Starting phenix.real_space_refine on Fri Mar 15 19:01:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7niw_12367/03_2024/7niw_12367_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7niw_12367/03_2024/7niw_12367.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7niw_12367/03_2024/7niw_12367.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7niw_12367/03_2024/7niw_12367.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7niw_12367/03_2024/7niw_12367_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7niw_12367/03_2024/7niw_12367_updated.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 1 5.49 5 S 41 5.16 5 C 8055 2.51 5 N 2067 2.21 5 O 2311 1.98 5 F 2 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 115": "NH1" <-> "NH2" Residue "A GLU 172": "OE1" <-> "OE2" Residue "A GLU 186": "OE1" <-> "OE2" Residue "A ARG 264": "NH1" <-> "NH2" Residue "A ARG 278": "NH1" <-> "NH2" Residue "A GLU 528": "OE1" <-> "OE2" Residue "A ARG 590": "NH1" <-> "NH2" Residue "A GLU 616": "OE1" <-> "OE2" Residue "A PHE 739": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 774": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 831": "NH1" <-> "NH2" Residue "A ARG 884": "NH1" <-> "NH2" Residue "A GLU 888": "OE1" <-> "OE2" Residue "A ARG 913": "NH1" <-> "NH2" Residue "A ARG 971": "NH1" <-> "NH2" Residue "A ARG 1013": "NH1" <-> "NH2" Residue "A ARG 1137": "NH1" <-> "NH2" Residue "A GLU 1165": "OE1" <-> "OE2" Residue "A GLU 1208": "OE1" <-> "OE2" Residue "A GLU 1222": "OE1" <-> "OE2" Residue "A ARG 1232": "NH1" <-> "NH2" Residue "B ARG 109": "NH1" <-> "NH2" Residue "B GLU 144": "OE1" <-> "OE2" Residue "C ARG 41": "NH1" <-> "NH2" Residue "C GLU 49": "OE1" <-> "OE2" Residue "C ARG 101": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 12477 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1140, 8831 Classifications: {'peptide': 1140} Link IDs: {'PTRANS': 29, 'TRANS': 1110} Chain breaks: 2 Chain: "B" Number of atoms: 1616 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 211, 1610 Classifications: {'peptide': 211} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 200} Conformer: "B" Number of residues, atoms: 211, 1607 Classifications: {'peptide': 211} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 200} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 1631 Chain: "C" Number of atoms: 1757 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 234, 1757 Classifications: {'peptide': 234} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 222} Chain: "A" Number of atoms: 273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 273 Unusual residues: {'CLR': 6, 'DLP': 1, 'X2N': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Time building chain proxies: 7.68, per 1000 atoms: 0.62 Number of scatterers: 12477 At special positions: 0 Unit cell: (120.12, 127.38, 128.04, 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 41 16.00 P 1 15.00 F 2 9.00 O 2311 8.00 N 2067 7.00 C 8055 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 24 " - pdb=" SG CYS B 89 " distance=2.03 Simple disulfide: pdb=" SG CYS B 135 " - pdb=" SG CYS B 195 " distance=2.04 Simple disulfide: pdb=" SG CYS C 25 " - pdb=" SG CYS C 99 " distance=2.02 Simple disulfide: pdb=" SG CYS C 160 " - pdb=" SG CYS C 216 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 5.05 Conformation dependent library (CDL) restraints added in 2.7 seconds 3154 Ramachandran restraints generated. 1577 Oldfield, 0 Emsley, 1577 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2922 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 43 helices and 16 sheets defined 45.0% alpha, 8.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.12 Creating SS restraints... Processing helix chain 'A' and resid 51 through 91 removed outlier: 4.351A pdb=" N MET A 63 " --> pdb=" O LEU A 59 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N GLY A 70 " --> pdb=" O ALA A 66 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N LEU A 71 " --> pdb=" O HIS A 67 " (cutoff:3.500A) Proline residue: A 72 - end of helix Processing helix chain 'A' and resid 107 through 158 Processing helix chain 'A' and resid 162 through 167 Processing helix chain 'A' and resid 171 through 189 Processing helix chain 'A' and resid 191 through 212 Processing helix chain 'A' and resid 214 through 251 removed outlier: 3.910A pdb=" N ILE A 223 " --> pdb=" O VAL A 219 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER A 224 " --> pdb=" O ILE A 220 " (cutoff:3.500A) Proline residue: A 225 - end of helix Processing helix chain 'A' and resid 254 through 258 Processing helix chain 'A' and resid 263 through 269 Processing helix chain 'A' and resid 273 through 324 removed outlier: 4.277A pdb=" N HIS A 282 " --> pdb=" O ARG A 278 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASN A 285 " --> pdb=" O LYS A 281 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N GLU A 288 " --> pdb=" O GLU A 284 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ILE A 289 " --> pdb=" O ASN A 285 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LYS A 292 " --> pdb=" O GLU A 288 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N VAL A 323 " --> pdb=" O GLY A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 348 removed outlier: 3.898A pdb=" N VAL A 336 " --> pdb=" O ASN A 332 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE A 337 " --> pdb=" O ALA A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 371 removed outlier: 4.581A pdb=" N PHE A 357 " --> pdb=" O CYS A 353 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N VAL A 366 " --> pdb=" O GLY A 362 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ILE A 367 " --> pdb=" O ALA A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 442 Processing helix chain 'A' and resid 465 through 471 Processing helix chain 'A' and resid 486 through 494 removed outlier: 3.703A pdb=" N ARG A 494 " --> pdb=" O ILE A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 508 Processing helix chain 'A' and resid 536 through 547 Processing helix chain 'A' and resid 565 through 578 Processing helix chain 'A' and resid 614 through 618 Processing helix chain 'A' and resid 623 through 628 Processing helix chain 'A' and resid 698 through 704 removed outlier: 4.506A pdb=" N ASN A 704 " --> pdb=" O VAL A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 722 Processing helix chain 'A' and resid 724 through 739 removed outlier: 3.813A pdb=" N PHE A 739 " --> pdb=" O ILE A 735 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 795 removed outlier: 3.901A pdb=" N GLN A 749 " --> pdb=" O ALA A 745 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE A 766 " --> pdb=" O GLY A 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 804 No H-bonds generated for 'chain 'A' and resid 802 through 804' Processing helix chain 'A' and resid 810 through 852 removed outlier: 3.867A pdb=" N ALA A 821 " --> pdb=" O LEU A 817 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N ALA A 822 " --> pdb=" O ALA A 818 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N GLN A 825 " --> pdb=" O ALA A 821 