Starting phenix.real_space_refine on Sat Aug 8 13:58:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9z4q_73811/08_2026/9z4q_73811.cif Found real_map, /net/cci-nas-00/data/ceres_data/9z4q_73811/08_2026/9z4q_73811.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9z4q_73811/08_2026/9z4q_73811.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9z4q_73811/08_2026/9z4q_73811.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9z4q_73811/08_2026/9z4q_73811.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9z4q_73811/08_2026/9z4q_73811.map" } resolution = 4.1 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= 0.001 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 133 5.16 5 C 17177 2.51 5 N 4814 2.21 5 O 5406 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 27538 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 11231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1376, 11231 Classifications: {'peptide': 1376} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 1347} Chain breaks: 3 Chain: "B" Number of atoms: 11304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1386, 11304 Classifications: {'peptide': 1386} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 1357} Chain breaks: 3 Chain: "C" Number of atoms: 1170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1170 Classifications: {'peptide': 149} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 145} Chain: "D" Number of atoms: 1311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1311 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 155} Chain: "E" Number of atoms: 1286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1286 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 152} Chain: "F" Number of atoms: 1170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1170 Classifications: {'peptide': 149} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 145} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 5.51, per 1000 atoms: 0.20 Number of scatterers: 27538 At special positions: 0 Unit cell: (223.66, 227.9, 171.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 133 16.00 P 6 15.00 Mg 2 11.99 O 5406 8.00 N 4814 7.00 C 17177 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: 2.34 Conformation dependent library (CDL) restraints added in 1.1 seconds 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6470 Finding SS restraints... Secondary structure from input PDB file: 125 helices and 21 sheets defined 71.8% alpha, 5.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'A' and resid 74 through 76 No H-bonds generated for 'chain 'A' and resid 74 through 76' Processing helix chain 'A' and resid 81 through 85 Processing helix chain 'A' and resid 89 through 93 Processing helix chain 'A' and resid 97 through 111 Processing helix chain 'A' and resid 135 through 143 Processing helix chain 'A' and resid 146 through 150 Processing helix chain 'A' and resid 153 through 169 removed outlier: 3.709A pdb=" N ILE A 157 " --> pdb=" O HIS A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 199 Processing helix chain 'A' and resid 212 through 229 removed outlier: 3.993A pdb=" N ASN A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Proline residue: A 223 - end of helix removed outlier: 3.741A pdb=" N PHE A 228 " --> pdb=" O ILE A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 272 Processing helix chain 'A' and resid 281 through 291 removed outlier: 4.184A pdb=" N TYR A 285 " --> pdb=" O PHE A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 299 Processing helix chain 'A' and resid 303 through 307 removed outlier: 3.991A pdb=" N TYR A 307 " --> pdb=" O PHE A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 336 Processing helix chain 'A' and resid 339 through 357 removed outlier: 3.840A pdb=" N GLY A 357 " --> pdb=" O VAL A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 386 removed outlier: 3.848A pdb=" N LEU A 384 " --> pdb=" O LYS A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 398 Processing helix chain 'A' and resid 413 through 445 Processing helix chain 'A' and resid 470 through 492 Processing helix chain 'A' and resid 492 through 502 removed outlier: 3.561A pdb=" N TYR A 499 " --> pdb=" O GLU A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 524 removed outlier: 4.009A pdb=" N ILE A 522 " --> pdb=" O CYS A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 541 Processing helix chain 'A' and resid 545 through 558 Processing helix chain 'A' and resid 590 through 597 Processing helix chain 'A' and resid 600 through 609 Processing helix chain 'A' and resid 612 through 619 Processing helix chain 'A' and resid 652 through 669 Processing helix chain 'A' and resid 691 through 702 Processing helix chain 'A' and resid 703 through 714 Processing helix chain 'A' and resid 721 through 728 Processing helix chain 'A' and resid 729 through 732 Processing helix chain 'A' and resid 742 through 754 Processing helix chain 'A' and resid 757 through 759 No H-bonds generated for 'chain 'A' and resid 757 through 759' Processing helix chain 'A' and resid 773 through 822 removed outlier: 3.641A pdb=" N HIS A 777 " --> pdb=" O GLY A 773 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LEU A 778 " --> pdb=" O VAL A 774 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASP A 788 " --> pdb=" O LEU A 784 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ILE A 789 " --> pdb=" O LYS A 785 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N PHE A 792 " --> pdb=" O ASP A 788 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL A 818 " --> pdb=" O SER A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 823 through 828 Processing helix chain 'A' and resid 837 through 1011 Proline residue: A 843 - end of helix removed outlier: 3.660A pdb=" N VAL A 847 " --> pdb=" O PRO A 843 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N GLN A 850 " --> pdb=" O GLN A 846 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N GLU A 851 " --> pdb=" O VAL A 847 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASP A 858 " --> pdb=" O LEU A 854 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLU A 899 " --> pdb=" O GLN A 895 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N THR A 900 " --> pdb=" O LEU A 896 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLN A 949 " --> pdb=" O LYS A 945 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N GLU A 957 " --> pdb=" O GLN A 953 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLN A 958 " --> pdb=" O ASP A 954 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU A 986 " --> pdb=" O LYS A 982 " (cutoff:3.500A) Processing helix chain 'A' and resid 1312 through 1523 removed outlier: 4.229A pdb=" N LYS A1520 " --> pdb=" O LEU A1516 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N ASP A1521 " --> pdb=" O MET A1517 " (cutoff:3.500A) Processing helix chain 'A' and resid 1534 through 1725 removed outlier: 3.954A pdb=" N LEU A1594 " --> pdb=" O LYS A1590 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N GLN A1597 " --> pdb=" O LEU A1593 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ARG A1659 " --> pdb=" O LYS A1655 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N GLU A1660 " --> pdb=" O ASP A1656 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLN