Starting phenix.real_space_refine on Thu Mar 5 15:19:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dl2_30708/03_2026/7dl2_30708.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dl2_30708/03_2026/7dl2_30708.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7dl2_30708/03_2026/7dl2_30708.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dl2_30708/03_2026/7dl2_30708.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7dl2_30708/03_2026/7dl2_30708.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dl2_30708/03_2026/7dl2_30708.map" } resolution = 4.4 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= 0.001 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 115 5.16 5 C 14811 2.51 5 N 4075 2.21 5 O 4284 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 100 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23285 Number of models: 1 Model: "" Number of chains: 6 Chain: "D" Number of atoms: 1575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1575 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 92} Link IDs: {'TRANS': 225} Unresolved non-hydrogen bonds: 329 Unresolved non-hydrogen angles: 412 Unresolved non-hydrogen dihedrals: 267 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'ASP:plan': 4, 'GLN:plan1': 14, 'TRP:plan': 1, 'GLU:plan': 10, 'ARG:plan': 6, 'TYR:plan': 2, 'ASN:plan1': 6, 'HIS:plan': 3, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 200 Chain: "A" Number of atoms: 9016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1127, 9016 Classifications: {'peptide': 1127} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 50, 'TRANS': 1076} Chain breaks: 9 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 7952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1042, 7952 Classifications: {'peptide': 1042} Incomplete info: {'truncation_to_alanine': 109} Link IDs: {'PTRANS': 49, 'TRANS': 992} Chain breaks: 16 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 394 Unresolved non-hydrogen angles: 510 Unresolved non-hydrogen dihedrals: 329 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'PHE:plan': 6, 'ASP:plan': 9, 'TYR:plan': 5, 'ASN:plan1': 5, 'GLU:plan': 8, 'HIS:plan': 3, 'ARG:plan': 5, 'GLN:plan1': 3, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 215 Chain: "C" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1558 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 91} Link IDs: {'TRANS': 223} Unresolved non-hydrogen bonds: 328 Unresolved non-hydrogen angles: 411 Unresolved non-hydrogen dihedrals: 266 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'ASP:plan': 4, 'GLN:plan1': 14, 'TRP:plan': 1, 'GLU:plan': 10, 'ARG:plan': 6, 'TYR:plan': 2, 'ASN:plan1': 6, 'HIS:plan': 3, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 200 Chain: "E" Number of atoms: 2169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2169 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 15, 'TRANS': 251} Chain: "F" Number of atoms: 1015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1015 Classifications: {'peptide': 203} Incomplete info: {'truncation_to_alanine': 203} Link IDs: {'TRANS': 202} Chain breaks: 8 Unresolved non-hydrogen bonds: 406 Unresolved non-hydrogen angles: 609 Unresolved non-hydrogen dihedrals: 203 Planarities with less than four sites: {'UNK:plan-1': 203} Unresolved non-hydrogen planarities: 203 Time building chain proxies: 5.01, per 1000 atoms: 0.22 Number of scatterers: 23285 At special positions: 0 Unit cell: (151.872, 402.732, 150.516, 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 115 16.00 O 4284 8.00 N 4075 7.00 C 14811 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.05 Conformation dependent library (CDL) restraints added in 1.0 seconds 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5996 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 5 sheets defined 73.7% alpha, 3.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'D' and resid 746 through 870 removed outlier: 3.809A pdb=" N TRP D 750 " --> pdb=" O ASP D 746 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N SER D 836 " --> pdb=" O SER D 832 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU D 855 " --> pdb=" O GLN D 851 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLY D 856 " --> pdb=" O LEU D 852 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU D 857 " --> pdb=" O LEU D 853 " (cutoff:3.500A) Processing helix chain 'D' and resid 874 through 970 removed outlier: 3.758A pdb=" N MET D 879 " --> pdb=" O LYS D 875 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N MET D 880 " --> pdb=" O GLU D 876 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LYS D 881 " --> pdb=" O VAL D 877 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N TYR D 884 " --> pdb=" O MET D 880 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR D 904 " --> pdb=" O GLN D 900 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER D 914 " --> pdb=" O LEU D 910 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N HIS D 915 " --> pdb=" O GLU D 911 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ALA D 917 " --> pdb=" O GLU D 913 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA D 944 " --> pdb=" O GLN D 940 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ARG D 947 " --> pdb=" O ALA D 943 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N GLU D 970 " --> pdb=" O TYR D 966 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 147 Processing helix chain 'A' and resid 153 through 163 Processing helix chain 'A' and resid 177 through 183 Processing helix chain 'A' and resid 184 through 192 removed outlier: 3.897A pdb=" N ASP A 192 " --> pdb=" O SER A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 215 removed outlier: 3.861A pdb=" N ILE A 215 " --> pdb=" O SER A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 231 Processing helix chain 'A' and resid 232 through 234 No H-bonds generated for 'chain 'A' and resid 232 through 234' Processing helix chain 'A' and resid 241 through 248 Processing helix chain 'A' and resid 256 through 268 Processing helix chain 'A' and resid 273 through 281 Processing helix chain 'A' and resid 288 through 300 Processing helix chain 'A' and resid 301 through 303 No H-bonds generated for 'chain 'A' and resid 301 through 303' Processing helix chain 'A' and resid 315 through 327 Proline residue: A 321 - end of helix removed outlier: 3.654A pdb=" N TYR A 324 " --> pdb=" O LEU A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 346 Processing helix chain 'A' and resid 359 through 377 Processing helix chain 'A' and resid 384 through 399 Processing helix chain 'A' and resid 400 through 403 Processing helix chain 'A' and resid 407 through 416 removed outlier: 3.542A pdb=" N VAL A 411 " --> pdb=" O TYR A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 435 Processing helix chain 'A' and resid 441 through 453 Processing helix chain 'A' and resid 458 through 476 removed outlier: 3.545A pdb=" N ARG A 462 " --> pdb=" O ARG A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 490 removed outlier: 3.981A pdb=" N ILE A 490 " --> pdb=" O ASN A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 518 removed outlier: 4.193A pdb=" N VAL A 504 " --> pdb=" O LYS A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 536 removed outlier: 3.517A pdb=" N SER A 526 " --> pdb=" O HIS A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 546 removed outlier: 3.830A pdb=" N LEU A 545 " --> pdb=" O PRO A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 575 removed outlier: 4.493A pdb=" N ASP A 559 " --> pdb=" O ALA A 555 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N VAL A 560 " --> pdb=" O SER A 556 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU A 575 " --> pdb=" O LEU A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 601 Processing helix chain 'A' and resid 604 through 620 removed outlier: 4.068A pdb=" N LEU A 620 " --> pdb=" O ASP A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 700 Processing helix chain 'A' and resid 703 through 719 Proline residue: A 714 - end of helix removed outlier: 3.525A pdb=" N TYR A 719 " --> pdb=" O GLU A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 726 removed outlier: 4.132A pdb=" N ILE A 723 " --> pdb=" O TYR A 719 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER A 726 " --> pdb=" O LEU