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N GLY A 826 " --> pdb=" O ALA A 822 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA A 827 " --> pdb=" O GLN A 823 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N ARG A 831 " --> pdb=" O ALA A 827 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N LEU A 832 " --> pdb=" O THR A 828 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N THR A 844 " --> pdb=" O ALA A 840 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N GLY A 845 " --> pdb=" O ASN A 841 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ILE A 846 " --> pdb=" O LEU A 842 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 901 removed outlier: 4.120A pdb=" N VAL A 863 " --> pdb=" O LEU A 859 " (cutoff:3.500A) Proline residue: A 865 - end of helix removed outlier: 5.764A pdb=" N GLY A 871 " --> pdb=" O ILE A 867 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ILE A 872 " --> pdb=" O ALA A 868 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ALA A 899 " --> pdb=" O ILE A 895 " (cutoff:3.500A) Processing helix chain 'A' and resid 903 through 908 Processing helix chain 'A' and resid 912 through 965 removed outlier: 3.859A pdb=" N SER A 917 " --> pdb=" O ARG A 913 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LYS A 922 " --> pdb=" O MET A 918 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N GLY A 925 " --> pdb=" O GLU A 921 " (cutoff:3.500A) Proline residue: A 926 - end of helix removed outlier: 4.181A pdb=" N HIS A 935 " --> pdb=" O VAL A 931 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N THR A 940 " --> pdb=" O ILE A 936 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N MET A 948 " --> pdb=" O SER A 944 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N TYR A 949 " --> pdb=" O GLN A 945 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N PHE A 950 " --> pdb=" O ALA A 946 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N SER A 951 " --> pdb=" O PHE A 947 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N TYR A 952 " --> pdb=" O MET A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 993 removed outlier: 3.593A pdb=" N GLY A 983 " --> pdb=" O ALA A 979 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N HIS A 989 " --> pdb=" O VAL A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 1003 through 1012 removed outlier: 3.808A pdb=" N LEU A1010 " --> pdb=" O HIS A1006 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLU A1012 " --> pdb=" O PHE A1008 " (cutoff:3.500A) Processing helix chain 'A' and resid 1077 through 1083 removed outlier: 3.930A pdb=" N LEU A1082 " --> pdb=" O VAL A1078 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLU A1083 " --> pdb=" O VAL A1079 " (cutoff:3.500A) Processing helix chain 'A' and resid 1100 through 1102 No H-bonds generated for 'chain 'A' and resid 1100 through 1102' Processing helix chain 'A' and resid 1105 through 1111 removed outlier: 4.232A pdb=" N ALA A1110 " --> pdb=" O GLN A1106 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLN A1111 " --> pdb=" O TRP A1107 " (cutoff:3.500A) Processing helix chain 'A' and resid 1126 through 1133 removed outlier: 4.360A pdb=" N GLY A1133 " --> pdb=" O ASN A1129 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1150 Processing helix chain 'A' and resid 1154 through 1159 removed outlier: 3.652A pdb=" N GLU A1158 " --> pdb=" O HIS A1154 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N THR A1159 " --> pdb=" O PRO A1155 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1154 through 1159' Processing helix chain 'A' and resid 1180 through 1190 removed outlier: 3.628A pdb=" N ALA A1184 " --> pdb=" O LYS A1180 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ILE A1185 " --> pdb=" O GLN A1181 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ILE A1190 " --> pdb=" O ALA A1186 " (cutoff:3.500A) Processing helix chain 'A' and resid 1207 through 1221 removed outlier: 4.662A pdb=" N GLU A1215 " --> pdb=" O LYS A1211 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA A1216 " --> pdb=" O VAL A1212 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ALA A1220 " --> pdb=" O ALA A1216 " (cutoff:3.500A) Processing helix chain 'A' and resid 1233 through 1236 No H-bonds generated for 'chain 'A' and resid 1233 through 1236' Processing helix chain 'B' and resid 123 through 128 removed outlier: 4.361A pdb=" N LYS B 127 " --> pdb=" O ASP B 123 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N SER B 128 " --> pdb=" O SER B 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 123 through 128' Processing helix chain 'C' and resid 32 through 34 No H-bonds generated for 'chain 'C' and resid 32 through 34' Processing helix chain 'C' and resid 65 through 67 No H-bonds generated for 'chain 'C' and resid 65 through 67' Processing helix chain 'C' and resid 206 through 208 No H-bonds generated for 'chain 'C' and resid 206 through 208' Processing sheet with id= A, first strand: chain 'A' and resid 395 through 397 Processing sheet with id= B, first strand: chain 'A' and resid 425 through 427 removed outlier: 6.776A pdb=" N VAL A 599 " --> pdb=" O ALA A 426 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLU A 610 " --> pdb=" O GLY A 602 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 472 through 475 removed outlier: 6.289A pdb=" N ILE A 553 " --> pdb=" O GLY A 473 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N VAL A 475 " --> pdb=" O ILE A 553 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N LEU A 555 " --> pdb=" O VAL A 475 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N THR A 583 " --> pdb=" O LEU A 554 " (cutoff:3.500A) removed outlier: 8.298A pdb=" N LEU A 556 " --> pdb=" O THR A 583 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ILE A 585 " --> pdb=" O LEU A 556 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 1035 through 1037 removed outlier: 3.555A pdb=" N LEU A1057 " --> pdb=" O PHE A1036 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 1112 through 1114 removed outlier: 6.353A pdb=" N ILE A1195 " --> pdb=" O GLY A1113 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'B' and resid 20 through 22 Processing sheet with id= G, first strand: chain 'B' and resid 37 through 39 Processing sheet with id= H, first strand: chain 'B' and resid 91 through 93 Processing sheet with id= I, first strand: chain 'B' and resid 130 through 134 Processing sheet with id= J, first strand: chain 'B' and resid 146 through 151 Processing sheet with id= K, first strand: chain 'B' and resid 137 through 140 removed outlier: 5.695A pdb=" N TYR B 174 " --> pdb=" O ASN B 139 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 6 through 8 Processing sheet with id= M, first strand: chain 'C' and resid 37 through 39 removed outlier: 3.912A pdb=" N TYR C 122 " --> pdb=" O ARG C 101 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 52 through 55 Processing sheet with id= O, first strand: chain 'C' and resid 155 through 163 Processing sheet with id= P, first strand: chain 'C' and resid 171 through 174 removed outlier: 3.561A pdb=" N CYS C 216 " --> pdb=" O LYS C 229 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS C 229 " --> pdb=" O CYS C 216 " (cutoff:3.500A) 549 hydrogen bonds defined for protein. 