A1674 " --> pdb=" O GLU A1670 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS A1680 " --> pdb=" O LYS A1676 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ARG A1704 " --> pdb=" O GLU A1700 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N HIS A1705 " --> pdb=" O ARG A1701 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA A1706 " --> pdb=" O ALA A1702 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 76 Processing helix chain 'B' and resid 81 through 85 Processing helix chain 'B' and resid 89 through 93 Processing helix chain 'B' and resid 97 through 110 Processing helix chain 'B' and resid 135 through 143 Processing helix chain 'B' and resid 146 through 150 Processing helix chain 'B' and resid 153 through 169 Processing helix chain 'B' and resid 183 through 199 Processing helix chain 'B' and resid 200 through 202 No H-bonds generated for 'chain 'B' and resid 200 through 202' Processing helix chain 'B' and resid 212 through 217 removed outlier: 3.965A pdb=" N GLN B 217 " --> pdb=" O GLU B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 220 No H-bonds generated for 'chain 'B' and resid 218 through 220' Processing helix chain 'B' and resid 221 through 227 removed outlier: 3.882A pdb=" N LEU B 225 " --> pdb=" O ALA B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 272 Processing helix chain 'B' and resid 281 through 291 removed outlier: 3.664A pdb=" N TYR B 285 " --> pdb=" O PHE B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 299 Processing helix chain 'B' and resid 321 through 336 Processing helix chain 'B' and resid 339 through 357 Processing helix chain 'B' and resid 375 through 386 Processing helix chain 'B' and resid 388 through 398 Processing helix chain 'B' and resid 413 through 444 Processing helix chain 'B' and resid 470 through 493 Processing helix chain 'B' and resid 493 through 502 Processing helix chain 'B' and resid 515 through 524 removed outlier: 3.785A pdb=" N ILE B 519 " --> pdb=" O LEU B 515 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ILE B 522 " --> pdb=" O CYS B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 530 through 539 removed outlier: 3.820A pdb=" N GLU B 537 " --> pdb=" O ALA B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 557 Processing helix chain 'B' and resid 590 through 597 Processing helix chain 'B' and resid 600 through 609 Processing helix chain 'B' and resid 612 through 619 Processing helix chain 'B' and resid 621 through 625 Processing helix chain 'B' and resid 652 through 669 Processing helix chain 'B' and resid 691 through 702 Processing helix chain 'B' and resid 703 through 714 Processing helix chain 'B' and resid 723 through 727 Processing helix chain 'B' and resid 728 through 732 Processing helix chain 'B' and resid 744 through 754 removed outlier: 4.799A pdb=" N MET B 750 " --> pdb=" O ALA B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 759 No H-bonds generated for 'chain 'B' and resid 757 through 759' Processing helix chain 'B' and resid 773 through 822 Processing helix chain 'B' and resid 823 through 828 Processing helix chain 'B' and resid 831 through 841 Processing helix chain 'B' and resid 842 through 845 Processing helix chain 'B' and resid 847 through 852 Processing helix chain 'B' and resid 855 through 1013 removed outlier: 3.609A pdb=" N LEU B 969 " --> pdb=" O ALA B 965 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ILE B 980 " --> pdb=" O ALA B 976 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LYS B 981 " --> pdb=" O GLU B 977 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N LYS B 982 " --> pdb=" O ALA B 978 " (cutoff:3.500A) Processing helix chain 'B' and resid 1312 through 1451 Processing helix chain 'B' and resid 1452 through 1523 Processing helix chain 'B' and resid 1523 through 1528 removed outlier: 3.627A pdb=" N VAL B1527 " --> pdb=" O VAL B1523 " (cutoff:3.500A) Processing helix chain 'B' and resid 1533 through 1603 removed outlier: 3.741A pdb=" N VAL B1598 " --> pdb=" O LEU B1594 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG B1599 " --> pdb=" O ILE B1595 " (cutoff:3.500A) Processing helix chain 'B' and resid 1604 through 1630 removed outlier: 3.938A pdb=" N ASP B1628 " --> pdb=" O ILE B1624 " (cutoff:3.500A) Processing helix chain 'B' and resid 1630 through 1727 removed outlier: 4.195A pdb=" N ARG B1640 " --> pdb=" O ALA B1636 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ASP B1641 " --> pdb=" O ASN B1637 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLU B1670 " --> pdb=" O ALA B1666 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASP B1715 " --> pdb=" O ASP B1711 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU B1716 " --> pdb=" O GLU B1712 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N THR B1718 " --> pdb=" O ALA B1714 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 20 Processing helix chain 'C' and resid 29 through 39 removed outlier: 4.257A pdb=" N GLY C 33 " --> pdb=" O TYR C 29 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N ASP C 34 " --> pdb=" O SER C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 52 Processing helix chain 'C' and resid 56 through 61 removed outlier: 3.557A pdb=" N ASN C 61 " --> pdb=" O SER C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 79 Proline residue: C 72 - end of helix Processing helix chain 'C' and resid 85 through 95 removed outlier: 3.762A pdb=" N LEU C 93 " --> pdb=" O TYR C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 114 Processing helix chain 'C' and resid 121 through 130 Processing helix chain 'C' and resid 141 through 150 removed outlier: 3.545A pdb=" N SER C 150 " --> pdb=" O ARG C 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 25 Processing helix chain 'D' and resid 26 through 41 Processing helix chain 'D' and resid 49 through 59 Processing helix chain 'D' and resid 65 through 74 removed outlier: 3.919A pdb=" N ALA D 71 " --> pdb=" O ALA D 67 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N MET D 72 " --> pdb=" O TYR D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 91 Processing helix chain 'D' and resid 98 through 108 Processing helix chain 'D' and resid 119 through 129 Processing helix chain 'D' and resid 134 through 144 removed outlier: 4.158A pdb=" N GLU D 144 " --> pdb=" O GLU D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 164 Processing helix chain 'E' and resid 18 through 23 Processing helix chain 'E' and resid 26 through 41 Processing helix chain 'E' and resid 49 through 59 Processing helix chain 'E' and resid 65 through 76 Processing helix chain 'E' and resid 82 through 94 Processing helix chain 'E' and resid 98 through 105 Processing helix chain 'E' and resid 106 through 110 Processing helix chain 'E' and resid 118 through 127 Processing helix chain 'E' and resid 134 through 144 Processing helix chain 'E' and resid 155 through 165 Processing helix chain 'F' and resid 5 through 17 Processing helix chain 'F' and resid 18 through 20 No H-bonds generated for 'chain 'F' and resid 18 through 20' Processing helix chain 'F' and resid 31 through 39 Processing helix chain 'F' and resid 44 through 52 removed outlier: 3.569A pdb=" N LEU F 52 " --> pdb=" O VAL F 48 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 61 Processing helix