A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 742 removed outlier: 3.826A pdb=" N CYS A 734 " --> pdb=" O VAL A 730 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 774 Proline residue: A 768 - end of helix Processing helix chain 'A' and resid 775 through 780 removed outlier: 4.820A pdb=" N ASN A 778 " --> pdb=" O SER A 775 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU A 780 " --> pdb=" O HIS A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 795 Processing helix chain 'A' and resid 801 through 815 Processing helix chain 'A' and resid 815 through 830 removed outlier: 4.304A pdb=" N LYS A 821 " --> pdb=" O ASP A 817 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA A 822 " --> pdb=" O ILE A 818 " (cutoff:3.500A) Proline residue: A 824 - end of helix Processing helix chain 'A' and resid 839 through 852 removed outlier: 3.557A pdb=" N LEU A 843 " --> pdb=" O MET A 839 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 873 Processing helix chain 'A' and resid 874 through 877 removed outlier: 3.986A pdb=" N ASN A 877 " --> pdb=" O PRO A 874 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 874 through 877' Processing helix chain 'A' and resid 882 through 900 Processing helix chain 'A' and resid 907 through 920 removed outlier: 3.954A pdb=" N PHE A 911 " --> pdb=" O ASP A 907 " (cutoff:3.500A) Processing helix chain 'A' and resid 1016 through 1034 Processing helix chain 'A' and resid 1045 through 1052 Processing helix chain 'A' and resid 1076 through 1082 Processing helix chain 'A' and resid 1182 through 1185 removed outlier: 3.920A pdb=" N ALA A1185 " --> pdb=" O ASN A1182 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1182 through 1185' Processing helix chain 'A' and resid 1186 through 1193 removed outlier: 3.761A pdb=" N GLY A1193 " --> pdb=" O LEU A1189 " (cutoff:3.500A) Processing helix chain 'A' and resid 1233 through 1239 removed outlier: 3.561A pdb=" N ALA A1237 " --> pdb=" O ASN A1233 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLU A1239 " --> pdb=" O LEU A1235 " (cutoff:3.500A) Processing helix chain 'A' and resid 1497 through 1505 removed outlier: 4.038A pdb=" N PHE A1501 " --> pdb=" O PRO A1497 " (cutoff:3.500A) Processing helix chain 'A' and resid 1524 through 1537 Processing helix chain 'A' and resid 1568 through 1577 removed outlier: 3.543A pdb=" N GLY A1577 " --> pdb=" O GLU A1573 " (cutoff:3.500A) Processing helix chain 'A' and resid 1637 through 1643 Processing helix chain 'A' and resid 1658 through 1662 Processing helix chain 'A' and resid 1707 through 1728 Processing helix chain 'A' and resid 1738 through 1755 removed outlier: 3.723A pdb=" N CYS A1755 " --> pdb=" O ARG A1751 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 140 Proline residue: B 131 - end of helix Processing helix chain 'B' and resid 160 through 171 removed outlier: 3.693A pdb=" N VAL B 164 " --> pdb=" O LEU B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 199 Processing helix chain 'B' and resid 212 through 222 removed outlier: 3.636A pdb=" N LEU B 222 " --> pdb=" O SER B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 248 Processing helix chain 'B' and resid 265 through 273 Processing helix chain 'B' and resid 281 through 289 Processing helix chain 'B' and resid 293 through 305 Processing helix chain 'B' and resid 318 through 328 removed outlier: 4.320A pdb=" N SER B 322 " --> pdb=" O SER B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 346 removed outlier: 3.653A pdb=" N SER B 335 " --> pdb=" O ASN B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 377 Processing helix chain 'B' and resid 382 through 399 Processing helix chain 'B' and resid 409 through 418 removed outlier: 3.983A pdb=" N ARG B 418 " --> pdb=" O CYS B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 434 Processing helix chain 'B' and resid 443 through 451 removed outlier: 4.384A pdb=" N ALA B 447 " --> pdb=" O GLN B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 469 removed outlier: 3.714A pdb=" N ARG B 462 " --> pdb=" O ARG B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 493 removed outlier: 5.802A pdb=" N GLU B 482 " --> pdb=" O GLN B 478 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N GLU B 483 " --> pdb=" O PHE B 479 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASN B 486 " --> pdb=" O GLU B 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 517 removed outlier: 3.703A pdb=" N GLU B 517 " --> pdb=" O VAL B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 535 removed outlier: 3.630A pdb=" N SER B 526 " --> pdb=" O HIS B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 574 removed outlier: 4.566A pdb=" N ALA B 552 " --> pdb=" O ARG B 548 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ASP B 559 " --> pdb=" O ALA B 555 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL B 560 " --> pdb=" O SER B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 575 through 576 No H-bonds generated for 'chain 'B' and resid 575 through 576' Processing helix chain 'B' and resid 577 through 578 No H-bonds generated for 'chain 'B' and resid 577 through 578' Processing helix chain 'B' and resid 579 through 600 removed outlier: 3.922A pdb=" N ALA B 583 " --> pdb=" O PRO B 579 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N HIS B 600 " --> pdb=" O LEU B 596 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 619 Processing helix chain 'B' and resid 687 through 699 removed outlier: 3.755A pdb=" N ARG B 691 " --> pdb=" O SER B 687 " (cutoff:3.500A) Processing helix chain 'B' and resid 704 through 719 Proline residue: B 714 - end of helix Processing helix chain 'B' and resid 721 through 725 removed outlier: 3.653A pdb=" N PHE B 724 " --> pdb=" O VAL B 721 " (cutoff:3.500A) Processing helix chain 'B' and resid 729 through 740 removed outlier: 3.790A pdb=" N LEU B 733 " --> pdb=" O SER B 729 " (cutoff:3.500A) Processing helix chain 'B' and resid 759 through 774 Proline residue: B 768 - end of helix Processing helix chain 'B' and resid 781 through 797 removed outlier: 4.282A pdb=" N ILE B 797 " --> pdb=" O GLU B 793 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 815 Processing helix chain 'B' and resid 815 through 831 removed outlier: 3.544A pdb=" N ILE B 819 " --> pdb=" O MET B 815 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N LYS B 821 " --> pdb=" O ASP B 817 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ALA B 822 " --> pdb=" O ILE B 818 " (cutoff:3.500A) Proline residue: B 824 - end of helix Processing helix chain 'B' and resid 839 through 852 removed outlier: 3.696A pdb=" N LEU B 844 " --> pdb=" O ALA B 840 " (cutoff:3.500A) Processing helix chain 'B' and resid 861 through 873 removed outlier: 3.867A pdb=" N TYR B 865 " --> pdb=" O ALA B 861 " (cutoff:3.500A) Processing helix chain 'B' and resid 874 through 877 Processing helix chain 'B' and resid 882 through 900 Processing helix chain 'B' and resid 907 through 918 removed outlier: 4.674A pdb=" N PHE B 911 " --> pdb=" O ASP B 907 " (cutoff:3.500A) Processing helix chain 'B' and resid 1016 through 1034 Processing helix chain 'B' and resid 1045 through 1053 Processing helix chain 'B' and resid 1074 through 1082 Processing helix chain 'B' and resid 1181 through 1185 Processing helix chain 'B' and resid 1186 through 1192 removed outlier: 4.026A pdb=" N THR B1191 " --> pdb=" O VAL B1187 " (cutoff:3.500A) Processing helix chain 'B' and resid 1228 through 1242 Processing helix chain 'B' and resid 1497 through 1505 removed outlier: 3.602A pdb=" N PHE B1501 " --> pdb=" O PRO B1497 " (cutoff:3.500A) Processing helix chain 'B' and resid 1512 through 1516 Processing helix chain 'B' and resid 1524 through 1537 removed outlier: 4.121A pdb=" N GLU B1528 " --> pdb=" O SER B1524 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ILE B1537 " --> pdb=" O LEU B1533 " (cutoff:3.500A) Processing helix chain 'B' and resid 1568 through 1579 removed outlier: 4.093A pdb=" N GLY B1579 " --> pdb=" O LEU B1575 " (cutoff:3.500A) Processing helix chain 'B' and resid 1637 through 1644 removed outlier: 3.715A pdb=" N ASN B1643 " --> pdb=" O ARG B1639 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASP B1644 " --> pdb=" O HIS B1640 " (cutoff:3.500A) Processing helix chain 'B' and resid 1658 through 1662 Processing helix chain 'B' and resid 1704 through 1706 No H-bonds generated for 'chain 