1596 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.25 Time building geometry restraints manager: 5.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2020 1.31 - 1.44: 3442 1.44 - 1.57: 7203 1.57 - 1.70: 19 1.70 - 1.83: 64 Bond restraints: 12748 Sorted by residual: bond pdb=" CA LEU A1197 " pdb=" CB LEU A1197 " ideal model delta sigma weight residual 1.524 1.435 0.089 1.62e-02 3.81e+03 3.01e+01 bond pdb=" C31 DLP A1308 " pdb=" O2 DLP A1308 " ideal model delta sigma weight residual 1.331 1.438 -0.107 2.00e-02 2.50e+03 2.87e+01 bond pdb=" C11 DLP A1308 " pdb=" O3 DLP A1308 " ideal model delta sigma weight residual 1.327 1.420 -0.093 2.00e-02 2.50e+03 2.17e+01 bond pdb=" CBL X2N A1306 " pdb=" NBT X2N A1306 " ideal model delta sigma weight residual 1.406 1.331 0.075 2.00e-02 2.50e+03 1.41e+01 bond pdb=" CB GLN A 837 " pdb=" CG GLN A 837 " ideal model delta sigma weight residual 1.520 1.414 0.106 3.00e-02 1.11e+03 1.25e+01 ... (remaining 12743 not shown) Histogram of bond angle deviations from ideal: 95.22 - 103.00: 107 103.00 - 110.79: 4343 110.79 - 118.57: 5905 118.57 - 126.35: 6791 126.35 - 134.13: 149 Bond angle restraints: 17295 Sorted by residual: angle pdb=" N THR B 207 " pdb=" CA THR B 207 " pdb=" C THR B 207 " ideal model delta sigma weight residual 107.23 118.04 -10.81 1.67e+00 3.59e-01 4.19e+01 angle pdb=" N LEU A1089 " pdb=" CA LEU A1089 " pdb=" C LEU A1089 " ideal model delta sigma weight residual 111.36 106.02 5.34 1.09e+00 8.42e-01 2.40e+01 angle pdb=" CA TYR A 312 " pdb=" CB TYR A 312 " pdb=" CG TYR A 312 " ideal model delta sigma weight residual 113.90 122.61 -8.71 1.80e+00 3.09e-01 2.34e+01 angle pdb=" N PHE A 947 " pdb=" CA PHE A 947 " pdb=" C PHE A 947 " ideal model delta sigma weight residual 113.19 118.86 -5.67 1.19e+00 7.06e-01 2.27e+01 angle pdb=" N LEU B 136 " pdb=" CA LEU B 136 " pdb=" C LEU B 136 " ideal model delta sigma weight residual 109.79 116.91 -7.12 1.56e+00 4.11e-01 2.08e+01 ... (remaining 17290 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.83: 7324 25.83 - 51.65: 504 51.65 - 77.48: 47 77.48 - 103.31: 14 103.31 - 129.14: 2 Dihedral angle restraints: 7891 sinusoidal: 3326 harmonic: 4565 Sorted by residual: dihedral pdb=" CA ASN A 91 " pdb=" C ASN A 91 " pdb=" N PHE A 92 " pdb=" CA PHE A 92 " ideal model delta harmonic sigma weight residual 180.00 150.49 29.51 0 5.00e+00 4.00e-02 3.48e+01 dihedral pdb=" CA GLN A 911 " pdb=" C GLN A 911 " pdb=" N GLU A 912 " pdb=" CA GLU A 912 " ideal model delta harmonic sigma weight residual 180.00 153.00 27.00 0 5.00e+00 4.00e-02 2.91e+01 dihedral pdb=" CA VAL A 869 " pdb=" C VAL A 869 " pdb=" N SER A 870 " pdb=" CA SER A 870 " ideal model delta harmonic sigma weight residual 180.00 154.04 25.96 0 5.00e+00 4.00e-02 2.70e+01 ... (remaining 7888 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 1565 0.081 - 0.161: 353 0.161 - 0.242: 40 0.242 - 0.322: 10 0.322 - 0.403: 6 Chirality restraints: 1974 Sorted by residual: chirality pdb=" C17 CLR A1304 " pdb=" C13 CLR A1304 " pdb=" C16 CLR A1304 " pdb=" C20 CLR A1304 " both_signs ideal model delta sigma weight residual False 2.55 2.96 -0.40 2.00e-01 2.50e+01 4.05e+00 chirality pdb=" C17 CLR A1307 " pdb=" C13 CLR A1307 " pdb=" C16 CLR A1307 " pdb=" C20 CLR A1307 " both_signs ideal model delta sigma weight residual False 2.55 2.95 -0.40 2.00e-01 2.50e+01 3.97e+00 chirality pdb=" C17 CLR A1305 " pdb=" C13 CLR A1305 " pdb=" C16 CLR A1305 " pdb=" C20 CLR A1305 " both_signs ideal model delta sigma weight residual False 2.55 2.95 -0.39 2.00e-01 2.50e+01 3.84e+00 ... (remaining 1971 not shown) Planarity restraints: 2157 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A1132 " -0.025 2.00e-02 2.50e+03 1.88e-02 7.04e+00 pdb=" CG TYR A1132 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 TYR A1132 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR A1132 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR A1132 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR A1132 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR A1132 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR A1132 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 792 " -0.030 2.00e-02 2.50e+03 1.94e-02 6.62e+00 pdb=" CG PHE A 792 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 PHE A 792 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE A 792 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE A 792 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE A 792 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE A 792 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 99 " 0.024 2.00e-02 2.50e+03 1.81e-02 5.72e+00 pdb=" CG PHE B 99 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE B 99 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE B 99 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE B 99 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE B 99 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE B 99 " 0.009 2.00e-02 2.50e+03 ... (remaining 2154 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 392 2.64 - 3.21: 12940 3.21 - 3.77: 18886 3.77 - 4.34: 25333 4.34 - 4.90: 40627 Nonbonded interactions: 98178 Sorted by model distance: nonbonded pdb=" O ASN A 332 " pdb=" ND2 ASN A 332 " model vdw 2.078 2.520 nonbonded pdb=" OG SER A 476 " pdb=" OE1 GLN A 477 " model vdw 2.090 2.440 nonbonded pdb=" O SER A 69 " pdb=" OG SER A 69 " model vdw 2.110 2.440 nonbonded pdb=" N GLN A 272 " pdb=" OE1 GLN A 272 " model vdw 2.180 2.520 nonbonded pdb=" O SER B 31 " pdb=" OG SER B 31 " model vdw 2.189 2.440 ... (remaining 98173 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.30 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: 6.930 Set stop_for_unknowns flag: 0.010 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: 19.620 Check model and map are aligned: 0.150 Set scattering table: 0.110 Process input model: 37.700 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 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 : 0.015 0.117 12748 Z= 0.982 Angle : 1.289 11.748 17295 Z= 0.686 Chirality : 0.070 0.403 1974 Planarity : 0.006 0.053 2157 Dihedral : 17.102 129.137 4957 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 27.93 Ramachandran Plot: Outliers : 0.19 % Allowed : 15.49 % Favored : 84.32 % Rotamer: Outliers : 2.44 % Allowed : 13.98 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.23 (0.15), residues: 1577 helix: -3.16 (0.13), residues: 712 sheet: -3.13 (0.28), residues: 227 loop : -3.81 (0.18), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.004 TRP A 802 HIS 0.017 0.002 HIS A 67 PHE 0.040 0.004 PHE B 99 TYR 0.044 0.003 TYR A1132 ARG 0.012 0.001 ARG A1221 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3154 Ramachandran restraints generated. 1577 Oldfield, 0 Emsley, 1577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3154 Ramachandran restraints generated. 