chain 'F' and resid 66 through 69 Processing helix chain 'F' and resid 70 through 78 removed outlier: 3.855A pdb=" N THR F 76 " --> pdb=" O PRO F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 93 removed outlier: 3.561A pdb=" N TYR F 89 " --> pdb=" O THR F 85 " (cutoff:3.500A) Processing helix chain 'F' and resid 106 through 114 Processing helix chain 'F' and resid 121 through 130 Processing helix chain 'F' and resid 140 through 149 Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 40 removed outlier: 5.817A pdb=" N ILE A 50 " --> pdb=" O GLU A 61 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N GLU A 61 " --> pdb=" O ILE A 50 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 115 through 118 removed outlier: 6.705A pdb=" N CYS A 122 " --> pdb=" O ARG A 677 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N ILE A 679 " --> pdb=" O CYS A 122 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N VAL A 124 " --> pdb=" O ILE A 679 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N SER A 173 " --> pdb=" O ASN A 674 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N VAL A 676 " --> pdb=" O SER A 173 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N LEU A 175 " --> pdb=" O VAL A 676 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N CYS A 678 " --> pdb=" O LEU A 175 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N THR A 177 " --> pdb=" O CYS A 678 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N GLN A 172 " --> pdb=" O GLY A 456 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N LEU A 458 " --> pdb=" O GLN A 172 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ILE A 174 " --> pdb=" O LEU A 458 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY A 258 " --> pdb=" O ASN A 249 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 230 through 231 Processing sheet with id=AA4, first strand: chain 'A' and resid 362 through 363 Processing sheet with id=AA5, first strand: chain 'A' and resid 400 through 403 Processing sheet with id=AA6, first strand: chain 'A' and resid 563 through 564 Processing sheet with id=AA7, first strand: chain 'A' and resid 717 through 720 Processing sheet with id=AA8, first strand: chain 'B' and resid 70 through 71 removed outlier: 7.144A pdb=" N GLU B 57 " --> pdb=" O GLU B 53 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N GLU B 53 " --> pdb=" O GLU B 57 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N MET B 59 " --> pdb=" O LYS B 51 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 115 through 118 removed outlier: 6.883A pdb=" N CYS B 122 " --> pdb=" O ARG B 677 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N ILE B 679 " --> pdb=" O CYS B 122 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL B 124 " --> pdb=" O ILE B 679 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N SER B 173 " --> pdb=" O ASN B 674 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N VAL B 676 " --> pdb=" O SER B 173 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LEU B 175 " --> pdb=" O VAL B 676 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N CYS B 678 " --> pdb=" O LEU B 175 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N THR B 177 " --> pdb=" O CYS B 678 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY B 258 " --> pdb=" O ASN B 249 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 362 through 364 Processing sheet with id=AB2, first strand: chain 'B' and resid 400 through 403 Processing sheet with id=AB3, first strand: chain 'B' and resid 575 through 579 Processing sheet with id=AB4, first strand: chain 'B' and resid 717 through 720 Processing sheet with id=AB5, first strand: chain 'C' and resid 27 through 28 Processing sheet with id=AB6, first strand: chain 'C' and resid 103 through 105 Processing sheet with id=AB7, first strand: chain 'D' and resid 47 through 48 Processing sheet with id=AB8, first strand: chain 'D' and resid 116 through 118 Processing sheet with id=AB9, first strand: chain 'E' and resid 47 through 48 Processing sheet with id=AC1, first strand: chain 'E' and resid 116 through 117 Processing sheet with id=AC2, first strand: chain 'F' and resid 27 through 28 Processing sheet with id=AC3, first strand: chain 'F' and resid 104 through 105 1995 hydrogen bonds defined for protein. 5799 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: 5.56 Time building geometry restraints manager: 3.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 5920 1.32 - 1.45: 5704 1.45 - 1.57: 16043 1.57 - 1.70: 19 1.70 - 1.82: 228 Bond restraints: 27914 Sorted by residual: bond pdb=" O2A ADP B2001 " pdb=" PA ADP B2001 " ideal model delta sigma weight residual 1.510 1.611 -0.101 2.00e-02 2.50e+03 2.58e+01 bond pdb=" O2B ADP A2002 " pdb=" PB ADP A2002 " ideal model delta sigma weight residual 1.510 1.610 -0.100 2.00e-02 2.50e+03 2.48e+01 bond pdb=" O2B ADP B2001 " pdb=" PB ADP B2001 " ideal model delta sigma weight residual 1.510 1.609 -0.099 2.00e-02 2.50e+03 2.44e+01 bond pdb=" O3B ADP B2001 " pdb=" PB ADP B2001 " ideal model delta sigma weight residual 1.510 1.608 -0.098 2.00e-02 2.50e+03 2.40e+01 bond pdb=" O3B ADP A2002 " pdb=" PB ADP A2002 " ideal model delta sigma weight residual 1.510 1.608 -0.098 2.00e-02 2.50e+03 2.40e+01 ... (remaining 27909 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.34: 36350 2.34 - 4.69: 914 4.69 - 7.03: 141 7.03 - 9.37: 30 9.37 - 11.72: 10 Bond angle restraints: 37445 Sorted by residual: angle pdb=" C ASN A 80 " pdb=" N PRO A 81 " pdb=" CA PRO A 81 " ideal model delta sigma weight residual 119.66 126.75 -7.09 7.30e-01 1.88e+00 9.43e+01 angle pdb=" C MET A 150 " pdb=" N PRO A 151 " pdb=" CA PRO A 151 " ideal model delta sigma weight residual 119.66 126.04 -6.38 7.20e-01 1.93e+00 7.86e+01 angle pdb=" C PHE A 715 " pdb=" N PRO A 716 " pdb=" CA PRO A 716 " ideal model delta sigma weight residual 119.56 127.57 -8.01 1.01e+00 9.80e-01 6.29e+01 angle pdb=" C PRO B 81 " pdb=" N PRO B 82 " pdb=" CA PRO B 82 " ideal model delta sigma weight residual 119.56 127.64 -8.08 1.02e+00 9.61e-01 6.27e+01 angle pdb=" C ASN C 54 " pdb=" N PRO C 55 " pdb=" CA PRO C 55 " ideal model delta sigma weight residual 120.31 128.00 -7.69 9.80e-01 1.04e+00 6.15e+01 ... (remaining 37440 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.71: 16937 26.71 - 53.43: 415 53.43 - 80.14: 74 80.14 - 106.85: 14 106.85 - 133.56: 2 Dihedral angle restraints: 17442 sinusoidal: 7529 harmonic: 9913 Sorted by residual: dihedral pdb=" CD ARG A 651 " pdb=" NE ARG A 651 " pdb=" CZ ARG A 651 " pdb=" NH1 ARG A 651 " ideal model delta sinusoidal sigma weight residual 0.00 83.83 -83.83 1 1.00e+01 1.00e-02 8.57e+01 dihedral pdb=" O2A ADP A2002 " pdb=" O3A ADP A2002 " pdb=" PA ADP A2002 " pdb=" PB ADP A2002 " ideal model delta sinusoidal sigma weight residual -60.00 73.56 -133.56 1 2.00e+01 2.50e-03 4.05e+01 dihedral pdb=" C5' ADP B2001 " pdb=" O5' ADP B2001 " pdb=" PA ADP B2001 " pdb=" O2A ADP B2001 " ideal model delta sinusoidal sigma weight residual 300.00 177.52 122.48 1 2.00e+01 2.50e-03 3.69e+01 ... (remaining 17439 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 2862 0.050 - 0.101: 845 0.101 - 0.151: 316 0.151 - 0.202: 31 0.202 - 0.252: 9 Chirality restraints: 4063 Sorted by residual: chirality pdb=" CA GLU A 464 " pdb=" N GLU A 