'B' and resid 1704 through 1706' Processing helix chain 'B' and resid 1707 through 1730 Processing helix chain 'B' and resid 1738 through 1755 Processing helix chain 'C' and resid 747 through 841 removed outlier: 3.631A pdb=" N GLU C 766 " --> pdb=" O ASN C 762 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLN C 767 " --> pdb=" O GLN C 763 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLU C 809 " --> pdb=" O ASN C 805 " (cutoff:3.500A) Processing helix chain 'C' and resid 841 through 871 removed outlier: 3.802A pdb=" N ASN C 849 " --> pdb=" O MET C 845 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG C 850 " --> pdb=" O GLU C 846 " (cutoff:3.500A) Processing helix chain 'C' and resid 875 through 967 removed outlier: 3.736A pdb=" N GLU C 887 " --> pdb=" O ALA C 883 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N LYS C 890 " --> pdb=" O LYS C 886 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N SER C 905 " --> pdb=" O ARG C 901 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLN C 906 " --> pdb=" O LEU C 902 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS C 907 " --> pdb=" O ASP C 903 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 32 Processing helix chain 'E' and resid 39 through 49 Processing helix chain 'E' and resid 52 through 64 removed outlier: 4.257A pdb=" N ALA E 57 " --> pdb=" O SER E 53 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N LEU E 58 " --> pdb=" O MET E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 72 No H-bonds generated for 'chain 'E' and resid 70 through 72' Processing helix chain 'E' and resid 73 through 95 removed outlier: 3.609A pdb=" N VAL E 88 " --> pdb=" O GLN E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 116 removed outlier: 3.969A pdb=" N ARG E 110 " --> pdb=" O GLU E 106 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N MET E 111 " --> pdb=" O VAL E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 145 Processing helix chain 'E' and resid 147 through 165 Processing helix chain 'E' and resid 166 through 169 Processing helix chain 'E' and resid 172 through 183 removed outlier: 3.606A pdb=" N ALA E 176 " --> pdb=" O GLN E 172 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU E 183 " --> pdb=" O GLN E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 186 through 196 removed outlier: 3.527A pdb=" N HIS E 191 " --> pdb=" O ARG E 187 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N LEU E 192 " --> pdb=" O LEU E 188 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 201 Processing helix chain 'E' and resid 202 through 206 removed outlier: 3.853A pdb=" N LEU E 205 " --> pdb=" O PRO E 202 " (cutoff:3.500A) Processing helix chain 'E' and resid 216 through 219 Processing helix chain 'E' and resid 220 through 229 removed outlier: 3.746A pdb=" N TRP E 224 " --> pdb=" O LEU E 220 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LYS E 226 " --> pdb=" O ARG E 222 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 246 removed outlier: 3.513A pdb=" N PHE E 237 " --> pdb=" O LYS E 233 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR E 245 " --> pdb=" O GLU E 241 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 252 Processing helix chain 'E' and resid 255 through 265 Processing helix chain 'E' and resid 270 through 286 removed outlier: 3.767A pdb=" N ASP E 280 " --> pdb=" O SER E 276 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 34 Processing helix chain 'F' and resid 41 through 51 removed outlier: 4.016A pdb=" N UNK F 51 " --> pdb=" O UNK F 47 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 65 removed outlier: 3.869A pdb=" N UNK F 60 " --> pdb=" O UNK F 56 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N UNK F 65 " --> pdb=" O UNK F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 70 through 80 removed outlier: 3.717A pdb=" N UNK F 80 " --> pdb=" O UNK F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 96 Processing helix chain 'F' and resid 123 through 133 Processing helix chain 'F' and resid 143 through 156 Processing helix chain 'F' and resid 163 through 170 removed outlier: 4.149A pdb=" N UNK F 167 " --> pdb=" O UNK F 163 " (cutoff:3.500A) Processing helix chain 'F' and resid 186 through 191 Processing helix chain 'F' and resid 196 through 209 removed outlier: 3.916A pdb=" N UNK F 200 " --> pdb=" O UNK F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 217 through 226 Processing helix chain 'F' and resid 231 through 237 removed outlier: 4.113A pdb=" N UNK F 237 " --> pdb=" O UNK F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 245 through 260 removed outlier: 3.520A pdb=" N UNK F 249 " --> pdb=" O UNK F 245 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N UNK F 260 " --> pdb=" O UNK F 256 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 622 through 623 Processing sheet with id=AA2, first strand: chain 'A' and resid 1518 through 1519 removed outlier: 3.947A pdb=" N LEU A1209 " --> pdb=" O SER B1211 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N SER B1211 " --> pdb=" O LEU A1209 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1609 through 1611 removed outlier: 6.248A pdb=" N ASP A1541 " --> pdb=" O GLN A1616 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N VAL A1618 " --> pdb=" O ASP A1541 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N HIS A1543 " --> pdb=" O VAL A1618 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N HIS A1620 " --> pdb=" O HIS A1543 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N ILE A1545 " --> pdb=" O HIS A1620 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N VAL A1646 " --> pdb=" O LYS A1544 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N SER A1647 " --> pdb=" O VAL A1671 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N VAL A1673 " --> pdb=" O SER A1647 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N VAL A1649 " --> pdb=" O VAL A1673 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 1547 through 1549 removed outlier: 3.819A pdb=" N TYR B1650 " --> pdb=" O LEU B1548 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL B1671 " --> pdb=" O SER B1647 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 1609 through 1610 1510 hydrogen bonds defined for protein. 4440 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: 3.36 Time building geometry restraints manager: 2.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6748 1.33 - 1.45: 3650 1.45 - 1.58: 13114 1.58 - 1.70: 0 1.70 - 1.82: 174 Bond restraints: 23686 Sorted by residual: bond pdb=" N THR E 102 " pdb=" CA THR E 102 " ideal model delta sigma weight residual 1.455 1.489 -0.033 7.00e-03 2.04e+04 2.29e+01 bond pdb=" C GLN B1532 " pdb=" O GLN B1532 " ideal model delta sigma weight residual 1.236 1.275 -0.039 1.15e-02 7.56e+03 1.14e+01 bond pdb=" N GLN B1536 " pdb=" CA GLN B1536 " ideal model delta sigma weight residual 1.457 1.499 -0.042 1.29e-02 6.01e+03 1.05e+01 bond pdb=" N VAL B1646 " pdb=" CA VAL B1646 " ideal model delta sigma weight residual 1.456 1.493 -0.037 1.15e-02 7.56e+03 1.03e+01 bond pdb=" N GLN B1532 " pdb=" CA GLN B1532 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.17e-02 7.31e+03 9.93e+00 ... (remaining 23681 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 30415 1.93 - 3.85: 1573 3.85 - 5.78: 139 5.78 - 7.71: 29 7.71 - 9.63: 2 Bond angle restraints: 32158 Sorted by residual: angle pdb=" N PRO B 232 " pdb=" CA PRO B 232 " pdb=" CB PRO B 232 " ideal model delta sigma weight residual 103.00 110.49 -7.49 1.10e+00 8.26e-01 4.63e+01 angle pdb=" N PRO B 131 " pdb=" CA PRO B 131 " pdb=" CB PRO B 131 " ideal model delta sigma weight residual 103.39 110.35 -6.96 1.08e+00 8.57e-01 4.16e+01 angle pdb=" O ASP B1613 " pdb=" C ASP B1613 " pdb=" N ILE B1614 " ideal model delta sigma weight residual 122.09 115.67 6.42 1.04e+00 9.25e-01 3.81e+01 angle pdb=" N PRO B 290 " pdb=" CA PRO B 290 " pdb=" CB PRO B 290 " ideal model delta sigma weight residual 103.39 110.03 -6.64 1.08e+00 8.57e-01 3.78e+01 angle pdb=" N PRO B 237 " pdb=" CA PRO B 237 " pdb=" CB PRO B 237 " ideal model delta sigma weight residual 103.44 110.18 -6.74 1.12e+00 7.97e-01 3.63e+01 ... (remaining 32153 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 13041 17.64 - 35.28: 1122 35.28 - 52.92: 201 52.92 - 70.55: 29 70.55 - 88.19: 15 Dihedral angle restraints: 14408 sinusoidal: 