Starting phenix.real_space_refine on Fri Feb 6 20:05:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9r75_53711/02_2026/9r75_53711.cif Found real_map, /net/cci-nas-00/data/ceres_data/9r75_53711/02_2026/9r75_53711.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9r75_53711/02_2026/9r75_53711.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9r75_53711/02_2026/9r75_53711.map" model { file = "/net/cci-nas-00/data/ceres_data/9r75_53711/02_2026/9r75_53711.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9r75_53711/02_2026/9r75_53711.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 66 5.49 5 Mg 2 5.21 5 S 69 5.16 5 C 16996 2.51 5 N 4834 2.21 5 O 5205 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27174 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1792 Classifications: {'peptide': 228} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 213} Chain: "B" Number of atoms: 1797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1797 Classifications: {'peptide': 229} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 214} Chain: "C" Number of atoms: 8627 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1091, 8605 Classifications: {'peptide': 1091} Link IDs: {'PCIS': 1, 'PTRANS': 69, 'TRANS': 1020} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 1091, 8605 Classifications: {'peptide': 1091} Link IDs: {'PCIS': 1, 'PTRANS': 69, 'TRANS': 1020} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 8744 Chain: "D" Number of atoms: 10740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1361, 10740 Classifications: {'peptide': 1361} Link IDs: {'PCIS': 2, 'PTRANS': 66, 'TRANS': 1292} Chain breaks: 2 Chain: "E" Number of atoms: 754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 754 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 6, 'TRANS': 86} Chain: "F" Number of atoms: 2094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2094 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 13, 'TRANS': 246} Chain breaks: 1 Chain: "G" Number of atoms: 635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 635 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain breaks: 1 Chain: "H" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 731 Classifications: {'DNA': 35} Link IDs: {'rna3p': 34} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 2, ' ZN': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 20048 SG CYS D1112 99.115 85.036 91.381 1.00 64.59 S ATOM 20692 SG CYS D1194 95.872 85.028 89.330 1.00 66.32 S ATOM 20748 SG CYS D1201 98.888 83.185 87.993 1.00 64.26 S ATOM 20772 SG CYS D1204 97.099 81.815 90.929 1.00 59.80 S ATOM 12694 SG CYS D 58 76.557 126.390 43.868 1.00121.13 S ATOM 12705 SG CYS D 60 73.931 129.077 43.238 1.00121.97 S ATOM 12816 SG CYS D 73 76.808 130.103 45.022 1.00114.89 S ATOM 12842 SG CYS D 76 74.460 127.797 46.851 1.00121.15 S Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AARG C 409 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG C 409 " occ=0.50 residue: pdb=" N AARG C 945 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG C 945 " occ=0.50 Time building chain proxies: 6.70, per 1000 atoms: 0.25 Number of scatterers: 27174 At special positions: 0 Unit cell: (136.71, 180.891, 135.043, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 69 16.00 P 66 15.00 Mg 2 11.99 O 5205 8.00 N 4834 7.00 C 16996 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.36 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D2001 " pdb="ZN ZN D2001 " - pdb=" SG CYS D1204 " pdb="ZN ZN D2001 " - pdb=" SG CYS D1201 " pdb="ZN ZN D2001 " - pdb=" SG CYS D1194 " pdb="ZN ZN D2001 " - pdb=" SG CYS D1112 " pdb=" ZN D2002 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 73 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 60 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 76 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 58 " Number of angles added : 12 6492 Ramachandran restraints generated. 