464 " pdb=" C GLU A 464 " pdb=" CB GLU A 464 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" C3' ADP A2002 " pdb=" C2' ADP A2002 " pdb=" C4' ADP A2002 " pdb=" O3' ADP A2002 " both_signs ideal model delta sigma weight residual False -2.51 -2.74 0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" C3' ADP B2001 " pdb=" C2' ADP B2001 " pdb=" C4' ADP B2001 " pdb=" O3' ADP B2001 " both_signs ideal model delta sigma weight residual False -2.51 -2.74 0.23 2.00e-01 2.50e+01 1.30e+00 ... (remaining 4060 not shown) Planarity restraints: 4956 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' ADP A2002 " 0.264 2.00e-02 2.50e+03 1.05e-01 3.02e+02 pdb=" C2 ADP A2002 " -0.033 2.00e-02 2.50e+03 pdb=" C4 ADP A2002 " -0.077 2.00e-02 2.50e+03 pdb=" C5 ADP A2002 " -0.016 2.00e-02 2.50e+03 pdb=" C6 ADP A2002 " 0.039 2.00e-02 2.50e+03 pdb=" C8 ADP A2002 " -0.091 2.00e-02 2.50e+03 pdb=" N1 ADP A2002 " 0.029 2.00e-02 2.50e+03 pdb=" N3 ADP A2002 " -0.081 2.00e-02 2.50e+03 pdb=" N6 ADP A2002 " 0.112 2.00e-02 2.50e+03 pdb=" N7 ADP A2002 " -0.031 2.00e-02 2.50e+03 pdb=" N9 ADP A2002 " -0.115 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 651 " -1.107 9.50e-02 1.11e+02 4.96e-01 1.48e+02 pdb=" NE ARG A 651 " 0.066 2.00e-02 2.50e+03 pdb=" CZ ARG A 651 " 0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG A 651 " -0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG A 651 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' ADP B2001 " 0.160 2.00e-02 2.50e+03 6.35e-02 1.11e+02 pdb=" C2 ADP B2001 " -0.018 2.00e-02 2.50e+03 pdb=" C4 ADP B2001 " -0.044 2.00e-02 2.50e+03 pdb=" C5 ADP B2001 " -0.009 2.00e-02 2.50e+03 pdb=" C6 ADP B2001 " 0.028 2.00e-02 2.50e+03 pdb=" C8 ADP B2001 " -0.059 2.00e-02 2.50e+03 pdb=" N1 ADP B2001 " 0.019 2.00e-02 2.50e+03 pdb=" N3 ADP B2001 " -0.053 2.00e-02 2.50e+03 pdb=" N6 ADP B2001 " 0.062 2.00e-02 2.50e+03 pdb=" N7 ADP B2001 " -0.013 2.00e-02 2.50e+03 pdb=" N9 ADP B2001 " -0.073 2.00e-02 2.50e+03 ... (remaining 4953 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 291 2.62 - 3.19: 26765 3.19 - 3.76: 46389 3.76 - 4.33: 67654 4.33 - 4.90: 104472 Nonbonded interactions: 245571 Sorted by model distance: nonbonded pdb=" CB LYS B 235 " pdb=" OE2 GLU B 464 " model vdw 2.047 3.440 nonbonded pdb=" O ILE A 625 " pdb=" CG1 VAL A 626 " model vdw 2.117 3.460 nonbonded pdb=" NH2 ARG A 241 " pdb=" NH1 ARG A 270 " model vdw 2.169 3.200 nonbonded pdb=" OG1 THR A 185 " pdb="MG MG A2001 " model vdw 2.175 2.170 nonbonded pdb=" O1B ADP B2001 " pdb="MG MG B2003 " model vdw 2.175 2.170 ... (remaining 245566 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 33 through 204 or resid 211 through 1726)) selection = (chain 'B' and (resid 33 through 633 or resid 648 through 1011 or resid 1311 thr \ ough 1726)) } ncs_group { reference = chain 'C' selection = chain 'F' } ncs_group { reference = (chain 'D' and resid 13 through 171) selection = chain 'E' } 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: 8.280 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: 0.600 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 24.830 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 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 : 0.012 0.101 27914 Z= 0.688 Angle : 1.049 11.717 37445 Z= 0.745 Chirality : 0.055 0.252 4063 Planarity : 0.008 0.496 4956 Dihedral : 12.429 133.562 10972 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.09 % Allowed : 0.71 % Favored : 99.20 % Rotamer: Outliers : 0.24 % Allowed : 1.28 % Favored : 98.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.13), residues: 3357 helix: 0.34 (0.09), residues: 2256 sheet: 0.71 (0.35), residues: 180 loop : 1.33 (0.20), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 567 TYR 0.025 0.004 TYR A 142 PHE 0.023 0.003 PHE E 85 TRP 0.038 0.004 TRP A 834 HIS 0.004 0.001 HIS B1528 Details of bonding type rmsd/Z covalent geometry : bond 0.01243 / 0.69 (27914) covalent geometry : angle 1.04869 / 0.75 (37445) hydrogen bonds : bond 0.18931 / 12.70 ( 1995) hydrogen bonds : angle 7.04773 / 4.95 ( 5799) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 2972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 148 time to evaluate : 1.145 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: A 141 MET cc_start: 0.9222 (tmm) cc_final: 0.8657 (tmm) REVERT: A 165 MET cc_start: 0.9082 (ttp) cc_final: 0.8836 (ttm) REVERT: A 195 LEU cc_start: 0.9614 (mt) cc_final: 0.9297 (pp) REVERT: A 330 MET cc_start: 0.9259 (mtm) cc_final: 0.8853 (mtm) REVERT: A 750 MET cc_start: 0.8656 (mtp) cc_final: 0.8292 (mtp) REVERT: A 1353 GLU cc_start: 0.9128 (mt-10) cc_final: 0.8921 (tp30) REVERT: B 79 MET cc_start: 0.8405 (mtp) cc_final: 0.7958 (mtp) REVERT: B 336 MET cc_start: 0.8638 (mmm) cc_final: 0.8337 (tpt) REVERT: B 390 MET cc_start: 0.9204 (mmp) cc_final: 0.8845 (mpp) REVERT: B 491 MET cc_start: 0.9213 (ptt) cc_final: 0.8704 (ppp) REVERT: B 750 MET cc_start: 0.9055 (mtp) cc_final: 0.8455 (mmt) REVERT: B 909 MET cc_start: 0.8071 (mtm) cc_final: 0.7805 (tpt) REVERT: B 1711 ASP cc_start: 0.7646 (m-30) cc_final: 0.7359 (m-30) REVERT: C 73 MET cc_start: 0.9640 (mtm) cc_final: 0.9386 (mtt) REVERT: D 129 MET cc_start: 0.8403 (mmt) cc_final: 0.7950 (mmm) outliers start: 7 outliers final: 2 residues processed: 154 average time/residue: 0.1980 time to fit residues: 48.8558 Evaluate side-chains 113 residues out of total 2972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 111 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 0.7980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 43 HIS ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 355 GLN B 726 GLN E 94 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.040377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.027673 restraints weight = 510969.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.027734 restraints weight = 397161.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.027903 restraints weight = 338528.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.027672 restraints weight = 283400.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.027756 restraints weight = 250479.131| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.098 27914 Z= 0.172 Angle : 0.610 8.530 37445 Z= 0.332 Chirality : 0.038 0.324 4063 Planarity : 0.005 0.106 4956 Dihedral : 5.826 122.920 3671 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.06 % Allowed : 0.51 % Favored : 99.43 % Rotamer: Outliers : 0.03 % Allowed : 0.87 % Favored : 99.