1577 Oldfield, 0 Emsley, 1577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 161 time to evaluate : 1.367 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 151 GLN cc_start: 0.8105 (tm-30) cc_final: 0.7637 (tm-30) REVERT: A 190 ASP cc_start: 0.8689 (OUTLIER) cc_final: 0.8204 (t0) REVERT: A 383 ARG cc_start: 0.7644 (mtp180) cc_final: 0.6440 (ttp80) REVERT: A 553 ILE cc_start: 0.8832 (mp) cc_final: 0.8605 (mp) REVERT: A 875 MET cc_start: 0.3854 (mmm) cc_final: 0.3647 (tmm) REVERT: A 884 ARG cc_start: 0.5732 (tpp-160) cc_final: 0.5350 (mtt180) REVERT: A 947 PHE cc_start: 0.9014 (OUTLIER) cc_final: 0.8587 (t80) REVERT: B 139 ASN cc_start: 0.6873 (m-40) cc_final: 0.5915 (p0) REVERT: C 196 TYR cc_start: 0.7303 (m-80) cc_final: 0.6850 (m-80) REVERT: C 230 LYS cc_start: 0.7344 (ttpp) cc_final: 0.7136 (tttp) outliers start: 32 outliers final: 20 residues processed: 188 average time/residue: 0.2670 time to fit residues: 72.1064 Evaluate side-chains 131 residues out of total 1305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 109 time to evaluate : 1.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain A residue 197 GLN Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 717 CYS Chi-restraints excluded: chain A residue 753 ILE Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 844 THR Chi-restraints excluded: chain A residue 947 PHE Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 1021 SER Chi-restraints excluded: chain A residue 1022 GLU Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1225 THR Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 132 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 133 optimal weight: 7.9990 chunk 119 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 40 optimal weight: 20.0000 chunk 80 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 123 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 chunk 92 optimal weight: 0.3980 chunk 143 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 GLN A 282 HIS A 298 ASN ** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 397 ASN A 416 ASN A 443 GLN A 464 ASN A 752 ASN A 823 GLN A 837 GLN ** A 929 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 HIS A1104 ASN A1129 ASN B 39 GLN C 42 GLN ** C 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 12748 Z= 0.199 Angle : 0.674 8.011 17295 Z= 0.349 Chirality : 0.042 0.211 1974 Planarity : 0.004 0.039 2157 Dihedral : 11.060 130.406 2223 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 3.59 % Allowed : 17.80 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.15 (0.19), residues: 1577 helix: -0.98 (0.17), residues: 728 sheet: -2.59 (0.29), residues: 250 loop : -3.18 (0.21), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 234 HIS 0.003 0.001 HIS A 400 PHE 0.034 0.002 PHE A 728 TYR 0.022 0.002 TYR A 249 ARG 0.007 0.000 ARG B 109 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3154 Ramachandran restraints generated. 1577 Oldfield, 0 Emsley, 1577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3154 Ramachandran restraints generated. 1577 Oldfield, 0 Emsley, 1577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 147 time to evaluate : 1.383 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 119 TYR cc_start: 0.7791 (m-80) cc_final: 0.7525 (m-80) REVERT: A 218 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8303 (mm) REVERT: A 383 ARG cc_start: 0.7619 (mtp180) cc_final: 0.6507 (ttp-170) REVERT: A 553 ILE cc_start: 0.8785 (mp) cc_final: 0.8581 (mp) REVERT: A 556 LEU cc_start: 0.7034 (OUTLIER) cc_final: 0.6686 (mt) REVERT: A 875 MET cc_start: 0.3878 (mmm) cc_final: 0.3590 (tmm) REVERT: A 884 ARG cc_start: 0.5621 (tpp-160) cc_final: 0.5231 (mtm180) REVERT: A 947 PHE cc_start: 0.8995 (OUTLIER) cc_final: 0.8681 (t80) REVERT: B 50 TYR cc_start: 0.8600 (p90) cc_final: 0.8362 (p90) REVERT: B 139 ASN cc_start: 0.6768 (m-40) cc_final: 0.6037 (p0) REVERT: C 196 TYR cc_start: 0.6909 (m-80) cc_final: 0.6393 (m-80) outliers start: 47 outliers final: 27 residues processed: 186 average time/residue: 0.2220 time to fit residues: 61.8893 Evaluate side-chains 151 residues out of total 1305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 121 time to evaluate : 1.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 280 GLN Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 717 CYS Chi-restraints excluded: chain A residue 744 ASP Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 844 THR Chi-restraints excluded: chain A residue 867 ILE Chi-restraints excluded: chain A residue 905 THR Chi-restraints excluded: chain A residue 947 PHE Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 1021 SER Chi-restraints excluded: chain A residue 1049 VAL Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1078 VAL Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1173 THR Chi-restraints excluded: chain A residue 1195 ILE Chi-restraints excluded: chain A residue 1207 THR Chi-restraints excluded: chain A residue 1225 THR Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 171 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 79 optimal weight: 5.9990 chunk 44 optimal weight: 10.0000 chunk 119 optimal weight: 0.0470 chunk 97 optimal weight: 0.0970 chunk 39 optimal weight: 0.0980 chunk 143 optimal weight: 7.9990 chunk 155 optimal weight: 0.0470 chunk 128 optimal weight: 7.9990 chunk 142 optimal weight: 0.7980 chunk 49 optimal weight: 0.6980 chunk 115 optimal weight: 0.9990 overall best weight: 0.1974 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 GLN ** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 349 GLN A 443 GLN ** A 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 929 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12748 Z= 0.157 Angle : 0.578 7.244 17295 Z= 0.299 Chirality : 0.040 0.213 1974 Planarity : 0.003 0.040 2157 Dihedral : 9.795 129.088 2207 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 3.21 % Allowed : 19.71 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.20), residues: 1577 helix: 0.09 (0.19), residues: 728 sheet: -2.05 (0.31), residues: 244 loop : -2.80 (0.22), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 234 HIS 0.003 0.001 HIS A 282 PHE 0.020 0.001 PHE A1041 TYR 0.026 0.001 TYR A 919 ARG 0.007 0.000 ARG B 109 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3154 Ramachandran restraints generated. 1577 Oldfield, 0 Emsley, 1577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3154 Ramachandran restraints generated. 1577 Oldfield, 0 Emsley, 1577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 150 time to evaluate : 1.693 Fit side-chains revert: symmetry clash REVERT: A 383 ARG cc_start: 0.7573 (mtp180) cc_final: 0.6383 (ttp80) REVERT: A 556 LEU cc_start: 0.7049 (OUTLIER) cc_final: 0.6757 (mt) REVERT: A 875 MET cc_start: 0.4078 (mmm) cc_final: 0.3869 (tmm) REVERT: A 884 ARG cc_start: 0.5434 (tpp-160) cc_final: 0.5114 (mtm180) REVERT: A 947 PHE cc_start: 0.8928 (OUTLIER) cc_final: 0.8681 (t80) REVERT: B 50 TYR cc_start: 0.8560 (p90) cc_final: 0.8318 (p90) REVERT: B 139 ASN cc_start: 0.6716 (m-40) cc_final: 0.6120 (p0) REVERT: C 196 TYR cc_start: 0.6925 (m-80) cc_final: 0.6529 (m-80) outliers start: 42 outliers final: 29 residues processed: 183 average time/residue: 0.2390 time to fit residues: 64.3300 Evaluate side-chains 159 residues out of total 1305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 128 time to evaluate : 1.