3246 Oldfield, 0 Emsley, 3246 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6042 Finding SS restraints... Secondary structure from input PDB file: 125 helices and 50 sheets defined 43.1% alpha, 18.5% beta 20 base pairs and 48 stacking pairs defined. Time for finding SS restraints: 3.71 Creating SS restraints... Processing helix chain 'A' and resid 31 through 47 removed outlier: 3.599A pdb=" N THR A 35 " --> pdb=" O GLY A 31 " (cutoff:3.500A) Proline residue: A 39 - end of helix Processing helix chain 'A' and resid 74 through 83 Processing helix chain 'A' and resid 112 through 114 No H-bonds generated for 'chain 'A' and resid 112 through 114' Processing helix chain 'A' and resid 152 through 157 Processing helix chain 'A' and resid 206 through 224 removed outlier: 3.715A pdb=" N TYR A 224 " --> pdb=" O GLU A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 227 No H-bonds generated for 'chain 'A' and resid 225 through 227' Processing helix chain 'B' and resid 31 through 47 removed outlier: 3.633A pdb=" N THR B 35 " --> pdb=" O GLY B 31 " (cutoff:3.500A) Proline residue: B 39 - end of helix Processing helix chain 'B' and resid 74 through 84 removed outlier: 3.621A pdb=" N GLU B 84 " --> pdb=" O LEU B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 114 No H-bonds generated for 'chain 'B' and resid 112 through 114' Processing helix chain 'B' and resid 152 through 157 removed outlier: 3.780A pdb=" N HIS B 156 " --> pdb=" O PRO B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 223 Processing helix chain 'C' and resid 19 through 31 removed outlier: 4.073A pdb=" N SER C 25 " --> pdb=" O ILE C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 39 Processing helix chain 'C' and resid 43 through 52 Processing helix chain 'C' and resid 79 through 87 Processing helix chain 'C' and resid 193 through 200 Processing helix chain 'C' and resid 203 through 212 Processing helix chain 'C' and resid 216 through 222 Processing helix chain 'C' and resid 223 through 228 Processing helix chain 'C' and resid 230 through 243 Processing helix chain 'C' and resid 249 through 262 Processing helix chain 'C' and resid 270 through 282 Processing helix chain 'C' and resid 302 through 315 Processing helix chain 'C' and resid 335 through 362 Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 375 through 389 removed outlier: 3.572A pdb=" N SER C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 408 Processing helix chain 'C' and resid 419 through 423 removed outlier: 3.947A pdb=" N ALA C 423 " --> pdb=" O ARG C 420 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 435 Processing helix chain 'C' and resid 487 through 492 Processing helix chain 'C' and resid 525 through 529 Processing helix chain 'C' and resid 535 through 540 Processing helix chain 'C' and resid 543 through 547 Processing helix chain 'C' and resid 549 through 553 Processing helix chain 'C' and resid 554 through 565 Processing helix chain 'C' and resid 583 through 591 Processing helix chain 'C' and resid 683 through 687 removed outlier: 4.031A pdb=" N ASP C 686 " --> pdb=" O ASN C 683 " (cutoff:3.500A) Processing helix chain 'C' and resid 692 through 697 Processing helix chain 'C' and resid 730 through 734 removed outlier: 3.560A pdb=" N ALA C 733 " --> pdb=" O SER C 730 " (cutoff:3.500A) Processing helix chain 'C' and resid 854 through 858 Processing helix chain 'C' and resid 874 through 880 removed outlier: 4.687A pdb=" N SER C 878 " --> pdb=" O LEU C 874 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG C 879 " --> pdb=" O GLY C 875 " (cutoff:3.500A) Processing helix chain 'C' and resid 882 through 898 Processing helix chain 'C' and resid 910 through 932 removed outlier: 4.008A pdb=" N ARG C 929 " --> pdb=" O TYR C 925 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU C 932 " --> pdb=" O LYS C 928 " (cutoff:3.500A) Processing helix chain 'C' and resid 937 through 951 Processing helix chain 'C' and resid 958 through 969 Processing helix chain 'C' and resid 1000 through 1005 removed outlier: 3.737A pdb=" N LYS C1004 " --> pdb=" O MET C1000 " (cutoff:3.500A) Processing helix chain 'C' and resid 1033 through 1044 Processing helix chain 'C' and resid 1045 through 1055 Processing helix chain 'C' and resid 1059 through 1073 Processing helix chain 'C' and resid 1082 through 1094 removed outlier: 3.623A pdb=" N ARG C1086 " --> pdb=" O PRO C1082 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 22 Processing helix chain 'D' and resid 46 through 51 Processing helix chain 'D' and resid 82 through 88 Processing helix chain 'D' and resid 102 through 107 removed outlier: 3.781A pdb=" N ASP D 107 " --> pdb=" O TRP D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 116 Processing helix chain 'D' and resid 119 through 128 Processing helix chain 'D' and resid 154 through 163 Processing helix chain 'D' and resid 372 through 376 removed outlier: 3.588A pdb=" N GLU D 376 " --> pdb=" O PRO D 373 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 426 Processing helix chain 'D' and resid 456 through 468 removed outlier: 3.738A pdb=" N ALA D 460 " --> pdb=" O MET D 456 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU D 468 " --> pdb=" O LEU D 464 