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % 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: 1.75 (0.14), residues: 3357 helix: 1.37 (0.10), residues: 2251 sheet: 0.57 (0.36), residues: 173 loop : 1.07 (0.21), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1701 TYR 0.020 0.002 TYR E 68 PHE 0.034 0.002 PHE E 85 TRP 0.013 0.002 TRP A 619 HIS 0.012 0.001 HIS B1528 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.17 (27914) covalent geometry : angle 0.60958 / 0.33 (37445) hydrogen bonds : bond 0.06841 / 4.51 ( 1995) hydrogen bonds : angle 5.32979 / 3.76 ( 5799) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 2972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 123 time to evaluate : 1.003 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 MET cc_start: 0.8488 (tpt) cc_final: 0.7840 (tpp) REVERT: A 79 MET cc_start: 0.4898 (mtt) cc_final: 0.4197 (mtt) REVERT: A 195 LEU cc_start: 0.9252 (mt) cc_final: 0.9004 (pp) REVERT: A 387 MET cc_start: 0.7246 (ptp) cc_final: 0.6633 (mmp) REVERT: B 79 MET cc_start: 0.8122 (mtp) cc_final: 0.7733 (mtp) REVERT: B 330 MET cc_start: 0.9431 (mtp) cc_final: 0.9156 (mmm) REVERT: B 336 MET cc_start: 0.8622 (mmm) cc_final: 0.8294 (tpt) REVERT: B 390 MET cc_start: 0.9273 (mmp) cc_final: 0.8964 (mpp) REVERT: B 458 LEU cc_start: 0.9342 (mt) cc_final: 0.9099 (tt) REVERT: B 1569 MET cc_start: 0.8409 (mtt) cc_final: 0.8057 (mtt) REVERT: D 129 MET cc_start: 0.7788 (mmt) cc_final: 0.7530 (mmm) outliers start: 1 outliers final: 1 residues processed: 124 average time/residue: 0.1720 time to fit residues: 36.1121 Evaluate side-chains 110 residues out of total 2972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 109 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 145 optimal weight: 7.9990 chunk 262 optimal weight: 5.9990 chunk 109 optimal weight: 6.9990 chunk 78 optimal weight: 0.7980 chunk 197 optimal weight: 9.9990 chunk 207 optimal weight: 7.9990 chunk 315 optimal weight: 0.0050 chunk 195 optimal weight: 7.9990 chunk 88 optimal weight: 3.9990 chunk 175 optimal weight: 7.9990 chunk 110 optimal weight: 5.9990 overall best weight: 3.3600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 148 HIS A 222 ASN A 260 ASN A 500 GLN A 846 GLN ** A1587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 409 GLN B 925 HIS C 147 HIS ** F 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.039132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.026345 restraints weight = 525886.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.026475 restraints weight = 390511.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.026659 restraints weight = 322463.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.026627 restraints weight = 271830.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.026691 restraints weight = 250158.703| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 27914 Z= 0.241 Angle : 0.635 10.152 37445 Z= 0.346 Chirality : 0.038 0.188 4063 Planarity : 0.004 0.056 4956 Dihedral : 5.568 117.331 3671 Min Nonbonded Distance : 1.745 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.10 % Favored : 98.87 % Rotamer: Outliers : 0.10 % Allowed : 1.31 % Favored : 98.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % 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: 1.42 (0.14), residues: 3357 helix: 1.27 (0.10), residues: 2276 sheet: -0.22 (0.35), residues: 191 loop : 0.64 (0.21), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1701 TYR 0.018 0.002 TYR A 314 PHE 0.028 0.002 PHE E 85 TRP 0.027 0.003 TRP A 619 HIS 0.008 0.002 HIS A 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.24 (27914) covalent geometry : angle 0.63518 / 0.35 (37445) hydrogen bonds : bond 0.06185 / 4.09 ( 1995) hydrogen bonds : angle 5.16282 / 3.64 ( 5799) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 2972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 112 time to evaluate : 1.193 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: symmetry clash REVERT: A 79 MET cc_start: 0.5734 (mtt) cc_final: 0.4826 (mtt) REVERT: B 79 MET cc_start: 0.8153 (mtp) cc_final: 0.7809 (mpp) REVERT: B 330 MET cc_start: 0.9487 (mtp) cc_final: 0.9080 (mmm) REVERT: B 336 MET cc_start: 0.8693 (mmm) cc_final: 0.8270 (tpt) REVERT: B 390 MET cc_start: 0.9228 (mmp) cc_final: 0.8998 (mpp) REVERT: B 1569 MET cc_start: 0.8414 (mtt) cc_final: 0.8137 (mtt) REVERT: D 129 MET cc_start: 0.8185 (mmt) cc_final: 0.7851 (mmm) REVERT: F 73 MET cc_start: 0.7985 (mmp) cc_final: 0.7782 (mmp) outliers start: 3 outliers final: 2 residues processed: 115 average time/residue: 0.1848 time to fit residues: 36.0534 Evaluate side-chains 104 residues out of total 2972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 102 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 225 optimal weight: 3.9990 chunk 236 optimal weight: 0.6980 chunk 22 optimal weight: 9.9990 chunk 71 optimal weight: 9.9990 chunk 276 optimal weight: 9.9990 chunk 79 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 224 optimal weight: 0.9980 chunk 52 optimal weight: 4.9990 chunk 183 optimal weight: 6.9990 chunk 23 optimal weight: 1.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 379 GLN A1505 GLN A1528 HIS B 609 GLN B1372 GLN C 132 HIS D 152 ASN F 111 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.039388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.027091 restraints weight = 526631.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.027127 restraints weight = 389233.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.026999 restraints weight = 330847.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.027100 restraints weight = 270762.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.027072 restraints weight = 237035.477| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 27914 Z= 0.157 Angle : 0.548 11.142 37445 Z= 0.293 Chirality : 0.037 0.352 4063 Planarity : 0.003 0.048 4956 Dihedral : 5.403 113.478 3671 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.01 % Favored : 98.96 % Rotamer: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % 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: 1.55 (0.14), residues: 3357 helix: 1.45 (0.10), residues: 2271 sheet: -0.42 (0.36), residues: 184 loop : 0.49 (0.21), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 651 TYR 0.021 0.002 TYR A 142 PHE 0.025 0.002 PHE E 85 TRP 0.036 0.003 TRP B 591 HIS 0.006 0.001 HIS B 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.16 (27914) covalent geometry : angle 0.54770 / 0.29 (37445) hydrogen bonds : bond 0.05662 / 3.73 ( 1995) hydrogen bonds : angle 4.98691 / 3.52 ( 5799) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 2972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 1.125 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: A 59 MET cc_start: 0.8591 (mmm) cc_final: 0.8252 (mmm) REVERT: A 79 MET cc_start: 0.5694 (mtt) cc_final: 0.5021 (mtt) REVERT: A 165 MET cc_start: 0.7689 (ttt) cc_final: 0.7326 (tpp) REVERT: A 195 LEU cc_start: 0.9308 (mt) cc_final: 0.9041 (pp) REVERT: A 387 MET cc_start: 0.7305 (ptp) cc_final: 0.6681 (mmp) REVERT: A 649 MET cc_start: 0.4423 (tmm) cc_final: 0.3738 (ppp) REVERT: A 750 MET cc_start: 0.7638 (mtt) cc_final: 0.7220 (mtt) REVERT: B 70 MET cc_start: 0.7340 (ttp) cc_final: 0.7093 (ttp) REVERT: B 79 MET cc_start: 0.8162 (mtp) cc_final: 0.7816 (mpp) REVERT: B 330 MET cc_start: 0.9470 (mtp) cc_final: 0.9171 (mmm) REVERT: B 336 MET cc_start: 0.8702 (mmm) cc_final: 0.8228 (tpt) REVERT: B 390 MET cc_start: 0.9268 (mmp) cc_final: 0.9041 (mpp) REVERT: B 1569 MET cc_start: 0.8464 (mtt) cc_final: 0.8205 (mtt) REVERT: D 129 MET cc_start: 0.8154 (mmt) cc_final: 0.7859 (mmm) REVERT: E 72 MET cc_start: 0.5732 (mmt) cc_final: 0.4782 (mmt) REVERT: F 73 MET cc_start: 0.7837 (mmp) cc_final: 0.7488 (mmt) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.1731 time to fit residues: 32.4650 Evaluate side-chains 100 residues out of total 2972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 333 optimal weight: 9.9990 chunk 155 optimal weight: 2.9990 chunk 31 optimal weight: 7.9990 chunk 152 optimal weight: 7.9990 chunk 116 optimal weight: 20.0000 chunk 119 optimal weight: 8.9990 chunk 218 optimal weight: 8.9990 chunk 47 optimal weight: 0.4980 chunk 178 optimal weight: 9.9990 chunk 7 optimal weight: 6.9990 chunk 263 optimal weight: 6.9990 overall best weight: 5.