5272 harmonic: 9136 Sorted by residual: dihedral pdb=" CA ASP A1656 " pdb=" C ASP A1656 " pdb=" N PHE A1657 " pdb=" CA PHE A1657 " ideal model delta harmonic sigma weight residual -180.00 -152.79 -27.21 0 5.00e+00 4.00e-02 2.96e+01 dihedral pdb=" CA ASN A1731 " pdb=" C ASN A1731 " pdb=" N PRO A1732 " pdb=" CA PRO A1732 " ideal model delta harmonic sigma weight residual 180.00 156.61 23.39 0 5.00e+00 4.00e-02 2.19e+01 dihedral pdb=" C THR D 874 " pdb=" N THR D 874 " pdb=" CA THR D 874 " pdb=" CB THR D 874 " ideal model delta harmonic sigma weight residual -122.00 -133.30 11.30 0 2.50e+00 1.60e-01 2.04e+01 ... (remaining 14405 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 3318 0.079 - 0.158: 421 0.158 - 0.237: 73 0.237 - 0.316: 4 0.316 - 0.395: 3 Chirality restraints: 3819 Sorted by residual: chirality pdb=" CA LYS D 881 " pdb=" N LYS D 881 " pdb=" C LYS D 881 " pdb=" CB LYS D 881 " both_signs ideal model delta sigma weight residual False 2.51 2.90 -0.39 2.00e-01 2.50e+01 3.89e+00 chirality pdb=" CA GLN D 844 " pdb=" N GLN D 844 " pdb=" C GLN D 844 " pdb=" CB GLN D 844 " both_signs ideal model delta sigma weight residual False 2.51 2.87 -0.36 2.00e-01 2.50e+01 3.18e+00 chirality pdb=" CA THR D 874 " pdb=" N THR D 874 " pdb=" C THR D 874 " pdb=" CB THR D 874 " both_signs ideal model delta sigma weight residual False 2.53 2.18 0.34 2.00e-01 2.50e+01 2.95e+00 ... (remaining 3816 not shown) Planarity restraints: 4110 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN D 868 " 0.020 2.00e-02 2.50e+03 4.29e-02 1.84e+01 pdb=" C ASN D 868 " -0.074 2.00e-02 2.50e+03 pdb=" O ASN D 868 " 0.028 2.00e-02 2.50e+03 pdb=" N LYS D 869 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 776 " -0.039 2.00e-02 2.50e+03 2.78e-02 1.55e+01 pdb=" CG TYR B 776 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR B 776 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR B 776 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR B 776 " 0.016 2.00e-02 2.50e+03 pdb=" CE2 TYR B 776 " 0.016 2.00e-02 2.50e+03 pdb=" CZ TYR B 776 " 0.029 2.00e-02 2.50e+03 pdb=" OH TYR B 776 " -0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B1613 " -0.021 2.00e-02 2.50e+03 3.93e-02 1.54e+01 pdb=" C ASP B1613 " 0.068 2.00e-02 2.50e+03 pdb=" O ASP B1613 " -0.024 2.00e-02 2.50e+03 pdb=" N ILE B1614 " -0.023 2.00e-02 2.50e+03 ... (remaining 4107 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2777 2.74 - 3.28: 28541 3.28 - 3.82: 40053 3.82 - 4.36: 46607 4.36 - 4.90: 71843 Nonbonded interactions: 189821 Sorted by model distance: nonbonded pdb=" N GLU E 217 " pdb=" OE1 GLU E 217 " model vdw 2.202 3.120 nonbonded pdb=" O TYR A 553 " pdb=" OG SER A 556 " model vdw 2.205 3.040 nonbonded pdb=" O CYS A 206 " pdb=" OG1 THR A 209 " model vdw 2.210 3.040 nonbonded pdb=" O LEU A 713 " pdb=" OG SER A 716 " model vdw 2.210 3.040 nonbonded pdb=" O GLN B1229 " pdb=" OG SER B1232 " model vdw 2.211 3.040 ... (remaining 189816 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 127 through 141 and (name N or name CA or name C or name \ O or name CB )) or (resid 160 through 170 and (name N or name CA or name C or na \ me O or name CB )) or resid 171 or (resid 172 through 174 and (name N or name CA \ or name C or name O or name CB )) or (resid 185 through 200 and (name N or name \ CA or name C or name O or name CB )) or (resid 211 through 225 and (name N or n \ ame CA or name C or name O or name CB )) or (resid 232 through 250 and (name N o \ r name CA or name C or name O or name CB )) or (resid 262 through 264 and (name \ N or name CA or name C or name O or name CB )) or resid 265 or (resid 266 throug \ h 268 and (name N or name CA or name C or name O or name CB )) or resid 269 or ( \ resid 270 through 276 and (name N or name CA or name C or name O or name CB )) o \ r (resid 281 through 293 and (name N or name CA or name C or name O or name CB ) \ ) or (resid 294 through 299 and (name N or name CA or name C or name O or name C \ B )) or resid 300 or (resid 301 through 304 and (name N or name CA or name C or \ name O or name CB )) or resid 305 or resid 316 through 400 or resid 407 through \ 623 or resid 685 through 748 or resid 758 through 1242 or resid 1494 through 175 \ 5)) selection = (chain 'B' and (resid 127 through 936 or resid 1015 through 1082 or resid 1182 t \ hrough 1221 or resid 1230 through 1242 or resid 1494 through 1755)) } ncs_group { reference = (chain 'C' and ((resid 746 through 840 and (name N or name CA or name C or name \ O or name CB )) or resid 841 through 969)) selection = (chain 'D' and resid 746 through 969) } 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: 13.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.420 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 20.100 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 23686 Z= 0.395 Angle : 0.883 9.634 32158 Z= 0.586 Chirality : 0.056 0.395 3819 Planarity : 0.005 0.053 4110 Dihedral : 13.739 88.192 8412 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 35.54 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.08 % Favored : 89.77 % Rotamer: Outliers : 1.11 % Allowed : 9.17 % Favored : 89.71 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.66 (0.14), residues: 2826 helix: -1.53 (0.11), residues: 1774 sheet: -3.35 (0.34), residues: 148 loop : -3.93 (0.18), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1078 TYR 0.050 0.002 TYR B 776 PHE 0.024 0.002 PHE B 860 TRP 0.010 0.001 TRP A 304 HIS 0.009 0.001 HIS A 593 Details of bonding type rmsd covalent geometry : bond 0.00587 (23686) covalent geometry : angle 0.88328 (32158) hydrogen bonds : bond 0.15742 ( 1510) hydrogen bonds : angle 6.53233 ( 4440) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 159 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 954 ILE cc_start: 0.9365 (mt) cc_final: 0.7992 (mt) REVERT: A 267 HIS cc_start: 0.8653 (t-90) cc_final: 0.8198 (t-170) REVERT: A 276 MET cc_start: 0.9094 (tpt) cc_final: 0.8699 (tpp) REVERT: A 278 HIS cc_start: 0.8781 (m90) cc_final: 0.8564 (m90) REVERT: A 301 MET cc_start: 0.8161 (tpp) cc_final: 0.7761 (tpp) REVERT: A 449 MET cc_start: 0.8829 (tpt) cc_final: 0.8503 (ttp) REVERT: A 1022 LEU cc_start: 0.9374 (mm) cc_final: 0.9095 (mt) REVERT: A 1210 MET cc_start: 0.9154 (mmt) cc_final: 0.8786 (mmp) REVERT: B 740 MET cc_start: 0.9095 (ptt) cc_final: 0.8867 (mtm) REVERT: B 1029 MET cc_start: 0.8958 (tmm) cc_final: 0.8643 (tmm) REVERT: B 1030 MET cc_start: 0.9146 (mtm) cc_final: 0.8271 (mtm) REVERT: C 931 GLU cc_start: 0.8898 (OUTLIER) cc_final: 0.8637 (mm-30) REVERT: C 954 ILE cc_start: 0.9362 (OUTLIER) cc_final: 0.8902 (tp) outliers start: 26 outliers final: 12 residues processed: 181 average time/residue: 0.1643 time to fit residues: 46.5035 Evaluate side-chains 128 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 114 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 0.0070 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 0.0970 chunk 298 optimal weight: 9.9990 overall best weight: 0.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 868 ASN D 897 GLN ** D 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 915 HIS ** D 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 936 GLN D 940 GLN D 956 GLN A 248 ASN ** A 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 486 ASN ** A 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 763 HIS A 891 HIS A1064 ASN A1503 GLN ** A1588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1640 HIS A1714 GLN A1726 HIS B 363 ASN ** B 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 503 GLN B 525 ASN ** B 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 600 HIS ** B 890 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1182 ASN B1503 GLN B1616 GLN B1651 ASN B1714 GLN B1727 HIS ** C 900 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 71 HIS E 113 GLN ** E 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.049174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.035256 restraints weight = 221784.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.036207 restraints weight = 126013.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.036834 restraints weight = 86629.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.037224 restraints weight = 67519.