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 481 Processing helix chain 'D' and resid 485 through 506 removed outlier: 3.685A pdb=" N VAL D 498 " --> pdb=" O LYS D 494 " (cutoff:3.500A) Processing helix chain 'D' and resid 508 through 511 Processing helix chain 'D' and resid 521 through 525 Processing helix chain 'D' and resid 538 through 560 removed outlier: 3.950A pdb=" N ASP D 542 " --> pdb=" O SER D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 563 through 584 Processing helix chain 'D' and resid 602 through 608 Processing helix chain 'D' and resid 612 through 618 Processing helix chain 'D' and resid 646 through 653 Processing helix chain 'D' and resid 653 through 664 Processing helix chain 'D' and resid 669 through 679 removed outlier: 4.013A pdb=" N ARG D 679 " --> pdb=" O ARG D 675 " (cutoff:3.500A) Processing helix chain 'D' and resid 680 through 683 Processing helix chain 'D' and resid 685 through 695 removed outlier: 3.580A pdb=" N ASP D 689 " --> pdb=" O ASP D 685 " (cutoff:3.500A) Processing helix chain 'D' and resid 709 through 711 No H-bonds generated for 'chain 'D' and resid 709 through 711' Processing helix chain 'D' and resid 729 through 731 No H-bonds generated for 'chain 'D' and resid 729 through 731' Processing helix chain 'D' and resid 732 through 737 Processing helix chain 'D' and resid 752 through 763 Processing helix chain 'D' and resid 764 through 768 Processing helix chain 'D' and resid 783 through 794 Processing helix chain 'D' and resid 808 through 819 Processing helix chain 'D' and resid 835 through 841 removed outlier: 3.502A pdb=" N LEU D 839 " --> pdb=" O SER D 835 " (cutoff:3.500A) Processing helix chain 'D' and resid 845 through 855 Processing helix chain 'D' and resid 876 through 891 Processing helix chain 'D' and resid 892 through 900 Processing helix chain 'D' and resid 907 through 923 Processing helix chain 'D' and resid 923 through 945 removed outlier: 3.687A pdb=" N THR D 944 " --> pdb=" O THR D 940 " (cutoff:3.500A) Processing helix chain 'D' and resid 950 through 954 Processing helix chain 'D' and resid 958 through 980 removed outlier: 3.952A pdb=" N GLN D 962 " --> pdb=" O GLU D 958 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU D 972 " --> pdb=" O ASP D 968 " (cutoff:3.500A) Processing helix chain 'D' and resid 984 through 1015 Processing helix chain 'D' and resid 1018 through 1026 Processing helix chain 'D' and resid 1031 through 1040 Processing helix chain 'D' and resid 1066 through 1103 removed outlier: 3.810A pdb=" N HIS D1075 " --> pdb=" O PHE D1071 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N GLY D1076 " --> pdb=" O ILE D1072 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ALA D1089 " --> pdb=" O ALA D1085 " (cutoff:3.500A) Processing helix chain 'D' and resid 1136 through 1145 Processing helix chain 'D' and resid 1167 through 1180 Processing helix chain 'D' and resid 1190 through 1194 Processing helix chain 'D' and resid 1202 through 1206 Processing helix chain 'D' and resid 1220 through 1234 Proline residue: D1232 - end of helix Processing helix chain 'D' and resid 1255 through 1264 Processing helix chain 'D' and resid 1331 through 1339 Processing helix chain 'D' and resid 1340 through 1359 removed outlier: 3.571A pdb=" N VAL D1344 " --> pdb=" O GLY D1340 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL D1355 " --> pdb=" O GLU D1351 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N TYR D1356 " --> pdb=" O ILE D1352 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN D1359 " --> pdb=" O VAL D1355 " (cutoff:3.500A) Processing helix chain 'D' and resid 1364 through 1376 removed outlier: 4.403A pdb=" N ILE D1368 " --> pdb=" O HIS D1364 " (cutoff:3.500A) Processing helix chain 'D' and resid 1397 through 1411 Processing helix chain 'D' and resid 1423 through 1430 Processing helix chain 'D' and resid 1433 through 1441 Processing helix chain 'D' and resid 1442 through 1454 Processing helix chain 'D' and resid 1461 through 1468 removed outlier: 4.162A pdb=" N ASN D1465 " --> pdb=" O GLY D1461 " (cutoff:3.500A) Processing helix chain 'D' and resid 1474 through 1478 Processing helix chain 'D' and resid 1489 through 1498 Processing helix chain 'E' and resid 5 through 12 Processing helix chain 'E' and resid 15 through 33 Processing helix chain 'E' and resid 59 through 71 removed outlier: 3.651A pdb=" N TRP E 63 " --> pdb=" O ASN E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 93 Processing helix chain 'F' and resid 79 through 90 removed outlier: 3.593A pdb=" N GLN F 83 " --> pdb=" O ASP F 79 " (cutoff:3.500A) Processing helix chain 'F' and resid 95 through 121 Processing helix chain 'F' and resid 123 through 137 removed outlier: 3.610A pdb=" N ILE F 127 " --> pdb=" O ASP F 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 152 through 165 Processing helix chain 'F' and resid 171 through 200 removed outlier: 3.689A pdb=" N HIS F 175 " --> pdb=" O LYS F 171 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N ARG F 193 " --> pdb=" O GLU F 189 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N LEU F 194 " --> pdb=" O ALA F 190 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N VAL F 195 " --> pdb=" O ASN F 191 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL F 196 " --> pdb=" O LEU F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 208 through 227 Processing helix chain 'F' and resid 228 through 232 removed outlier: 3.899A pdb=" N ARG F 231 " --> pdb=" O GLU F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 255 removed outlier: 3.867A pdb=" N TYR F 238 " --> pdb=" O LYS F 234 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N TRP F 241 " --> pdb=" O THR F 237 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N TRP F 242 " --> pdb=" O TYR F 238 " (cutoff:3.500A) Processing helix chain 'F' and resid 261 through 283 Processing helix chain 'F' and resid 287 through 296 Processing helix chain 'F' and resid 300 through 311 Processing helix chain 'F' and resid 330 through 333 Processing helix chain 'F' and resid 340 through 345 Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 16 removed outlier: 6.586A pdb=" N ASP A 193 " --> pdb=" O PRO A 27 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 96 through 104 removed outlier: 7.206A pdb=" N ASN A 139 " --> pdb=" O ILE A 58 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ILE A 58 " --> pdb=" O ASN A 139 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N GLU A 141 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N VAL A 56 " --> pdb=" O GLU A 141 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ARG A 143 " --> pdb=" O THR A 54 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 87 through 89 Processing sheet with id=AA4, first strand: chain 'A' and resid 107 through 110 Processing sheet with id=AA5, first strand: chain 'A' and resid 150 through 151 Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 13 removed outlier: 6.415A pdb=" N ASP B 193 " --> pdb=" O PRO B 27 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N THR B 190 " --> pdb=" O LEU B 186 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N LEU B 186 " --> pdb=" O THR B 190 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 97 through 104 removed outlier: 8.345A pdb=" N ASN B 139 " --> pdb=" O ILE B 58 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N ILE B 58 " --> pdb=" O ASN B 139 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N GLU B 141 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N VAL B 56 " --> pdb=" O GLU B 141 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ARG B 143 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL B 56 " --> pdb=" O ILE B 165 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 87 through 89 Processing sheet with id=AA9, first strand: chain 'B' and resid 107 through 110 Processing sheet with id=AB1, first strand: chain 'B' and resid 150 through 151 Processing sheet with id=AB2, first strand: chain 'C' and resid 3 through 5 Processing sheet with id=AB3, first strand: chain 'C' and resid 54 through 55 removed outlier: 3.589A pdb=" N LEU C 66 " --> pdb=" O ILE C 54 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N LEU C 66 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N ILE C 101 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N PHE C 68 " --> pdb=" O GLN C 99 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N GLN C 99 " --> pdb=" O PHE C 68 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU C 70 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ALA C 92 " --> pdb=" O HIS C 117 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N HIS C 117 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N LEU C 94 " --> pdb=" O LEU C 115 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 127 through 129 Processing sheet with id=AB5, first strand: chain 'C' and resid 331 through 334 removed outlier: 6.327A pdb=" N SER C 138 " --> pdb=" O SER C 411 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 145 through 150 removed outlier: 6.496A pdb=" N TYR C 158 " --> pdb=" O VAL C 176 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N VAL C 176 " --> pdb=" O TYR C 158 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE C 191 " --> pdb=" O MET C 184 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 291 through 294 Processing sheet with id=AB8, first strand: chain 'C' and resid 460 through 461 removed outlier: 5.567A pdb=" N GLU C 482 " --> pdb=" O ARG C 473 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N VAL C 475 " --> pdb=" O THR C 480 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N THR C 480 " --> pdb=" O VAL C 475 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 460 through 461 Processing sheet with id=AC1, first strand: chain 'C' and resid 503 through 504 Processing sheet with id=AC2, first strand: chain 'C' and resid 595 through 596 removed outlier: 6.673A pdb=" N LEU C 595 " --> pdb=" O LEU C 655 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 620 through 624 removed outlier: 6.713A pdb=" N ARG C 610 " --> pdb=" O VAL C 606 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N VAL C 606 " --> pdb=" O ARG C 610 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N VAL C 612 " --> pdb=" O ALA C 604 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 629 through 630 removed outlier: 3.609A pdb=" N TYR C 629 " --> pdb=" O LEU C 637 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 661 through 662 Processing sheet with id=AC6, first strand: chain 'C' and resid 971 through 972 removed outlier: 7.237A pdb=" N ILE C 688 " --> pdb=" O ALA C 850 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ILE C 852 " --> pdb=" O ILE C 688 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N ILE C 690 " --> pdb=" O ILE C 852 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL C 689 " --> pdb=" O ILE C 870 " (cutoff:3.500A) removed outlier: 8.960A pdb=" N VAL C 869 " --> pdb=" O ASN C 671 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LEU C 673 " --> pdb=" O VAL C 869 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N LEU C 871 " --> pdb=" O LEU C 673 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ALA C 675 " --> pdb=" O LEU C 871 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N VAL C 988 " --> pdb=" O ILE C 676 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 702 through 713 removed outlier: 8.185A pdb=" N ARG C 820 " --> pdb=" O ARG C 807 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N ARG C 807 " --> pdb=" O ARG C 820 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N VAL C 822 " --> pdb=" O ARG C 805 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ARG C 805 " --> pdb=" O VAL C 822 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ARG C 824 " --> pdb=" O THR C 803 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N THR C 803 " --> pdb=" O ARG C 824 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N TYR C 826 " --> pdb=" O VAL C 801 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 754 through 756 removed outlier: 6.913A pdb=" N LEU C 790 " --> pdb=" O LEU C 755 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 759 through 760 Processing sheet with id=AD1, first strand: chain 'C' and resid 1006 through 1008 removed outlier: 6.309A pdb=" N CYS D 642 " --> pdb=" O VAL D 719 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N VAL D 721 " --> pdb=" O CYS D 642 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N LEU D 644 " --> pdb=" O VAL D 721 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 1031 through 1032 Processing sheet with id=AD3, first strand: chain 'C' and resid 1097 through 1102 Processing sheet with id=AD4, first strand: chain 'D' and resid 91 through 100 removed outlier: 7.029A pdb=" N GLU D 515 " --> pdb=" O LEU D 95 " (cutoff:3.500A) removed outlier: 10.930A pdb=" N THR D 97 " --> pdb=" O ILE D 513 " (cutoff:3.500A) removed outlier: 10.423A pdb=" N ILE D 513 " --> pdb=" O THR D 97 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 152 through 153 removed outlier: 3.728A pdb=" N ILE D 133 " --> pdb=" O ARG D 455 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG D 455 " --> pdb=" O ILE D 133 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASP D 453 " --> pdb=" O LEU D 135 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 141 through 142 Processing sheet with id=AD7, first strand: chain 'D' and resid 166 through 170 removed outlier: 6.966A pdb=" N VAL D 385 " --> pdb=" O VAL D 213 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL D 213 " --> pdb=" O VAL D 385 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N LEU D 387 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL D 211 " --> pdb=" O LEU