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 496 GLN A 812 GLN ** B 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 222 ASN ** B 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 555 GLN B 777 HIS ** B1441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 GLN ** D 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 54 HIS ** F 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.038093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.025748 restraints weight = 547223.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.025817 restraints weight = 415757.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.025702 restraints weight = 332315.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.025840 restraints weight = 284287.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.025873 restraints weight = 252143.249| |-----------------------------------------------------------------------------| r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.3448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 27914 Z= 0.304 Angle : 0.745 13.202 37445 Z= 0.398 Chirality : 0.039 0.195 4063 Planarity : 0.005 0.051 4956 Dihedral : 5.773 119.099 3671 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 22.26 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.76 % Favored : 98.21 % Rotamer: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % 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: 0.88 (0.14), residues: 3357 helix: 0.99 (0.10), residues: 2288 sheet: -0.86 (0.37), residues: 167 loop : 0.08 (0.21), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 431 TYR 0.024 0.003 TYR A 314 PHE 0.028 0.003 PHE B1502 TRP 0.032 0.003 TRP A 619 HIS 0.008 0.002 HIS A 831 Details of bonding type rmsd/Z covalent geometry : bond 0.00595 / 0.30 (27914) covalent geometry : angle 0.74459 / 0.40 (37445) hydrogen bonds : bond 0.06008 / 3.98 ( 1995) hydrogen bonds : angle 5.26775 / 3.71 ( 5799) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 2972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 1.147 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: A 59 MET cc_start: 0.8677 (mmm) cc_final: 0.8347 (mmm) REVERT: A 70 MET cc_start: 0.9051 (tpp) cc_final: 0.8703 (tpp) REVERT: A 79 MET cc_start: 0.6648 (mtt) cc_final: 0.5755 (mtt) REVERT: A 387 MET cc_start: 0.7517 (ptp) cc_final: 0.6558 (mmp) REVERT: A 750 MET cc_start: 0.7908 (mtt) cc_final: 0.7480 (mtt) REVERT: B 79 MET cc_start: 0.8298 (mtp) cc_final: 0.7909 (mpp) REVERT: B 330 MET cc_start: 0.9512 (mtp) cc_final: 0.9116 (mmm) REVERT: B 336 MET cc_start: 0.8776 (mmm) cc_final: 0.8318 (tpt) REVERT: B 346 MET cc_start: 0.8280 (ppp) cc_final: 0.8034 (ppp) REVERT: B 390 MET cc_start: 0.9277 (mmp) cc_final: 0.9074 (mpp) REVERT: B 750 MET cc_start: 0.8779 (mtp) cc_final: 0.8318 (mmm) REVERT: B 1569 MET cc_start: 0.8516 (mtt) cc_final: 0.8264 (mtt) REVERT: D 129 MET cc_start: 0.8401 (mmt) cc_final: 0.8101 (mmm) REVERT: E 72 MET cc_start: 0.5709 (mmt) cc_final: 0.4723 (mmt) outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.1673 time to fit residues: 30.4468 Evaluate side-chains 98 residues out of total 2972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 147 optimal weight: 2.9990 chunk 50 optimal weight: 10.0000 chunk 178 optimal weight: 0.9990 chunk 90 optimal weight: 9.9990 chunk 190 optimal weight: 0.9990 chunk 186 optimal weight: 9.9990 chunk 286 optimal weight: 0.0670 chunk 227 optimal weight: 6.9990 chunk 107 optimal weight: 0.9980 chunk 3 optimal weight: 10.0000 chunk 173 optimal weight: 0.9990 overall best weight: 0.8124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 80 ASN A 260 ASN ** A 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 ASN B 500 GLN B1632 GLN D 152 ASN E 94 ASN ** F 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 111 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.039158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.027404 restraints weight = 529503.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.027530 restraints weight = 406937.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.027197 restraints weight = 308415.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.027355 restraints weight = 284327.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.027478 restraints weight = 251609.486| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.3385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 27914 Z= 0.139 Angle : 0.548 10.509 37445 Z= 0.289 Chirality : 0.037 0.209 4063 Planarity : 0.003 0.038 4956 Dihedral : 5.452 110.102 3671 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.31 % Favored : 98.66 % Rotamer: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % 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: 1.37 (0.14), residues: 3357 helix: 1.41 (0.10), residues: 2285 sheet: -0.91 (0.36), residues: 176 loop : 0.22 (0.21), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1583 TYR 0.016 0.002 TYR A 826 PHE 0.040 0.002 PHE A 487 TRP 0.023 0.002 TRP B 591 HIS 0.012 0.001 HIS F 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.14 (27914) covalent geometry : angle 0.54828 / 0.29 (37445) hydrogen bonds : bond 0.05363 / 3.52 ( 1995) hydrogen bonds : angle 4.93496 / 3.48 ( 5799) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 2972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 1.137 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: A 59 MET cc_start: 0.8452 (mmm) cc_final: 0.8161 (mmm) REVERT: A 70 MET cc_start: 0.8897 (tpp) cc_final: 0.8632 (tpp) REVERT: A 79 MET cc_start: 0.6321 (mtt) cc_final: 0.5633 (mtt) REVERT: A 195 LEU cc_start: 0.9288 (mt) cc_final: 0.9020 (pp) REVERT: A 387 MET cc_start: 0.7462 (ptp) cc_final: 0.6616 (mmp) REVERT: A 1513 MET cc_start: 0.2067 (mmp) cc_final: 0.1793 (mmp) REVERT: B 79 MET cc_start: 0.8209 (mtp) cc_final: 0.7852 (mpp) REVERT: B 330 MET cc_start: 0.9522 (mtp) cc_final: 0.9255 (mmm) REVERT: B 336 MET cc_start: 0.8699 (mmm) cc_final: 0.8265 (tpt) REVERT: B 390 MET cc_start: 0.9396 (mmp) cc_final: 0.9182 (mpp) REVERT: B 983 MET cc_start: 0.7213 (ptt) cc_final: 0.6948 (ptt) REVERT: B 1569 MET cc_start: 0.8444 (mtt) cc_final: 0.8176 (mtt) REVERT: E 72 MET cc_start: 0.5981 (mmt) cc_final: 0.5276 (mmt) outliers start: 0 outliers final: 0 residues processed: 107 average time/residue: 0.1689 time to fit residues: 31.6655 Evaluate side-chains 100 residues out of total 2972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 92 optimal weight: 5.9990 chunk 296 optimal weight: 0.7980 chunk 48 optimal weight: 7.9990 chunk 69 optimal weight: 7.9990 chunk 156 optimal weight: 4.9990 chunk 311 optimal weight: 9.9990 chunk 180 optimal weight: 9.9990 chunk 85 optimal weight: 5.9990 chunk 36 optimal weight: 10.0000 chunk 322 optimal weight: 10.0000 chunk 216 optimal weight: 0.6980 overall best weight: 3.