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 206 PHE Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 717 CYS Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain A residue 744 ASP Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 905 THR Chi-restraints excluded: chain A residue 947 PHE Chi-restraints excluded: chain A residue 1034 ILE Chi-restraints excluded: chain A residue 1049 VAL Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1168 VAL Chi-restraints excluded: chain A residue 1173 THR Chi-restraints excluded: chain A residue 1195 ILE Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 227 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 142 optimal weight: 0.9990 chunk 108 optimal weight: 8.9990 chunk 74 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 96 optimal weight: 8.9990 chunk 144 optimal weight: 2.9990 chunk 152 optimal weight: 0.0070 chunk 75 optimal weight: 1.9990 chunk 136 optimal weight: 10.0000 chunk 41 optimal weight: 6.9990 overall best weight: 1.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 GLN ** A 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 902 ASN ** A 929 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1141 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12748 Z= 0.215 Angle : 0.594 10.086 17295 Z= 0.305 Chirality : 0.041 0.149 1974 Planarity : 0.003 0.040 2157 Dihedral : 9.622 131.298 2200 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 4.74 % Allowed : 20.70 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.20), residues: 1577 helix: 0.33 (0.19), residues: 729 sheet: -1.85 (0.31), residues: 245 loop : -2.60 (0.23), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 802 HIS 0.005 0.001 HIS A 67 PHE 0.020 0.002 PHE A 769 TYR 0.017 0.002 TYR C 53 ARG 0.003 0.000 ARG B 109 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3154 Ramachandran restraints generated. 1577 Oldfield, 0 Emsley, 1577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3154 Ramachandran restraints generated. 1577 Oldfield, 0 Emsley, 1577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 139 time to evaluate : 1.421 Fit side-chains revert: symmetry clash REVERT: A 379 SER cc_start: 0.8688 (OUTLIER) cc_final: 0.7962 (t) REVERT: A 383 ARG cc_start: 0.7539 (mtp180) cc_final: 0.6419 (ttp80) REVERT: A 556 LEU cc_start: 0.7079 (OUTLIER) cc_final: 0.6771 (mt) REVERT: A 875 MET cc_start: 0.4014 (mmm) cc_final: 0.3808 (tmm) REVERT: A 884 ARG cc_start: 0.5415 (tpp-160) cc_final: 0.5057 (mtm180) REVERT: A 947 PHE cc_start: 0.9012 (OUTLIER) cc_final: 0.8727 (t80) REVERT: A 1036 PHE cc_start: 0.7460 (m-80) cc_final: 0.7202 (m-80) REVERT: B 50 TYR cc_start: 0.8569 (p90) cc_final: 0.8333 (p90) REVERT: B 139 ASN cc_start: 0.6769 (m-40) cc_final: 0.6209 (p0) REVERT: C 196 TYR cc_start: 0.6998 (m-80) cc_final: 0.6762 (m-80) outliers start: 62 outliers final: 45 residues processed: 187 average time/residue: 0.2277 time to fit residues: 63.7981 Evaluate side-chains 176 residues out of total 1305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 128 time to evaluate : 1.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 85 PHE Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 206 PHE Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 717 CYS Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain A residue 744 ASP Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 844 THR Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 867 ILE Chi-restraints excluded: chain A residue 869 VAL Chi-restraints excluded: chain A residue 905 THR Chi-restraints excluded: chain A residue 947 PHE Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 1049 VAL Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1168 VAL Chi-restraints excluded: chain A residue 1173 THR Chi-restraints excluded: chain A residue 1195 ILE Chi-restraints excluded: chain A residue 1202 THR Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 227 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 127 optimal weight: 0.8980 chunk 86 optimal weight: 0.5980 chunk 2 optimal weight: 0.4980 chunk 113 optimal weight: 9.9990 chunk 63 optimal weight: 0.9980 chunk 130 optimal weight: 20.0000 chunk 105 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 77 optimal weight: 5.9990 chunk 137 optimal weight: 0.6980 chunk 38 optimal weight: 9.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 464 ASN A 902 ASN ** C 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 12748 Z= 0.160 Angle : 0.559 9.561 17295 Z= 0.286 Chirality : 0.039 0.187 1974 Planarity : 0.003 0.041 2157 Dihedral : 9.315 130.384 2200 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 4.20 % Allowed : 21.85 % Favored : 73.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.21), residues: 1577 helix: 0.58 (0.19), residues: 731 sheet: -1.59 (0.32), residues: 244 loop : -2.44 (0.23), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 234 HIS 0.003 0.001 HIS A 67 PHE 0.022 0.001 PHE A 769 TYR 0.020 0.001 TYR A 119 ARG 0.006 0.000 ARG A 884 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3154 Ramachandran restraints generated. 1577 Oldfield, 0 Emsley, 1577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3154 Ramachandran restraints generated. 1577 Oldfield, 0 Emsley, 1577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 138 time to evaluate : 1.435 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 TYR cc_start: 0.7288 (t80) cc_final: 0.7059 (t80) REVERT: A 154 PHE cc_start: 0.7823 (t80) cc_final: 0.7385 (t80) REVERT: A 349 GLN cc_start: 0.5848 (mm-40) cc_final: 0.5543 (mm-40) REVERT: A 379 SER cc_start: 0.8651 (OUTLIER) cc_final: 0.7978 (t) REVERT: A 383 ARG cc_start: 0.7525 (mtp180) cc_final: 0.6347 (ttp80) REVERT: A 556 LEU cc_start: 0.7108 (OUTLIER) cc_final: 0.6809 (mt) REVERT: A 875 MET cc_start: 0.3908 (mmm) cc_final: 0.3701 (tmm) REVERT: A 884 ARG cc_start: 0.5420 (tpp-160) cc_final: 0.5096 (mtm180) REVERT: A 947 PHE cc_start: 0.8966 (OUTLIER) cc_final: 0.8734 (t80) REVERT: A 1036 PHE cc_start: 0.7454 (m-80) cc_final: 0.6947 (m-80) REVERT: B 50 TYR cc_start: 0.8552 (p90) cc_final: 0.8330 (p90) REVERT: B 139 ASN cc_start: 0.6808 (m-40) cc_final: 0.6408 (p0) REVERT: C 196 TYR cc_start: 0.6903 (m-80) cc_final: 0.6614 (m-80) outliers start: 55 outliers final: 44 residues processed: 183 average time/residue: 0.2286 time to fit residues: 62.3334 Evaluate side-chains 176 residues out of total 1305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 129 time to evaluate : 1.