D 387 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N GLU D 389 " --> pdb=" O ARG D 209 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N PHE D 207 " --> pdb=" O ALA D 391 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE D 393 " --> pdb=" O TYR D 205 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N TYR D 205 " --> pdb=" O ILE D 393 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL D 395 " --> pdb=" O ALA D 203 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ALA D 203 " --> pdb=" O VAL D 395 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 166 through 170 removed outlier: 6.966A pdb=" N VAL D 385 " --> pdb=" O VAL D 213 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL D 213 " --> pdb=" O VAL D 385 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N LEU D 387 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL D 211 " --> pdb=" O LEU D 387 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N GLU D 389 " --> pdb=" O ARG D 209 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N PHE D 207 " --> pdb=" O ALA D 391 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE D 393 " --> pdb=" O TYR D 205 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N TYR D 205 " --> pdb=" O ILE D 393 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL D 395 " --> pdb=" O ALA D 203 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ALA D 203 " --> pdb=" O VAL D 395 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 190 through 192 Processing sheet with id=AE1, first strand: chain 'D' and resid 366 through 368 removed outlier: 6.899A pdb=" N VAL D 377 " --> pdb=" O ILE D 367 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 398 through 402 removed outlier: 3.909A pdb=" N ASP D 413 " --> pdb=" O VAL D 435 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 528 through 529 Processing sheet with id=AE4, first strand: chain 'D' and resid 805 through 806 Processing sheet with id=AE5, first strand: chain 'D' and resid 842 through 843 Processing sheet with id=AE6, first strand: chain 'D' and resid 1106 through 1109 Processing sheet with id=AE7, first strand: chain 'D' and resid 1118 through 1121 Processing sheet with id=AE8, first strand: chain 'D' and resid 1123 through 1125 Processing sheet with id=AE9, first strand: chain 'D' and resid 1153 through 1155 Processing sheet with id=AF1, first strand: chain 'D' and resid 1300 through 1305 removed outlier: 3.730A pdb=" N LEU D1305 " --> pdb=" O LEU D1290 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N LEU D1290 " --> pdb=" O LEU D1305 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY D1279 " --> pdb=" O VAL D1319 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 1394 through 1396 removed outlier: 5.494A pdb=" N VAL D1381 " --> pdb=" O LYS D1418 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N LYS D1418 " --> pdb=" O VAL D1381 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 1484 through 1488 Processing sheet with id=AF4, first strand: chain 'E' and resid 47 through 49 Processing sheet with id=AF5, first strand: chain 'F' and resid 320 through 321 removed outlier: 4.257A pdb=" N SER F 327 " --> pdb=" O ILE F 321 " (cutoff:3.500A) 1209 hydrogen bonds defined for protein. 3347 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 52 hydrogen bonds 104 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 48 stacking parallelities Total time for adding SS restraints: 7.03 Time building geometry restraints manager: 3.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8873 1.34 - 1.46: 4855 1.46 - 1.58: 13817 1.58 - 1.70: 129 1.70 - 1.82: 125 Bond restraints: 27799 Sorted by residual: bond pdb=" SD MET D 661 " pdb=" CE MET D 661 " ideal model delta sigma weight residual 1.791 1.708 0.083 2.50e-02 1.60e+03 1.11e+01 bond pdb=" CB MET D 661 " pdb=" CG MET D 661 " ideal model delta sigma weight residual 1.520 1.423 0.097 3.00e-02 1.11e+03 1.05e+01 bond pdb=" N ILE D 761 " pdb=" CA ILE D 761 " ideal model delta sigma weight residual 1.456 1.496 -0.039 1.30e-02 5.92e+03 9.12e+00 bond pdb=" N VAL C 176 " pdb=" CA VAL C 176 " ideal model delta sigma weight residual 1.460 1.493 -0.033 1.10e-02 8.26e+03 9.05e+00 bond pdb=" N VAL C 181 " pdb=" CA VAL C 181 " ideal model delta sigma weight residual 1.455 1.493 -0.038 1.38e-02 5.25e+03 7.53e+00 ... (remaining 27794 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.23: 37105 2.23 - 4.45: 703 4.45 - 6.68: 66 6.68 - 8.90: 12 8.90 - 11.13: 6 Bond angle restraints: 37892 Sorted by residual: angle pdb=" CB ILE B 58 " pdb=" CG1 ILE B 58 " pdb=" CD1 