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 187 ASN ** A 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 ASN ** B1441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 31 GLN ** F 54 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 = 0.3527 r_free = 0.3527 target = 0.038270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.026375 restraints weight = 546125.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.025887 restraints weight = 414405.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 70)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.025796 restraints weight = 327751.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.025885 restraints weight = 285774.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.025961 restraints weight = 253640.131| |-----------------------------------------------------------------------------| r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.3764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 27914 Z= 0.231 Angle : 0.633 10.048 37445 Z= 0.340 Chirality : 0.038 0.236 4063 Planarity : 0.004 0.042 4956 Dihedral : 5.545 108.222 3671 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 18.51 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.97 % Favored : 98.00 % Rotamer: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % 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: 1.16 (0.14), residues: 3357 helix: 1.27 (0.10), residues: 2278 sheet: -0.82 (0.37), residues: 167 loop : 0.02 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 651 TYR 0.020 0.002 TYR A 314 PHE 0.044 0.002 PHE B 997 TRP 0.021 0.002 TRP A 619 HIS 0.009 0.002 HIS A 489 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.23 (27914) covalent geometry : angle 0.63259 / 0.34 (37445) hydrogen bonds : bond 0.05524 / 3.65 ( 1995) hydrogen bonds : angle 5.09829 / 3.58 ( 5799) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 2972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 1.165 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: A 59 MET cc_start: 0.8529 (mmm) cc_final: 0.8283 (mmm) REVERT: A 70 MET cc_start: 0.8933 (tpp) cc_final: 0.8480 (tpp) REVERT: A 79 MET cc_start: 0.6505 (mtt) cc_final: 0.5699 (mtt) REVERT: A 195 LEU cc_start: 0.9329 (mt) cc_final: 0.9039 (pp) REVERT: A 387 MET cc_start: 0.7837 (ptp) cc_final: 0.6793 (mmp) REVERT: A 1513 MET cc_start: 0.1591 (mmp) cc_final: 0.1073 (mmm) REVERT: B 79 MET cc_start: 0.8213 (mtp) cc_final: 0.7791 (mpp) REVERT: B 330 MET cc_start: 0.9498 (mtp) cc_final: 0.9163 (mmm) REVERT: B 336 MET cc_start: 0.8779 (mmm) cc_final: 0.8310 (tpt) REVERT: B 346 MET cc_start: 0.8121 (ppp) cc_final: 0.7902 (ppp) REVERT: B 390 MET cc_start: 0.9262 (mmp) cc_final: 0.9057 (mpp) REVERT: B 983 MET cc_start: 0.7408 (ptt) cc_final: 0.7166 (ptt) REVERT: B 1569 MET cc_start: 0.8429 (mtt) cc_final: 0.8175 (mtt) REVERT: D 129 MET cc_start: 0.7970 (mmp) cc_final: 0.7623 (mmm) REVERT: E 72 MET cc_start: 0.6113 (mmt) cc_final: 0.5293 (mmt) outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.1716 time to fit residues: 31.1027 Evaluate side-chains 97 residues out of total 2972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 113 optimal weight: 3.9990 chunk 223 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 132 optimal weight: 10.0000 chunk 78 optimal weight: 10.0000 chunk 302 optimal weight: 3.9990 chunk 134 optimal weight: 20.0000 chunk 72 optimal weight: 2.9990 chunk 220 optimal weight: 3.9990 chunk 279 optimal weight: 6.9990 chunk 157 optimal weight: 10.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 80 ASN ** A 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 ASN ** F 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.038373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.026188 restraints weight = 546979.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.026188 restraints weight = 401174.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.026188 restraints weight = 401142.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.026188 restraints weight = 401142.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.026188 restraints weight = 401142.506| |-----------------------------------------------------------------------------| r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.3997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 27914 Z= 0.186 Angle : 0.586 11.357 37445 Z= 0.313 Chirality : 0.037 0.178 4063 Planarity : 0.004 0.041 4956 Dihedral : 5.548 106.136 3671 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 16.91 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.03 % Favored : 97.94 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % 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: 1.15 (0.14), residues: 3357 helix: 1.31 (0.10), residues: 2282 sheet: -0.90 (0.38), residues: 164 loop : -0.12 (0.21), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 752 TYR 0.019 0.002 TYR A 142 PHE 0.027 0.002 PHE B 997 TRP 0.019 0.002 TRP B 591 HIS 0.007 0.001 HIS B 951 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.19 (27914) covalent geometry : angle 0.58595 / 0.31 (37445) hydrogen bonds : bond 0.05342 / 3.53 ( 1995) hydrogen bonds : angle 5.03434 / 3.53 ( 5799) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 2972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 1.158 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: A 59 MET cc_start: 0.8600 (mmm) cc_final: 0.8295 (mmm) REVERT: A 70 MET cc_start: 0.8986 (tpp) cc_final: 0.8528 (tpp) REVERT: A 195 LEU cc_start: 0.9457 (mt) cc_final: 0.9140 (pp) REVERT: A 387 MET cc_start: 0.7905 (ptp) cc_final: 0.6707 (mmp) REVERT: B 79 MET cc_start: 0.8402 (mtp) cc_final: 0.8002 (mpp) REVERT: B 330 MET cc_start: 0.9533 (mtp) cc_final: 0.9213 (mmm) REVERT: B 336 MET cc_start: 0.8794 (mmm) cc_final: 0.8388 (tpt) REVERT: B 983 MET cc_start: 0.7408 (ptt) cc_final: 0.7175 (ptt) REVERT: B 1569 MET cc_start: 0.8350 (mtt) cc_final: 0.8109 (mtt) REVERT: D 129 MET cc_start: 0.7844 (mmp) cc_final: 0.7601 (mmm) REVERT: E 72 MET cc_start: 0.4766 (mmt) cc_final: 0.3776 (mmm) outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.1665 time to fit residues: 30.2027 Evaluate side-chains 98 residues out of total 2972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 167 optimal weight: 0.8980 chunk 220 optimal weight: 7.9990 chunk 154 optimal weight: 0.0770 chunk 318 optimal weight: 9.9990 chunk 271 optimal weight: 20.0000 chunk 43 optimal weight: 0.8980 chunk 190 optimal weight: 9.9990 chunk 277 optimal weight: 9.9990 chunk 170 optimal weight: 30.0000 chunk 181 optimal weight: 7.9990 chunk 239 optimal weight: 7.9990 overall best weight: 3.5742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 412 GLN A 496 GLN ** A 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 ASN ** B1441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 54 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 = 0.3519 r_free = 0.3519 target = 0.038097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.026024 restraints weight = 549972.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.026159 restraints weight = 407430.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.026144 restraints weight = 326480.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.026067 restraints weight = 275343.