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 PHE Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 206 PHE Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 312 TYR Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 717 CYS Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain A residue 744 ASP Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 867 ILE Chi-restraints excluded: chain A residue 869 VAL Chi-restraints excluded: chain A residue 902 ASN Chi-restraints excluded: chain A residue 905 THR Chi-restraints excluded: chain A residue 947 PHE Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 1009 MET Chi-restraints excluded: chain A residue 1022 GLU Chi-restraints excluded: chain A residue 1034 ILE Chi-restraints excluded: chain A residue 1049 VAL Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1168 VAL Chi-restraints excluded: chain A residue 1173 THR Chi-restraints excluded: chain A residue 1195 ILE Chi-restraints excluded: chain A residue 1202 THR Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 227 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 51 optimal weight: 10.0000 chunk 137 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 89 optimal weight: 0.7980 chunk 37 optimal weight: 20.0000 chunk 152 optimal weight: 0.0870 chunk 126 optimal weight: 20.0000 chunk 70 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 80 optimal weight: 6.9990 overall best weight: 1.9562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 ASN ** A 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 12748 Z= 0.261 Angle : 0.616 10.927 17295 Z= 0.316 Chirality : 0.042 0.194 1974 Planarity : 0.004 0.041 2157 Dihedral : 9.375 131.675 2196 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 5.58 % Allowed : 21.31 % Favored : 73.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.21), residues: 1577 helix: 0.50 (0.19), residues: 731 sheet: -1.64 (0.32), residues: 243 loop : -2.39 (0.23), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 112 HIS 0.006 0.001 HIS A 67 PHE 0.017 0.002 PHE A 769 TYR 0.019 0.002 TYR C 53 ARG 0.011 0.000 ARG B 109 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3154 Ramachandran restraints generated. 1577 Oldfield, 0 Emsley, 1577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3154 Ramachandran restraints generated. 1577 Oldfield, 0 Emsley, 1577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 133 time to evaluate : 1.382 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 TYR cc_start: 0.7413 (t80) cc_final: 0.7185 (t80) REVERT: A 146 ILE cc_start: 0.8512 (OUTLIER) cc_final: 0.8155 (tp) REVERT: A 154 PHE cc_start: 0.7878 (t80) cc_final: 0.7421 (t80) REVERT: A 379 SER cc_start: 0.8668 (OUTLIER) cc_final: 0.8003 (t) REVERT: A 383 ARG cc_start: 0.7512 (mtp180) cc_final: 0.6371 (ttp80) REVERT: A 537 GLN cc_start: 0.5667 (mt0) cc_final: 0.5285 (mt0) REVERT: A 556 LEU cc_start: 0.7098 (OUTLIER) cc_final: 0.6794 (mt) REVERT: A 884 ARG cc_start: 0.5292 (tpp-160) cc_final: 0.4981 (mtm180) REVERT: A 886 LYS cc_start: 0.7006 (OUTLIER) cc_final: 0.6688 (tptt) REVERT: A 947 PHE cc_start: 0.9044 (OUTLIER) cc_final: 0.8771 (t80) REVERT: A 1112 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8582 (mt) REVERT: B 50 TYR cc_start: 0.8591 (p90) cc_final: 0.8364 (p90) REVERT: B 139 ASN cc_start: 0.6534 (m-40) cc_final: 0.6289 (p0) outliers start: 73 outliers final: 57 residues processed: 192 average time/residue: 0.2122 time to fit residues: 61.6420 Evaluate side-chains 188 residues out of total 1305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 125 time to evaluate : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 85 PHE Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 312 TYR Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 717 CYS Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain A residue 744 ASP Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 784 THR Chi-restraints excluded: chain A residue 815 THR Chi-restraints excluded: chain A residue 844 THR Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 867 ILE Chi-restraints excluded: chain A residue 869 VAL Chi-restraints excluded: chain A residue 886 LYS Chi-restraints excluded: chain A residue 905 THR Chi-restraints excluded: chain A residue 947 PHE Chi-restraints excluded: chain A residue 1009 MET Chi-restraints excluded: chain A residue 1022 GLU Chi-restraints excluded: chain A residue 1034 ILE Chi-restraints excluded: chain A residue 1049 VAL Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1078 VAL Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain A residue 1112 LEU Chi-restraints excluded: chain A residue 1168 VAL Chi-restraints excluded: chain A residue 1173 THR Chi-restraints excluded: chain A residue 1195 ILE Chi-restraints excluded: chain A residue 1202 THR Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 227 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 147 optimal weight: 0.8980 chunk 17 optimal weight: 0.1980 chunk 87 optimal weight: 0.9980 chunk 111 optimal weight: 6.9990 chunk 86 optimal weight: 0.8980 chunk 128 optimal weight: 9.9990 chunk 85 optimal weight: 0.7980 chunk 152 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 92 optimal weight: 5.9990 chunk 70 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 902 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.3266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 12748 Z= 0.161 Angle : 0.563 9.757 17295 Z= 0.286 Chirality : 0.040 0.196 1974 Planarity : 0.003 0.063 2157 Dihedral : 9.059 128.050 2196 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 4.58 % Allowed : 23.22 % Favored : 72.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.21), residues: 1577 helix: 0.75 (0.19), residues: 732 sheet: -1.37 (0.33), residues: 231 loop : -2.20 (0.24), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 234 HIS 0.003 0.001 HIS C 38 PHE 0.013 0.001 PHE A 316 TYR 0.017 0.001 TYR A 467 ARG 0.013 0.000 ARG B 109 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3154 Ramachandran restraints generated. 1577 Oldfield, 0 Emsley, 1577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3154 Ramachandran restraints generated. 1577 Oldfield, 0 Emsley, 1577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 140 time to evaluate : 1.347 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 TYR cc_start: 0.7266 (t80) cc_final: 0.7007 (t80) REVERT: A 154 PHE cc_start: 0.7788 (t80) cc_final: 0.7300 (t80) REVERT: A 379 SER cc_start: 0.8596 (OUTLIER) cc_final: 0.7961 (t) REVERT: A 383 ARG cc_start: 0.7506 (mtp180) cc_final: 0.6331 (ttp80) REVERT: A 537 GLN cc_start: 0.5623 (mt0) cc_final: 0.5306 (mt0) REVERT: A 556 LEU cc_start: 0.7183 (OUTLIER) cc_final: 0.6884 (mt) REVERT: A 884 ARG cc_start: 0.5278 (tpp-160) cc_final: 0.4994 (mtm180) REVERT: A 886 LYS cc_start: 0.7085 (mtmm) cc_final: 0.6714 (tptt) REVERT: A 947 PHE cc_start: 0.8981 (OUTLIER) cc_final: 0.8715 (t80) REVERT: A 1112 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8544 (mt) REVERT: B 50 TYR cc_start: 0.8544 (p90) cc_final: 0.8339 (p90) REVERT: C 195 LEU cc_start: 0.6070 (mt) cc_final: 0.5859 (tp) outliers start: 60 outliers final: 43 residues processed: 190 average time/residue: 0.2064 time to fit residues: 59.3154 Evaluate side-chains 176 residues out of total 1305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 129 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 