ILE B 58 " ideal model delta sigma weight residual 113.80 105.02 8.78 2.10e+00 2.27e-01 1.75e+01 angle pdb=" C GLU A 59 " pdb=" N ASP A 60 " pdb=" CA ASP A 60 " ideal model delta sigma weight residual 122.08 128.16 -6.08 1.47e+00 4.63e-01 1.71e+01 angle pdb=" CA GLU D 57 " pdb=" CB GLU D 57 " pdb=" CG GLU D 57 " ideal model delta sigma weight residual 114.10 121.83 -7.73 2.00e+00 2.50e-01 1.49e+01 angle pdb=" CB LYS C 167 " pdb=" CG LYS C 167 " pdb=" CD LYS C 167 " ideal model delta sigma weight residual 111.30 119.96 -8.66 2.30e+00 1.89e-01 1.42e+01 angle pdb=" N GLU F 305 " pdb=" CA GLU F 305 " pdb=" CB GLU F 305 " ideal model delta sigma weight residual 110.12 115.65 -5.53 1.47e+00 4.63e-01 1.41e+01 ... (remaining 37887 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.92: 15752 29.92 - 59.83: 1061 59.83 - 89.75: 92 89.75 - 119.66: 0 119.66 - 149.58: 1 Dihedral angle restraints: 16906 sinusoidal: 7515 harmonic: 9391 Sorted by residual: dihedral pdb=" CA SER A 46 " pdb=" C SER A 46 " pdb=" N SER A 47 " pdb=" CA SER A 47 " ideal model delta harmonic sigma weight residual -180.00 -157.94 -22.06 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA TYR D1207 " pdb=" C TYR D1207 " pdb=" N ASP D1208 " pdb=" CA ASP D1208 " ideal model delta harmonic sigma weight residual 180.00 158.26 21.74 0 5.00e+00 4.00e-02 1.89e+01 dihedral pdb=" C4' DA G 26 " pdb=" C3' DA G 26 " pdb=" O3' DA G 26 " pdb=" P DA G 27 " ideal model delta sinusoidal sigma weight residual 220.00 70.42 149.58 1 3.50e+01 8.16e-04 1.46e+01 ... (remaining 16903 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 3339 0.055 - 0.110: 781 0.110 - 0.165: 125 0.165 - 0.220: 19 0.220 - 0.275: 8 Chirality restraints: 4272 Sorted by residual: chirality pdb=" P DA G 27 " pdb=" OP1 DA G 27 " pdb=" OP2 DA G 27 " pdb=" O5' DA G 27 " both_signs ideal model delta sigma weight residual True 2.35 -2.62 -0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" P DA H 18 " pdb=" OP1 DA H 18 " pdb=" OP2 DA H 18 " pdb=" O5' DA H 18 " both_signs ideal model delta sigma weight residual True 2.35 -2.61 -0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CB ILE F 198 " pdb=" CA ILE F 198 " pdb=" CG1 ILE F 198 " pdb=" CG2 ILE F 198 " both_signs ideal model delta sigma weight residual False 2.64 2.91 -0.26 2.00e-01 2.50e+01 1.70e+00 ... (remaining 4269 not shown) Planarity restraints: 4732 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG F 140 " -0.223 9.50e-02 1.11e+02 1.01e-01 8.13e+00 pdb=" NE ARG F 140 " 0.022 2.00e-02 2.50e+03 pdb=" CZ ARG F 140 " -0.022 2.00e-02 2.50e+03 pdb=" NH1 ARG F 140 " 0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG F 140 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 132 " -0.217 9.50e-02 1.11e+02 9.81e-02 7.59e+00 pdb=" NE ARG F 132 " 0.021 2.00e-02 2.50e+03 pdb=" CZ ARG F 132 " -0.021 2.00e-02 2.50e+03 pdb=" NH1 ARG F 132 " 0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG F 132 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 237 " -0.221 9.50e-02 1.11e+02 9.95e-02 7.40e+00 pdb=" NE ARG C 237 " 0.020 2.00e-02 2.50e+03 pdb=" CZ ARG C 237 " -0.018 2.00e-02 2.50e+03 pdb=" NH1 ARG C 237 " 0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG C 237 " -0.001 2.00e-02 2.50e+03 ... (remaining 4729 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 90 2.61 - 3.18: 22624 3.18 - 3.76: 41489 3.76 - 4.33: 57001 4.33 - 4.90: 93896 Nonbonded interactions: 215100 Sorted by model distance: nonbonded pdb=" OD1 ASP D 743 " pdb="MG MG D2003 " model vdw 2.039 2.170 nonbonded pdb=" O ASP D 107 " pdb=" OD1 ASP D 107 " model vdw 2.132 3.040 nonbonded pdb=" N GLU F 97 " pdb=" OE1 GLU F 97 " model vdw 2.204 3.120 nonbonded pdb=" OG1 THR F 95 " pdb=" OE1 GLU F 97 " model vdw 2.248 3.040 nonbonded pdb=" O LYS D 840 " pdb="MG MG D2004 " model vdw 2.294 2.170 ... (remaining 215095 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 4 through 231) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.460 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 33.070 Find NCS groups from input model: 0.160 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: 0.000 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 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 : 0.004 0.097 27807 Z= 0.168 Angle : 0.712 11.126 37904 Z= 0.383 Chirality : 0.049 0.275 4272 Planarity : 0.009 0.101 4732 Dihedral : 18.094 149.580 10864 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.00 % Allowed : 22.34 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.14), residues: 3246 helix: 1.42 (0.15), residues: 1212 sheet: -0.01 (0.24), residues: 457 loop : 0.14 (0.15), residues: 1577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.002 ARG F 140 TYR 0.024 0.001 TYR B 20 PHE 0.016 0.001 PHE C 293 TRP 0.020 0.002 TRP E 63 HIS 0.011 0.001 HIS D 350 Details of bonding type rmsd covalent geometry : bond 0.00359 (27799) covalent geometry : angle 0.70918 (37892) hydrogen bonds : bond 0.14450 ( 1253) hydrogen bonds : angle 6.02168 ( 3451) metal coordination : bond 0.00549 ( 8) metal coordination : angle 3.83281 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6492 Ramachandran restraints generated. 