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.026048 restraints weight = 251384.709| |-----------------------------------------------------------------------------| r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.4233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 27914 Z= 0.217 Angle : 0.624 9.370 37445 Z= 0.334 Chirality : 0.038 0.176 4063 Planarity : 0.004 0.046 4956 Dihedral : 5.646 105.995 3671 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 19.64 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.32 % Favored : 97.65 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % 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: 0.97 (0.14), residues: 3357 helix: 1.20 (0.10), residues: 2280 sheet: -0.98 (0.38), residues: 157 loop : -0.29 (0.21), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A1007 TYR 0.019 0.002 TYR A 314 PHE 0.029 0.002 PHE B 997 TRP 0.021 0.002 TRP A 832 HIS 0.007 0.001 HIS F 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.22 (27914) covalent geometry : angle 0.62362 / 0.33 (37445) hydrogen bonds : bond 0.05385 / 3.56 ( 1995) hydrogen bonds : angle 5.09230 / 3.56 ( 5799) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 2972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.895 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: A 59 MET cc_start: 0.8756 (mmm) cc_final: 0.8523 (mmm) REVERT: A 195 LEU cc_start: 0.9825 (mt) cc_final: 0.9557 (pp) REVERT: A 387 MET cc_start: 0.8939 (ptp) cc_final: 0.7889 (mmm) REVERT: A 750 MET cc_start: 0.8891 (mtp) cc_final: 0.8614 (mtp) REVERT: B 330 MET cc_start: 0.9490 (mtp) cc_final: 0.9174 (mmm) REVERT: B 336 MET cc_start: 0.8296 (mmm) cc_final: 0.8045 (tpt) REVERT: B 593 MET cc_start: 0.9059 (mmp) cc_final: 0.8497 (tmm) REVERT: B 596 MET cc_start: 0.8241 (ptp) cc_final: 0.7749 (ptt) REVERT: B 983 MET cc_start: 0.8001 (ptt) cc_final: 0.7794 (ptt) REVERT: B 1569 MET cc_start: 0.9170 (mtt) cc_final: 0.8949 (mtt) REVERT: C 120 MET cc_start: 0.8888 (mmp) cc_final: 0.8598 (mmm) REVERT: D 129 MET cc_start: 0.8952 (mmp) cc_final: 0.8501 (mmm) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.1679 time to fit residues: 30.2158 Evaluate side-chains 97 residues out of total 2972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 269 optimal weight: 20.0000 chunk 32 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 12 optimal weight: 8.9990 chunk 297 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 248 optimal weight: 4.9990 chunk 265 optimal weight: 4.9990 chunk 218 optimal weight: 5.9990 chunk 169 optimal weight: 0.9990 chunk 258 optimal weight: 0.9980 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 496 GLN ** A 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.038335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.025841 restraints weight = 551621.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.025870 restraints weight = 423964.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.025599 restraints weight = 337214.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.025689 restraints weight = 289294.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.025715 restraints weight = 258053.054| |-----------------------------------------------------------------------------| r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.4321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.095 27914 Z= 0.176 Angle : 0.589 8.812 37445 Z= 0.314 Chirality : 0.038 0.274 4063 Planarity : 0.004 0.046 4956 Dihedral : 5.626 104.329 3671 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 17.16 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.11 % Favored : 97.86 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % 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: 1.05 (0.14), residues: 3357 helix: 1.28 (0.10), residues: 2287 sheet: -1.17 (0.37), residues: 173 loop : -0.26 (0.21), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 143 TYR 0.018 0.002 TYR A 728 PHE 0.030 0.002 PHE B 997 TRP 0.018 0.002 TRP A 832 HIS 0.005 0.001 HIS B 489 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.18 (27914) covalent geometry : angle 0.58938 / 0.31 (37445) hydrogen bonds : bond 0.05246 / 3.47 ( 1995) hydrogen bonds : angle 5.02743 / 3.51 ( 5799) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 2972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.953 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: A 59 MET cc_start: 0.8407 (mmm) cc_final: 0.8076 (mmm) REVERT: A 70 MET cc_start: 0.8971 (tpp) cc_final: 0.8746 (tpp) REVERT: A 195 LEU cc_start: 0.9296 (mt) cc_final: 0.9012 (pp) REVERT: A 387 MET cc_start: 0.7790 (ptp) cc_final: 0.6569 (mmp) REVERT: B 330 MET cc_start: 0.9510 (mtp) cc_final: 0.9219 (mmm) REVERT: B 336 MET cc_start: 0.8761 (mmm) cc_final: 0.8251 (tpt) REVERT: B 593 MET cc_start: 0.8940 (mmp) cc_final: 0.8499 (tmm) REVERT: B 596 MET cc_start: 0.8209 (ptp) cc_final: 0.7709 (ptt) REVERT: B 1544 MET cc_start: 0.8050 (ptt) cc_final: 0.7756 (ptt) REVERT: B 1569 MET cc_start: 0.8444 (mtt) cc_final: 0.8184 (mtt) REVERT: D 129 MET cc_start: 0.8160 (mmp) cc_final: 0.7809 (mmm) outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.1639 time to fit residues: 29.7126 Evaluate side-chains 97 residues out of total 2972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 121 optimal weight: 0.9990 chunk 330 optimal weight: 5.9990 chunk 322 optimal weight: 0.9980 chunk 79 optimal weight: 0.0470 chunk 231 optimal weight: 9.9990 chunk 225 optimal weight: 9.9990 chunk 170 optimal weight: 2.9990 chunk 259 optimal weight: 1.9990 chunk 128 optimal weight: 20.0000 chunk 289 optimal weight: 0.1980 chunk 262 optimal weight: 0.1980 overall best weight: 0.4880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 54 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.038974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.027521 restraints weight = 536193.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.026758 restraints weight = 417246.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.026800 restraints weight = 340812.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.026346 restraints weight = 276777.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.026465 restraints weight = 238909.407| |-----------------------------------------------------------------------------| r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.4285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.083 27914 Z= 0.127 Angle : 0.551 9.451 37445 Z= 0.288 Chirality : 0.037 0.169 4063 Planarity : 0.003 0.040 4956 Dihedral : 5.382 96.071 3671 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.40 % Favored : 98.57 % Rotamer: Outliers : 0.00 % Allowed : 0.07 % Favored : 99.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.14), residues: 3357 helix: 1.51 (0.10), residues: 2287 sheet: -0.93 (0.37), residues: 181 loop : -0.15 (0.21), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 910 TYR 0.015 0.001 TYR A 728 PHE 0.030 0.002 PHE B 997 TRP 0.016 0.002 TRP B 37 HIS 0.004 0.001 HIS B 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.13 (27914) covalent geometry : angle 0.55105 / 0.29 (37445) hydrogen bonds : bond 0.04969 / 3.28 ( 1995) hydrogen bonds : angle 4.83943 / 3.39 ( 5799) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8117.58 seconds wall clock time: 139 minutes 53.29 seconds (8393.29 seconds total)