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.037509 restraints weight = 57259.790| |-----------------------------------------------------------------------------| r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 23686 Z= 0.167 Angle : 0.705 9.756 32158 Z= 0.359 Chirality : 0.041 0.206 3819 Planarity : 0.005 0.069 4110 Dihedral : 5.076 26.563 3289 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 0.17 % Allowed : 6.47 % Favored : 93.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.90 (0.15), residues: 2826 helix: -0.17 (0.12), residues: 1829 sheet: -2.61 (0.37), residues: 154 loop : -3.35 (0.19), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 81 TYR 0.028 0.002 TYR C 884 PHE 0.036 0.002 PHE B 860 TRP 0.013 0.002 TRP E 282 HIS 0.011 0.001 HIS D 894 Details of bonding type rmsd covalent geometry : bond 0.00347 (23686) covalent geometry : angle 0.70500 (32158) hydrogen bonds : bond 0.05341 ( 1510) hydrogen bonds : angle 5.13800 ( 4440) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 146 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 921 HIS cc_start: 0.8698 (t-90) cc_final: 0.8337 (t-170) REVERT: D 954 ILE cc_start: 0.9543 (mt) cc_final: 0.8874 (mt) REVERT: D 958 PHE cc_start: 0.9304 (m-10) cc_final: 0.8773 (m-80) REVERT: D 966 TYR cc_start: 0.8984 (m-80) cc_final: 0.8782 (m-80) REVERT: A 248 ASN cc_start: 0.9431 (OUTLIER) cc_final: 0.8971 (t0) REVERT: A 278 HIS cc_start: 0.9200 (m90) cc_final: 0.8942 (m90) REVERT: A 301 MET cc_start: 0.8280 (tpp) cc_final: 0.7783 (tpp) REVERT: A 320 LEU cc_start: 0.9464 (mt) cc_final: 0.9228 (mt) REVERT: A 449 MET cc_start: 0.9067 (tpt) cc_final: 0.8794 (ttp) REVERT: A 740 MET cc_start: 0.8987 (tpp) cc_final: 0.8649 (tpp) REVERT: A 1022 LEU cc_start: 0.9555 (mm) cc_final: 0.9338 (mt) REVERT: A 1721 MET cc_start: 0.9500 (mtp) cc_final: 0.9190 (mmm) REVERT: B 449 MET cc_start: 0.8600 (ppp) cc_final: 0.8365 (ppp) REVERT: B 740 MET cc_start: 0.8939 (ptt) cc_final: 0.8708 (mtm) REVERT: B 845 GLU cc_start: 0.9433 (mt-10) cc_final: 0.9086 (mt-10) REVERT: B 1028 ASP cc_start: 0.9048 (m-30) cc_final: 0.8743 (m-30) REVERT: B 1030 MET cc_start: 0.9338 (mtm) cc_final: 0.8596 (mtm) REVERT: B 1210 MET cc_start: 0.9002 (mtp) cc_final: 0.8751 (mtm) REVERT: B 1540 TYR cc_start: 0.6861 (m-80) cc_final: 0.6613 (m-80) REVERT: B 1613 ASP cc_start: 0.9059 (p0) cc_final: 0.8837 (p0) REVERT: C 958 PHE cc_start: 0.9354 (m-80) cc_final: 0.9085 (m-80) outliers start: 4 outliers final: 1 residues processed: 150 average time/residue: 0.1593 time to fit residues: 38.0547 Evaluate side-chains 118 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 116 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 280 optimal weight: 4.9990 chunk 69 optimal weight: 0.7980 chunk 141 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 234 optimal weight: 0.9980 chunk 188 optimal weight: 0.8980 chunk 7 optimal weight: 40.0000 chunk 16 optimal weight: 0.2980 chunk 110 optimal weight: 0.8980 chunk 251 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 868 ASN ** D 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 373 GLN ** A 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 732 GLN ** A1588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 890 HIS B1503 GLN C 842 GLN ** C 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 900 GLN C 926 GLN E 254 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.048843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.035302 restraints weight = 215859.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.036230 restraints weight = 125890.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.036846 restraints weight = 87678.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.037252 restraints weight = 68480.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.037518 restraints weight = 57831.773| |-----------------------------------------------------------------------------| r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23686 Z= 0.146 Angle : 0.648 8.942 32158 Z= 0.329 Chirality : 0.040 0.361 3819 Planarity : 0.004 0.067 4110 Dihedral : 4.861 24.415 3289 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 0.04 % Allowed : 4.93 % Favored : 95.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.16), residues: 2826 helix: 0.53 (0.12), residues: 1826 sheet: -2.16 (0.37), residues: 156 loop : -3.05 (0.20), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 151 TYR 0.016 0.001 TYR A 779 PHE 0.033 0.002 PHE B 860 TRP 0.012 0.001 TRP A 441 HIS 0.009 0.001 HIS A1506 Details of bonding type rmsd covalent geometry : bond 0.00301 (23686) covalent geometry : angle 0.64820 (32158) hydrogen bonds : bond 0.04752 ( 1510) hydrogen bonds : angle 4.78192 ( 4440) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 144 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 845 MET cc_start: 0.9277 (tmm) cc_final: 0.9070 (tmm) REVERT: D 847 PHE cc_start: 0.9013 (t80) cc_final: 0.8806 (t80) REVERT: D 884 TYR cc_start: 0.9157 (t80) cc_final: 0.8741 (t80) REVERT: D 954 ILE cc_start: 0.9595 (mt) cc_final: 0.8737 (mt) REVERT: D 958 PHE cc_start: 0.9276 (m-10) cc_final: 0.8929 (m-80) REVERT: A 245 ARG cc_start: 0.8762 (mtt90) cc_final: 0.8513 (mtt-85) REVERT: A 301 MET cc_start: 0.8202 (tpp) cc_final: 0.7817 (tpp) REVERT: A 320 LEU cc_start: 0.9546 (mt) cc_final: 0.9235 (mt) REVERT: A 327 MET cc_start: 0.8783 (tpt) cc_final: 0.8537 (tpt) REVERT: A 392 GLU cc_start: 0.9440 (tp30) cc_final: 0.9233 (tp30) REVERT: A 449 MET cc_start: 0.9235 (tpt) cc_final: 0.8946 (ttp) REVERT: A 740 MET cc_start: 0.8997 (tpp) cc_final: 0.8641 (tpp) REVERT: A 1022 LEU cc_start: 0.9553 (mm) cc_final: 0.9336 (mt) REVERT: A 1210 MET cc_start: 0.9479 (mmp) cc_final: 0.8830 (mmp) REVERT: A 1721 MET cc_start: 0.9441 (mtp) cc_final: 0.9161 (mmm) REVERT: B 449 MET cc_start: 0.8580 (ppp) cc_final: 0.8343 (ppp) REVERT: B 788 MET cc_start: 0.8871 (ptp) cc_final: 0.8130 (ptp) REVERT: B 845 GLU cc_start: 0.9415 (mt-10) cc_final: 0.9053 (mt-10) REVERT: B 1030 MET cc_start: 0.9327 (mtm) cc_final: 0.8445 (mtm) REVERT: B 1540 TYR cc_start: 0.6821 (m-80) cc_final: 0.6524 (m-80) REVERT: C 958 PHE cc_start: 0.9382 (m-80) cc_final: 0.8945 (m-80) outliers start: 1 outliers final: 0 residues processed: 145 average time/residue: 0.1618 time to fit residues: 37.1622 Evaluate side-chains 110 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 204 optimal weight: 0.7980 chunk 287 optimal weight: 10.0000 chunk 253 optimal weight: 2.9990 chunk 91 optimal weight: 0.0270 chunk 304 optimal weight: 9.9990 chunk 182 optimal weight: 0.9990 chunk 257 optimal weight: 2.9990 chunk 219 optimal weight: 5.9990 chunk 122 optimal weight: 0.9990 chunk 297 optimal weight: 10.0000 chunk 165 optimal weight: 0.9990 overall best weight: 0.7644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 868 ASN ** D 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 417 GLN ** A 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 363 ASN ** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 890 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.049252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.035369 restraints weight = 221444.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.036343 restraints weight = 124965.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.036973 restraints weight = 85739.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.037387 restraints weight = 66718.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.037660 restraints weight = 56307.108| |-----------------------------------------------------------------------------| r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 23686 Z= 0.141 Angle : 0.634 9.964 32158 Z= 0.322 Chirality : 0.039 0.206 3819 Planarity : 0.004 0.051 4110 Dihedral : 4.712 23.039 3289 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 0.04 % Allowed : 3.99 % Favored : 95.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.16), residues: 2826 helix: 0.81 (0.12), residues: 1842 sheet: -1.94 (0.37), residues: 155 loop : -2.98 (0.20), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 505 TYR 0.020 0.001 TYR D 966 PHE 0.022 0.002 PHE B 860 TRP 0.011 0.001 TRP A 441 HIS 0.008 0.001 HIS A1506 Details of bonding type rmsd covalent geometry : bond 0.00294 (23686) covalent geometry : angle 0.63445 (32158) hydrogen bonds : bond 0.04443 ( 1510) hydrogen bonds : angle 4.63892 ( 4440) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 137 time to evaluate : 0.