PHE Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 312 TYR Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain A residue 744 ASP Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 784 THR Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 867 ILE Chi-restraints excluded: chain A residue 869 VAL Chi-restraints excluded: chain A residue 905 THR Chi-restraints excluded: chain A residue 947 PHE Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 1002 LEU Chi-restraints excluded: chain A residue 1009 MET Chi-restraints excluded: chain A residue 1034 ILE Chi-restraints excluded: chain A residue 1049 VAL Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1078 VAL Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1112 LEU Chi-restraints excluded: chain A residue 1168 VAL Chi-restraints excluded: chain A residue 1173 THR Chi-restraints excluded: chain A residue 1195 ILE Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 227 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 94 optimal weight: 6.9990 chunk 60 optimal weight: 0.9990 chunk 90 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 96 optimal weight: 5.9990 chunk 103 optimal weight: 9.9990 chunk 75 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 119 optimal weight: 0.0040 chunk 138 optimal weight: 1.9990 overall best weight: 0.9396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 902 ASN B 139 ASN ** C 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.3369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 12748 Z= 0.179 Angle : 0.566 9.687 17295 Z= 0.288 Chirality : 0.040 0.182 1974 Planarity : 0.003 0.047 2157 Dihedral : 8.966 127.298 2195 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 4.89 % Allowed : 23.45 % Favored : 71.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.21), residues: 1577 helix: 0.83 (0.19), residues: 734 sheet: -1.35 (0.33), residues: 236 loop : -2.10 (0.24), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 112 HIS 0.003 0.000 HIS C 38 PHE 0.012 0.001 PHE A 337 TYR 0.016 0.001 TYR A 467 ARG 0.009 0.000 ARG B 109 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3154 Ramachandran restraints generated. 1577 Oldfield, 0 Emsley, 1577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3154 Ramachandran restraints generated. 1577 Oldfield, 0 Emsley, 1577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 132 time to evaluate : 1.519 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 TYR cc_start: 0.7293 (t80) cc_final: 0.7087 (t80) REVERT: A 146 ILE cc_start: 0.8502 (OUTLIER) cc_final: 0.8172 (tp) REVERT: A 379 SER cc_start: 0.8562 (OUTLIER) cc_final: 0.7930 (t) REVERT: A 383 ARG cc_start: 0.7499 (mtp180) cc_final: 0.6338 (ttp80) REVERT: A 537 GLN cc_start: 0.5656 (mt0) cc_final: 0.5338 (mt0) REVERT: A 556 LEU cc_start: 0.7170 (OUTLIER) cc_final: 0.6887 (mt) REVERT: A 884 ARG cc_start: 0.5281 (tpp-160) cc_final: 0.4992 (mtm180) REVERT: A 886 LYS cc_start: 0.7215 (mtmm) cc_final: 0.6756 (tptt) REVERT: A 947 PHE cc_start: 0.8997 (OUTLIER) cc_final: 0.8732 (t80) REVERT: A 1112 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8527 (mt) REVERT: B 50 TYR cc_start: 0.8578 (p90) cc_final: 0.8365 (p90) outliers start: 63 outliers final: 49 residues processed: 185 average time/residue: 0.2134 time to fit residues: 59.8005 Evaluate side-chains 183 residues out of total 1305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 129 time to evaluate : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 PHE Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 312 TYR Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 608 ILE Chi-restraints excluded: chain A residue 700 VAL Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain A residue 744 ASP Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 784 THR Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 867 ILE Chi-restraints excluded: chain A residue 869 VAL Chi-restraints excluded: chain A residue 905 THR Chi-restraints excluded: chain A residue 947 PHE Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 1002 LEU Chi-restraints excluded: chain A residue 1022 GLU Chi-restraints excluded: chain A residue 1034 ILE Chi-restraints excluded: chain A residue 1049 VAL Chi-restraints excluded: chain A residue 1078 VAL Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1112 LEU Chi-restraints excluded: chain A residue 1168 VAL Chi-restraints excluded: chain A residue 1173 THR Chi-restraints excluded: chain A residue 1195 ILE Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 139 ASN Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 227 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 145 optimal weight: 1.9990 chunk 133 optimal weight: 30.0000 chunk 141 optimal weight: 0.2980 chunk 85 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 111 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 chunk 128 optimal weight: 5.9990 chunk 134 optimal weight: 8.9990 chunk 93 optimal weight: 0.9980 chunk 150 optimal weight: 50.0000 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 902 ASN A1117 GLN ** B 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.3239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 12748 Z= 0.276 Angle : 0.618 8.821 17295 Z= 0.317 Chirality : 0.042 0.182 1974 Planarity : 0.004 0.047 2157 Dihedral : 9.121 127.505 2194 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 5.35 % Allowed : 22.92 % Favored : 71.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.21), residues: 1577 helix: 0.72 (0.19), residues: 732 sheet: -1.43 (0.33), residues: 234 loop : -2.11 (0.24), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 112 HIS 0.009 0.001 HIS A 67 PHE 0.016 0.002 PHE B 99 TYR 0.020 0.002 TYR C 53 ARG 0.007 0.000 ARG B 109 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3154 Ramachandran restraints generated. 1577 Oldfield, 0 Emsley, 1577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3154 Ramachandran restraints generated. 1577 Oldfield, 0 Emsley, 1577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 129 time to evaluate : 1.361 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 TYR cc_start: 0.7394 (t80) cc_final: 0.7141 (t80) REVERT: A 154 PHE cc_start: 0.7831 (t80) cc_final: 0.7380 (t80) REVERT: A 379 SER cc_start: 0.8572 (OUTLIER) cc_final: 0.7935 (t) REVERT: A 383 ARG cc_start: 0.7503 (mtp180) cc_final: 0.6356 (ttp80) REVERT: A 537 GLN cc_start: 0.5675 (mt0) cc_final: 0.5335 (mt0) REVERT: A 556 LEU cc_start: 0.7214 (OUTLIER) cc_final: 0.6913 (mt) REVERT: A 593 THR cc_start: 0.4323 (OUTLIER) cc_final: 0.4085 (m) REVERT: A 884 ARG cc_start: 0.5349 (tpp-160) cc_final: 0.5029 (mtm180) REVERT: A 886 LYS cc_start: 0.7319 (mtmm) cc_final: 0.6800 (tptt) REVERT: A 947 PHE cc_start: 0.9038 (OUTLIER) cc_final: 0.8749 (t80) REVERT: A 1112 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8604 (mt) REVERT: B 50 TYR cc_start: 0.8610 (p90) cc_final: 0.8381 (p90) outliers start: 69 outliers final: 60 residues processed: 185 average time/residue: 0.2060 time to fit residues: 58.5429 Evaluate side-chains 193 residues out of total 1305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 128 time to evaluate : 1.