PHE cc_start: 0.8259 (t80) cc_final: 0.7595 (t80) REVERT: A 1331 MET cc_start: 0.7044 (ttm) cc_final: 0.6033 (tmm) REVERT: A 1507 TYR cc_start: 0.8595 (m-80) cc_final: 0.8175 (m-10) outliers start: 21 outliers final: 18 residues processed: 115 average time/residue: 0.0911 time to fit residues: 16.9792 Evaluate side-chains 116 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 96 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 337 MET Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 448 MET Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 596 ASN Chi-restraints excluded: chain A residue 620 TYR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 787 ILE Chi-restraints excluded: chain A residue 896 PHE Chi-restraints excluded: chain A residue 988 GLN Chi-restraints excluded: chain A residue 1459 ILE Chi-restraints excluded: chain A residue 1542 THR Chi-restraints excluded: chain C residue 80 TYR Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 212 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 100 optimal weight: 0.0370 chunk 103 optimal weight: 8.9990 chunk 180 optimal weight: 9.9990 chunk 118 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 25 optimal weight: 0.0980 chunk 15 optimal weight: 5.9990 chunk 134 optimal weight: 0.0010 chunk 102 optimal weight: 5.9990 chunk 146 optimal weight: 0.7980 chunk 150 optimal weight: 2.9990 overall best weight: 0.5866 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 108 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.108689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.078494 restraints weight = 32456.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.080909 restraints weight = 17256.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.082516 restraints weight = 11574.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.083601 restraints weight = 8954.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.084195 restraints weight = 7584.618| |-----------------------------------------------------------------------------| r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 13702 Z= 0.096 Angle : 0.484 9.414 18725 Z= 0.256 Chirality : 0.043 0.287 2245 Planarity : 0.003 0.040 2436 Dihedral : 4.130 57.703 2073 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.11 % Allowed : 16.22 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % 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: -0.06 (0.19), residues: 1925 helix: 1.59 (0.22), residues: 631 sheet: -0.58 (0.25), residues: 426 loop : -0.95 (0.20), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 499 TYR 0.009 0.001 TYR A1508 PHE 0.036 0.001 PHE A1593 TRP 0.010 0.001 TRP C 172 HIS 0.001 0.000 HIS C 35 Details of bonding type rmsd covalent geometry : bond 0.00211 (13700) covalent geometry : angle 0.48364 (18721) SS BOND : bond 0.00160 ( 2) SS BOND : angle 0.54717 ( 4) hydrogen bonds : bond 0.02862 ( 659) hydrogen bonds : angle 4.28652 ( 1896) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2484.55 seconds wall clock time: 43 minutes 30.15 seconds (2610.15 seconds total)