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 845 MET cc_start: 0.9291 (tmm) cc_final: 0.9086 (tmm) REVERT: D 847 PHE cc_start: 0.9000 (t80) cc_final: 0.8780 (t80) REVERT: D 884 TYR cc_start: 0.9105 (t80) cc_final: 0.8720 (t80) REVERT: D 954 ILE cc_start: 0.9612 (mt) cc_final: 0.8729 (mt) REVERT: D 958 PHE cc_start: 0.9226 (m-10) cc_final: 0.8876 (m-80) REVERT: A 278 HIS cc_start: 0.9180 (m90) cc_final: 0.8970 (m90) REVERT: A 301 MET cc_start: 0.8250 (tpp) cc_final: 0.7608 (tpp) REVERT: A 320 LEU cc_start: 0.9584 (mt) cc_final: 0.9305 (mt) REVERT: A 392 GLU cc_start: 0.9377 (tp30) cc_final: 0.9136 (tp30) REVERT: A 449 MET cc_start: 0.9133 (tpt) cc_final: 0.8810 (ttp) REVERT: A 464 LYS cc_start: 0.9357 (tppp) cc_final: 0.9141 (tppp) REVERT: A 740 MET cc_start: 0.8938 (tpp) cc_final: 0.8658 (tpp) REVERT: A 839 MET cc_start: 0.8259 (mmt) cc_final: 0.8039 (mmt) REVERT: A 1022 LEU cc_start: 0.9538 (mm) cc_final: 0.9334 (mt) REVERT: A 1721 MET cc_start: 0.9431 (mtp) cc_final: 0.9119 (mmm) REVERT: B 449 MET cc_start: 0.8595 (ppp) cc_final: 0.8366 (ppp) REVERT: B 788 MET cc_start: 0.8861 (ptp) cc_final: 0.8582 (ptp) REVERT: B 845 GLU cc_start: 0.9406 (mt-10) cc_final: 0.9021 (mt-10) REVERT: B 1030 MET cc_start: 0.9320 (mtm) cc_final: 0.8430 (mtm) REVERT: B 1540 TYR cc_start: 0.7204 (m-80) cc_final: 0.6808 (m-80) REVERT: C 958 PHE cc_start: 0.9454 (m-80) cc_final: 0.9121 (m-80) outliers start: 1 outliers final: 1 residues processed: 138 average time/residue: 0.1532 time to fit residues: 34.5779 Evaluate side-chains 114 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 113 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 238 optimal weight: 5.9990 chunk 289 optimal weight: 10.0000 chunk 95 optimal weight: 0.9990 chunk 302 optimal weight: 10.0000 chunk 252 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 305 optimal weight: 8.9990 chunk 218 optimal weight: 0.8980 chunk 210 optimal weight: 0.9990 chunk 223 optimal weight: 0.0980 chunk 179 optimal weight: 0.9980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 868 ASN ** D 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 267 HIS A 370 GLN ** A 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 593 HIS ** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 890 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1707 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.049239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.035485 restraints weight = 220297.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.036456 restraints weight = 124422.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.037066 restraints weight = 85110.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.037487 restraints weight = 66178.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.037756 restraints weight = 56003.643| |-----------------------------------------------------------------------------| r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 23686 Z= 0.134 Angle : 0.625 9.360 32158 Z= 0.314 Chirality : 0.040 0.397 3819 Planarity : 0.004 0.050 4110 Dihedral : 4.599 23.400 3289 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 0.09 % Allowed : 3.13 % Favored : 96.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.16), residues: 2826 helix: 1.07 (0.12), residues: 1836 sheet: -1.69 (0.37), residues: 155 loop : -2.88 (0.20), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 585 TYR 0.029 0.001 TYR D 966 PHE 0.031 0.001 PHE B 860 TRP 0.010 0.001 TRP A 441 HIS 0.018 0.001 HIS A 593 Details of bonding type rmsd covalent geometry : bond 0.00281 (23686) covalent geometry : angle 0.62475 (32158) hydrogen bonds : bond 0.04247 ( 1510) hydrogen bonds : angle 4.46898 ( 4440) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 142 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 845 MET cc_start: 0.9375 (tmm) cc_final: 0.9147 (tmm) REVERT: D 847 PHE cc_start: 0.9073 (t80) cc_final: 0.8788 (t80) REVERT: D 884 TYR cc_start: 0.9038 (t80) cc_final: 0.8663 (t80) REVERT: D 921 HIS cc_start: 0.8810 (t-90) cc_final: 0.8346 (t70) REVERT: D 954 ILE cc_start: 0.9608 (mt) cc_final: 0.8702 (mt) REVERT: D 958 PHE cc_start: 0.9310 (m-10) cc_final: 0.8951 (m-80) REVERT: A 278 HIS cc_start: 0.9139 (m90) cc_final: 0.8885 (m90) REVERT: A 301 MET cc_start: 0.8191 (tpp) cc_final: 0.7720 (tpp) REVERT: A 392 GLU cc_start: 0.9374 (tp30) cc_final: 0.9172 (tp30) REVERT: A 429 TYR cc_start: 0.8393 (t80) cc_final: 0.8108 (t80) REVERT: A 449 MET cc_start: 0.9170 (tpt) cc_final: 0.8808 (ttp) REVERT: A 466 LEU cc_start: 0.9811 (tp) cc_final: 0.9567 (tt) REVERT: A 510 GLN cc_start: 0.9104 (mm-40) cc_final: 0.8803 (mm-40) REVERT: A 1022 LEU cc_start: 0.9586 (mm) cc_final: 0.9384 (mt) REVERT: A 1721 MET cc_start: 0.9424 (mtp) cc_final: 0.9135 (mmm) REVERT: B 449 MET cc_start: 0.8612 (ppp) cc_final: 0.8404 (ppp) REVERT: B 788 MET cc_start: 0.8845 (ptp) cc_final: 0.8529 (ptp) REVERT: B 845 GLU cc_start: 0.9370 (mt-10) cc_final: 0.8992 (mt-10) REVERT: B 1030 MET cc_start: 0.9307 (mtm) cc_final: 0.8465 (mtm) REVERT: B 1210 MET cc_start: 0.8510 (mpp) cc_final: 0.8034 (mpp) REVERT: B 1540 TYR cc_start: 0.7251 (m-80) cc_final: 0.6801 (m-80) REVERT: B 1613 ASP cc_start: 0.8713 (p0) cc_final: 0.8458 (p0) REVERT: C 958 PHE cc_start: 0.9501 (m-80) cc_final: 0.9118 (m-80) outliers start: 2 outliers final: 1 residues processed: 144 average time/residue: 0.1450 time to fit residues: 34.6958 Evaluate side-chains 118 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 117 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 279 optimal weight: 0.1980 chunk 274 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 chunk 139 optimal weight: 0.0000 chunk 148 optimal weight: 5.9990 chunk 300 optimal weight: 9.9990 chunk 192 optimal weight: 0.6980 chunk 280 optimal weight: 0.7980 chunk 156 optimal weight: 0.0060 chunk 212 optimal weight: 0.9980 overall best weight: 0.3200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 868 ASN ** D 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 425 ASN ** A 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1192 GLN B 435 HIS ** B 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 890 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1707 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.049450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.035961 restraints weight = 213719.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.036874 restraints weight = 126660.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.037479 restraints weight = 89137.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.037884 restraints weight = 69994.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.038126 restraints weight = 59376.831| |-----------------------------------------------------------------------------| r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.3197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 23686 Z= 0.122 Angle : 0.624 9.513 32158 Z= 0.311 Chirality : 0.040 0.437 3819 Planarity : 0.004 0.050 4110 Dihedral : 4.477 23.156 3289 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.16), residues: 2826 helix: 1.23 (0.12), residues: 1839 sheet: -1.58 (0.39), residues: 157 loop : -2.71 (0.21), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG E 56 TYR 0.047 0.001 TYR D 966 PHE 0.031 0.001 PHE B 860 TRP 0.009 0.001 TRP A 441 HIS 0.007 0.001 HIS B1506 Details of bonding type rmsd covalent geometry : bond 0.00250 (23686) covalent geometry : angle 0.62362 (32158) hydrogen bonds : bond 0.04071 ( 1510) hydrogen bonds : angle 4.31369 ( 4440) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 845 MET cc_start: 0.9389 (tmm) cc_final: 0.9160 (tmm) REVERT: D 847 PHE cc_start: 0.9073 (t80) cc_final: 0.8826 (t80) REVERT: D 884 TYR cc_start: 0.8970 (t80) cc_final: 0.8619 (t80) REVERT: D 921 HIS cc_start: 0.8786 (t-90) cc_final: 0.8316 (t70) REVERT: D 954 ILE cc_start: 0.9561 (mt) cc_final: 0.8614 (mt) REVERT: D 958 PHE cc_start: 0.9189 (m-10) cc_final: 0.8776 (m-80) REVERT: A 301 MET cc_start: 0.8154 (tpp) cc_final: 0.7705 (tpp) REVERT: A 429 TYR cc_start: 0.8355 (t80) cc_final: 0.8114 (t80) REVERT: A 449 MET cc_start: 0.9303 (tpt) cc_final: 0.9052 (ttp) REVERT: A 464 LYS cc_start: 0.9445 (tppp) cc_final: 0.9144 (tppt) REVERT: A 510 GLN cc_start: 0.9079 (mm-40) cc_final: 0.8793 (mm-40) REVERT: A 839 MET cc_start: 0.8311 (mmt) cc_final: 0.8106 (mmt) REVERT: A 1721 MET cc_start: 0.9412 (mtp) cc_final: 0.9138 (mmm) REVERT: B 740 MET cc_start: 0.9233 (ptp) cc_final: 0.8923 (ptt) REVERT: B 788 MET cc_start: 0.8869 (ptp) cc_final: 0.8539 (ptp) REVERT: B 845 GLU cc_start: 0.9378 (mt-10) cc_final: 0.8945 (mt-10) REVERT: B 1030 MET cc_start: 0.9298 (mtm) cc_final: 0.8469 (ptp) REVERT: B 1540 TYR cc_start: 0.7359 (m-80) cc_final: 0.6887 (m-80) REVERT: B 1613 ASP cc_start: 0.8750 (p0) cc_final: 0.8457 (p0) REVERT: C 903 ASP cc_start: 0.9452 (t70) cc_final: 0.9241 (t0) REVERT: C 958 PHE cc_start: 0.9569 (m-80) cc_final: 0.9201 (m-80) outliers start: 0 outliers final: 0 residues processed: 144 average time/residue: 0.1394 time to fit residues: 33.4511 Evaluate side-chains 113 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 268 optimal weight: 1.9990 chunk 100 optimal weight: 0.6980 chunk 276 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 77 optimal weight: 0.0060 chunk 16 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 42 optimal weight: 0.0980 chunk 64 optimal weight: 0.7980 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 868 ASN ** D 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 267 HIS ** A 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 890 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 890 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1707 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 926 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.049735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.035829 restraints weight = 220615.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.036821 restraints weight = 124114.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.037469 restraints weight = 84859.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.037897 restraints weight = 65592.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.038167 restraints weight = 55161.197| |-----------------------------------------------------------------------------| r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.3364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23686 Z= 0.124 Angle : 0.614 9.290 32158 Z= 0.308 Chirality : 0.040 0.465 3819 Planarity : 0.004 0.047 4110 Dihedral : 4.385 21.626 3289 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.16), residues: 2826 helix: 1.32 (0.12), residues: 1834 sheet: -1.36 (0.39), residues: 154 loop : -2.60 (0.21), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 622 TYR 0.014 0.001 TYR A 274 PHE 0.028 0.001 PHE B 860 TRP 0.010 0.001 TRP A 441 HIS 0.007 0.001 HIS B1506 Details of bonding type rmsd covalent geometry : bond 0.00251 (23686) covalent geometry : angle 0.61387 (32158) hydrogen bonds : bond 0.03957 ( 1510) hydrogen bonds : angle 4.26120 ( 4440) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 845 MET cc_start: 0.9395 (tmm) cc_final: 0.9168 (tmm) REVERT: D 847 PHE cc_start: 0.9048 (t80) cc_final: 0.8809 (t80) REVERT: D 884 TYR cc_start: 0.8986 (t80) cc_final: 0.8726 (t80) REVERT: D 921 HIS cc_start: 0.8783 (t-90) cc_final: 0.8300 (t70) REVERT: D 954 ILE cc_start: 0.9543 (mt) cc_final: 0.8592 (mt) REVERT: D 958 PHE cc_start: 0.9231 (m-10) cc_final: 0.8832 (m-80) REVERT: D 966 TYR cc_start: 0.8977 (m-80) cc_final: 0.8766 (m-80) REVERT: A 280 MET cc_start: 0.9074 (mtm) cc_final: 0.8500 (ptp) REVERT: A 301 MET cc_start: 0.8134 (tpp) cc_final: 0.7710 (tpp) REVERT: A 392 GLU cc_start: 0.9387 (tp30) cc_final: 0.9169 (tp30) REVERT: A 429 TYR cc_start: 0.8369 (t80) cc_final: 0.8164 (t80) REVERT: A 449 MET cc_start: 0.9244 (tpt) cc_final: 0.8981 (ttp) REVERT: A 464 LYS cc_start: 0.9357 (tppp) cc_final: 0.9108 (tppp) REVERT: A 510 GLN cc_start: 0.8978 (mm-40) cc_final: 0.8733 (mm110) REVERT: A 1721 MET cc_start: 0.9503 (mtp) cc_final: 0.9058 (mmm) REVERT: B 449 MET cc_start: 0.8641 (ppp) cc_final: 0.8321 (ppp) REVERT: B 845 GLU cc_start: 0.9366 (mt-10) cc_final: 0.8923 (mt-10) REVERT: B 1030 MET cc_start: 0.9174 (mtm) cc_final: 0.8458 (ptp) REVERT: B 1210 MET cc_start: 0.8430 (mpp) cc_final: 0.8003 (mpp) REVERT: B 1540 TYR cc_start: 0.7167 (m-80) cc_final: 0.6673 (m-80) REVERT: B 1613 ASP cc_start: 0.8765 (p0) cc_final: 0.8516 (p0) REVERT: C 903 ASP cc_start: 0.9458 (t70) cc_final: 0.9245 (t0) REVERT: C 958 PHE cc_start: 0.9522 (m-80) cc_final: 0.9172 (m-80) outliers start: 0 outliers final: 0 residues processed: 139 average time/residue: 0.1391 time to fit residues: 32.1131 Evaluate side-chains 114 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 71 optimal weight: 5.9990 chunk 35 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 247 optimal weight: 3.9990 chunk 229 optimal weight: 1.9990 chunk 2 optimal weight: 30.0000 chunk 246 optimal weight: 8.9990 chunk 233 optimal weight: 0.9980 chunk 213 optimal weight: 3.9990 chunk 277 optimal weight: 0.2980 chunk 142 optimal weight: 40.0000 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 868 ASN ** D 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 890 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 890 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1229 GLN B1554 GLN ** B1707 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 844 GLN C 906 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.048541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.034756 restraints weight = 223143.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.035703 restraints weight = 127104.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.036321 restraints weight = 87942.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.036727 restraints weight = 68705.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.036985 restraints weight = 58184.210| |-----------------------------------------------------------------------------| r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.3307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 23686 Z= 0.177 Angle : 0.644 8.789 32158 Z= 0.327 Chirality : 0.040 0.467 3819 Planarity : 0.004 0.049 4110 Dihedral : 4.509 22.150 3289 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.16), residues: 2826 helix: 1.16 (0.12), residues: 1864 sheet: -1.43 (0.40), residues: 155 loop : -2.63 (0.22), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 56 TYR 0.015 0.002 TYR B1540 PHE 0.034 0.002 PHE A 298 TRP 0.016 0.001 TRP B1208 HIS 0.006 0.001 HIS A 777 Details of bonding type rmsd covalent geometry : bond 0.00375 (23686) covalent geometry : angle 0.64394 (32158) hydrogen bonds : bond 0.04049 ( 1510) hydrogen bonds : angle 4.40072 ( 4440) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 845 MET cc_start: 0.9413 (tmm) cc_final: 0.9144 (tmm) REVERT: D 921 HIS cc_start: 0.8845 (t-90) cc_final: 0.8346 (t-170) REVERT: D 954 ILE cc_start: 0.9567 (mt) cc_final: 0.8828 (mt) REVERT: D 958 PHE cc_start: 0.9344 (m-10) cc_final: 0.9001 (m-80) REVERT: A 301 MET cc_start: 0.7967 (tpp) cc_final: 0.7604 (tpp) REVERT: A 449 MET cc_start: 0.9311 (tpt) cc_final: 0.8903 (ttp) REVERT: A 466 LEU cc_start: 0.9836 (tp) cc_final: 0.9580 (tt) REVERT: A 895 MET cc_start: 0.9270 (tpp) cc_final: 0.9056 (tpp) REVERT: A 1022 LEU cc_start: 0.9584 (mt) cc_final: 0.9302 (pp) REVERT: B 449 MET cc_start: 0.8660 (ppp) cc_final: 0.8397 (ppp) REVERT: B 788 MET cc_start: 0.8908 (ptp) cc_final: 0.8391 (ptp) REVERT: B 845 GLU cc_start: 0.9378 (mt-10) cc_final: 0.8994 (mt-10) REVERT: B 1030 MET cc_start: 0.9180 (mtm) cc_final: 0.8311 (mtm) REVERT: B 1210 MET cc_start: 0.8566 (mpp) cc_final: 0.8013 (mpp) REVERT: B 1540 TYR cc_start: 0.6970 (m-80) cc_final: 0.6572 (m-80) REVERT: B 1613 ASP cc_start: 0.8921 (p0) cc_final: 0.8651 (p0) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.1385 time to fit residues: 30.8217 Evaluate side-chains 104 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 76 optimal weight: 0.9980 chunk 284 optimal weight: 5.9990 chunk 292 optimal weight: 10.0000 chunk 297 optimal weight: 20.0000 chunk 215 optimal weight: 2.9990 chunk 68 optimal weight: 0.5980 chunk 185 optimal weight: 2.9990 chunk 92 optimal weight: 0.2980 chunk 144 optimal weight: 30.0000 chunk 147 optimal weight: 20.0000 chunk 42 optimal weight: 3.