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 PHE Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 312 TYR Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 608 ILE Chi-restraints excluded: chain A residue 700 VAL Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain A residue 744 ASP Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 784 THR Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 867 ILE Chi-restraints excluded: chain A residue 869 VAL Chi-restraints excluded: chain A residue 875 MET Chi-restraints excluded: chain A residue 905 THR Chi-restraints excluded: chain A residue 947 PHE Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 1002 LEU Chi-restraints excluded: chain A residue 1022 GLU Chi-restraints excluded: chain A residue 1034 ILE Chi-restraints excluded: chain A residue 1049 VAL Chi-restraints excluded: chain A residue 1078 VAL Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain A residue 1112 LEU Chi-restraints excluded: chain A residue 1168 VAL Chi-restraints excluded: chain A residue 1173 THR Chi-restraints excluded: chain A residue 1195 ILE Chi-restraints excluded: chain A residue 1207 THR Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 139 ASN Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 227 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 91 optimal weight: 5.9990 chunk 71 optimal weight: 0.3980 chunk 104 optimal weight: 0.0020 chunk 157 optimal weight: 3.9990 chunk 144 optimal weight: 4.9990 chunk 125 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 76 optimal weight: 0.8980 chunk 99 optimal weight: 0.9990 chunk 133 optimal weight: 9.9990 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 902 ASN B 139 ASN ** C 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.3548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 12748 Z= 0.154 Angle : 0.560 11.400 17295 Z= 0.284 Chirality : 0.040 0.212 1974 Planarity : 0.003 0.046 2157 Dihedral : 8.794 123.143 2194 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 4.13 % Allowed : 23.83 % Favored : 72.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.21), residues: 1577 helix: 0.99 (0.19), residues: 733 sheet: -1.20 (0.33), residues: 231 loop : -1.98 (0.24), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 234 HIS 0.005 0.001 HIS A 67 PHE 0.015 0.001 PHE A 956 TYR 0.019 0.001 TYR A 120 ARG 0.007 0.000 ARG B 109 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3154 Ramachandran restraints generated. 1577 Oldfield, 0 Emsley, 1577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3154 Ramachandran restraints generated. 1577 Oldfield, 0 Emsley, 1577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 133 time to evaluate : 1.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 TYR cc_start: 0.7222 (t80) cc_final: 0.7006 (t80) REVERT: A 154 PHE cc_start: 0.7710 (t80) cc_final: 0.7216 (t80) REVERT: A 379 SER cc_start: 0.8504 (OUTLIER) cc_final: 0.7883 (t) REVERT: A 383 ARG cc_start: 0.7518 (mtp180) cc_final: 0.6314 (ttp80) REVERT: A 537 GLN cc_start: 0.5694 (mt0) cc_final: 0.5362 (mt0) REVERT: A 556 LEU cc_start: 0.7127 (OUTLIER) cc_final: 0.6846 (mt) REVERT: A 593 THR cc_start: 0.4248 (OUTLIER) cc_final: 0.4002 (m) REVERT: A 884 ARG cc_start: 0.5309 (tpp-160) cc_final: 0.5028 (mtm180) REVERT: A 886 LYS cc_start: 0.7322 (mtmm) cc_final: 0.6758 (tptt) REVERT: A 947 PHE cc_start: 0.8974 (OUTLIER) cc_final: 0.8705 (t80) REVERT: B 5 MET cc_start: 0.8209 (tpt) cc_final: 0.7943 (mmm) REVERT: B 50 TYR cc_start: 0.8562 (p90) cc_final: 0.8350 (p90) outliers start: 53 outliers final: 44 residues processed: 178 average time/residue: 0.2274 time to fit residues: 60.9593 Evaluate side-chains 175 residues out of total 1305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 127 time to evaluate : 1.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 PHE Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 312 TYR Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 700 VAL Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain A residue 744 ASP Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 784 THR Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 867 ILE Chi-restraints excluded: chain A residue 869 VAL Chi-restraints excluded: chain A residue 902 ASN Chi-restraints excluded: chain A residue 905 THR Chi-restraints excluded: chain A residue 947 PHE Chi-restraints excluded: chain A residue 1002 LEU Chi-restraints excluded: chain A residue 1022 GLU Chi-restraints excluded: chain A residue 1034 ILE Chi-restraints excluded: chain A residue 1049 VAL Chi-restraints excluded: chain A residue 1078 VAL Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain A residue 1168 VAL Chi-restraints excluded: chain A residue 1173 THR Chi-restraints excluded: chain A residue 1195 ILE Chi-restraints excluded: chain A residue 1207 THR Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 139 ASN Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 227 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 38 optimal weight: 10.0000 chunk 115 optimal weight: 0.3980 chunk 18 optimal weight: 4.9990 chunk 34 optimal weight: 10.0000 chunk 125 optimal weight: 7.9990 chunk 52 optimal weight: 0.6980 chunk 128 optimal weight: 10.0000 chunk 15 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 110 optimal weight: 6.9990 chunk 7 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 902 ASN ** C 220 HIS ** 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 = 0.4223 r_free = 0.4223 target = 0.173164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.136569 restraints weight = 34107.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.138787 restraints weight = 45265.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.142069 restraints weight = 17952.027| |-----------------------------------------------------------------------------| r_work (final): 0.3820 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3820 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3820 r_free = 0.3820 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3820 r_free = 0.3820 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3820 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.3570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.216 12748 Z= 0.250 Angle : 0.922 59.200 17295 Z= 0.565 Chirality : 0.045 0.816 1974 Planarity : 0.005 0.137 2157 Dihedral : 8.757 123.127 2190 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.25 % Favored : 95.68 % Rotamer: Outliers : 4.13 % Allowed : 23.91 % Favored : 71.96 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.21), residues: 1577 helix: 0.99 (0.19), residues: 734 sheet: -1.19 (0.33), residues: 231 loop : -1.97 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 234 HIS 0.004 0.000 HIS A 67 PHE 0.013 0.001 PHE A 956 TYR 0.018 0.001 TYR A 120 ARG 0.007 0.000 ARG B 109 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2868.07 seconds wall clock time: 54 minutes 54.58 seconds (3294.58 seconds total)