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 868 ASN ** D 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 267 HIS ** A 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 890 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 890 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1229 GLN ** B1707 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.048008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.034618 restraints weight = 218439.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.035517 restraints weight = 128082.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.036110 restraints weight = 89781.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.036496 restraints weight = 70588.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.036765 restraints weight = 60058.139| |-----------------------------------------------------------------------------| r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.3354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 23686 Z= 0.183 Angle : 0.652 9.477 32158 Z= 0.331 Chirality : 0.041 0.425 3819 Planarity : 0.004 0.049 4110 Dihedral : 4.569 22.434 3289 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.16), residues: 2826 helix: 1.14 (0.12), residues: 1860 sheet: -1.45 (0.40), residues: 152 loop : -2.66 (0.21), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 885 TYR 0.034 0.002 TYR D 966 PHE 0.027 0.002 PHE B 860 TRP 0.016 0.001 TRP B1208 HIS 0.006 0.001 HIS A1506 Details of bonding type rmsd covalent geometry : bond 0.00384 (23686) covalent geometry : angle 0.65198 (32158) hydrogen bonds : bond 0.04061 ( 1510) hydrogen bonds : angle 4.46294 ( 4440) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 1.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 845 MET cc_start: 0.9386 (tmm) cc_final: 0.9116 (tmm) REVERT: D 921 HIS cc_start: 0.8875 (t-90) cc_final: 0.8433 (t-170) REVERT: D 954 ILE cc_start: 0.9542 (mt) cc_final: 0.8737 (mt) REVERT: D 958 PHE cc_start: 0.9321 (m-10) cc_final: 0.9020 (m-80) REVERT: A 276 MET cc_start: 0.9325 (tpt) cc_final: 0.9000 (tpt) REVERT: A 301 MET cc_start: 0.8090 (tpp) cc_final: 0.7647 (tpp) REVERT: A 449 MET cc_start: 0.9330 (tpt) cc_final: 0.8813 (tpp) REVERT: A 895 MET cc_start: 0.9265 (tpp) cc_final: 0.9044 (tpp) REVERT: A 1721 MET cc_start: 0.9528 (mtp) cc_final: 0.8849 (mpp) REVERT: B 449 MET cc_start: 0.8656 (ppp) cc_final: 0.8418 (ppp) REVERT: B 815 MET cc_start: 0.8732 (mpp) cc_final: 0.8518 (mmt) REVERT: B 845 GLU cc_start: 0.9394 (mt-10) cc_final: 0.8980 (mt-10) REVERT: B 1030 MET cc_start: 0.9193 (mtm) cc_final: 0.8345 (mtm) REVERT: B 1210 MET cc_start: 0.8531 (mpp) cc_final: 0.8193 (mpp) REVERT: E 79 MET cc_start: 0.9465 (ptp) cc_final: 0.9235 (tmm) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.1329 time to fit residues: 28.2619 Evaluate side-chains 105 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 112 optimal weight: 5.9990 chunk 137 optimal weight: 0.7980 chunk 249 optimal weight: 0.9980 chunk 216 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 59 optimal weight: 0.5980 chunk 150 optimal weight: 0.9990 chunk 279 optimal weight: 4.9990 chunk 229 optimal weight: 0.0970 chunk 134 optimal weight: 30.0000 chunk 142 optimal weight: 40.0000 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 868 ASN ** D 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 267 HIS ** A 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 890 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1229 GLN ** B1707 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.049149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.035275 restraints weight = 223131.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.036250 restraints weight = 126324.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.036891 restraints weight = 86695.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.037262 restraints weight = 67288.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.037568 restraints weight = 57343.867| |-----------------------------------------------------------------------------| r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.3521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 23686 Z= 0.128 Angle : 0.626 8.843 32158 Z= 0.312 Chirality : 0.040 0.362 3819 Planarity : 0.004 0.047 4110 Dihedral : 4.452 21.282 3289 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.16), residues: 2826 helix: 1.29 (0.12), residues: 1857 sheet: -1.37 (0.41), residues: 151 loop : -2.61 (0.21), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 56 TYR 0.022 0.001 TYR D 966 PHE 0.029 0.001 PHE B 860 TRP 0.012 0.001 TRP B1208 HIS 0.006 0.001 HIS A1506 Details of bonding type rmsd covalent geometry : bond 0.00270 (23686) covalent geometry : angle 0.62635 (32158) hydrogen bonds : bond 0.03910 ( 1510) hydrogen bonds : angle 4.30688 ( 4440) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 845 MET cc_start: 0.9388 (tmm) cc_final: 0.9145 (tmm) REVERT: D 921 HIS cc_start: 0.8864 (t-90) cc_final: 0.8396 (t70) REVERT: D 954 ILE cc_start: 0.9558 (mt) cc_final: 0.8885 (mt) REVERT: D 958 PHE cc_start: 0.9275 (m-10) cc_final: 0.8907 (m-10) REVERT: A 245 ARG cc_start: 0.8473 (mtt90) cc_final: 0.7935 (mtt-85) REVERT: A 301 MET cc_start: 0.8059 (tpp) cc_final: 0.7714 (tpp) REVERT: A 449 MET cc_start: 0.9307 (tpt) cc_final: 0.8911 (ttp) REVERT: A 510 GLN cc_start: 0.8965 (mm-40) cc_final: 0.8734 (mm110) REVERT: A 839 MET cc_start: 0.8703 (tpp) cc_final: 0.8399 (tpp) REVERT: A 895 MET cc_start: 0.9299 (tpp) cc_final: 0.9050 (tpp) REVERT: A 1022 LEU cc_start: 0.9575 (mm) cc_final: 0.9326 (mt) REVERT: A 1721 MET cc_start: 0.9487 (mtp) cc_final: 0.8802 (mpp) REVERT: B 449 MET cc_start: 0.8643 (ppp) cc_final: 0.8347 (ppp) REVERT: B 589 MET cc_start: 0.9508 (tmm) cc_final: 0.8716 (mtt) REVERT: B 815 MET cc_start: 0.8643 (mpp) cc_final: 0.8394 (mmt) REVERT: B 845 GLU cc_start: 0.9369 (mt-10) cc_final: 0.8971 (mt-10) REVERT: B 1030 MET cc_start: 0.9167 (mtm) cc_final: 0.8337 (mtm) REVERT: B 1210 MET cc_start: 0.8561 (mpp) cc_final: 0.7962 (mpp) REVERT: E 79 MET cc_start: 0.9475 (ptp) cc_final: 0.9131 (ptt) outliers start: 0 outliers final: 0 residues processed: 131 average time/residue: 0.1480 time to fit residues: 32.7610 Evaluate side-chains 105 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 46 optimal weight: 7.9990 chunk 188 optimal weight: 0.1980 chunk 226 optimal weight: 0.5980 chunk 295 optimal weight: 10.0000 chunk 22 optimal weight: 0.8980 chunk 276 optimal weight: 0.1980 chunk 151 optimal weight: 7.9990 chunk 18 optimal weight: 0.8980 chunk 67 optimal weight: 0.8980 chunk 139 optimal weight: 0.0970 chunk 31 optimal weight: 2.9990 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 868 ASN ** D 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 267 HIS ** A 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 890 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1229 GLN ** B1707 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.049663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.035776 restraints weight = 221302.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.036763 restraints weight = 125150.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.037407 restraints weight = 85755.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.037832 restraints weight = 66532.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.038078 restraints weight = 56144.039| |-----------------------------------------------------------------------------| r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.3720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 23686 Z= 0.118 Angle : 0.623 11.050 32158 Z= 0.308 Chirality : 0.040 0.326 3819 Planarity : 0.004 0.048 4110 Dihedral : 4.337 20.261 3289 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.16), residues: 2826 helix: 1.39 (0.12), residues: 1859 sheet: -1.42 (0.41), residues: 154 loop : -2.56 (0.22), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 585 TYR 0.013 0.001 TYR A 429 PHE 0.030 0.001 PHE B 860 TRP 0.022 0.001 TRP B1208 HIS 0.007 0.001 HIS B1506 Details of bonding type rmsd covalent geometry : bond 0.00246 (23686) covalent geometry : angle 0.62315 (32158) hydrogen bonds : bond 0.03834 ( 1510) hydrogen bonds : angle 4.20786 ( 4440) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3914.80 seconds wall clock time: 68 minutes 42.08 seconds (4122.08 seconds total)