3246 Oldfield, 0 Emsley, 3246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6492 Ramachandran restraints generated. 3246 Oldfield, 0 Emsley, 3246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 248 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 252 LYS cc_start: 0.8911 (ttmt) cc_final: 0.7967 (tptt) REVERT: C 321 GLU cc_start: 0.7029 (pm20) cc_final: 0.6679 (pm20) REVERT: C 427 VAL cc_start: 0.9161 (m) cc_final: 0.8757 (t) REVERT: C 697 ARG cc_start: 0.8108 (ptp90) cc_final: 0.7882 (ptp90) REVERT: C 815 LEU cc_start: 0.8004 (mt) cc_final: 0.7500 (mm) REVERT: D 110 SER cc_start: 0.9090 (t) cc_final: 0.8735 (p) REVERT: D 832 ARG cc_start: 0.8251 (ptp90) cc_final: 0.7609 (ptm160) REVERT: D 859 ASP cc_start: 0.9017 (m-30) cc_final: 0.8787 (m-30) REVERT: D 862 ASP cc_start: 0.9070 (m-30) cc_final: 0.8596 (m-30) REVERT: D 1168 MET cc_start: 0.9304 (mmt) cc_final: 0.8986 (mmt) REVERT: D 1378 TYR cc_start: 0.8799 (m-80) cc_final: 0.8549 (m-80) REVERT: D 1496 GLU cc_start: 0.7406 (tm-30) cc_final: 0.7124 (tm-30) REVERT: E 37 ASN cc_start: 0.8661 (p0) cc_final: 0.8314 (p0) REVERT: F 90 GLN cc_start: 0.7949 (mm110) cc_final: 0.7407 (tt0) REVERT: F 194 LEU cc_start: 0.8926 (mt) cc_final: 0.8689 (tp) REVERT: F 313 GLU cc_start: 0.6306 (tp30) cc_final: 0.5311 (mp0) outliers start: 0 outliers final: 0 residues processed: 248 average time/residue: 0.1784 time to fit residues: 71.5097 Evaluate side-chains 241 residues out of total 2771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 241 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 0.0170 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 9.9990 overall best weight: 2.7624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 670 GLN C 728 HIS D 703 ASN D1116 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.114210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.082701 restraints weight = 79730.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.085555 restraints weight = 39113.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.087472 restraints weight = 24552.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.088698 restraints weight = 18279.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.089372 restraints weight = 15266.886| |-----------------------------------------------------------------------------| r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3061 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3061 r_free = 0.3061 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3061 r_free = 0.3061 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3061 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.0947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 27807 Z= 0.211 Angle : 0.616 9.332 37904 Z= 0.325 Chirality : 0.045 0.168 4272 Planarity : 0.005 0.048 4732 Dihedral : 13.729 142.542 4334 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.63 % Allowed : 18.77 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.15), residues: 3246 helix: 1.56 (0.15), residues: 1245 sheet: 0.04 (0.24), residues: 459 loop : 0.31 (0.16), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 154 TYR 0.013 0.001 TYR C 90 PHE 0.011 0.002 PHE C1032 TRP 0.015 0.002 TRP A 200 HIS 0.010 0.001 HIS A 156 Details of bonding type rmsd covalent geometry : bond 0.00506 (27799) covalent geometry : angle 0.61254 (37892) hydrogen bonds : bond 0.04902 ( 1253) hydrogen bonds : angle 4.94642 ( 3451) metal coordination : bond 0.01054 ( 8) metal coordination : angle 3.82478 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6492 Ramachandran restraints generated. 3246 Oldfield, 0 Emsley, 3246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6492 Ramachandran restraints generated. 3246 Oldfield, 0 Emsley, 3246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 249 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 115 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8566 (pp) REVERT: C 179 ASN cc_start: 0.8335 (OUTLIER) cc_final: 0.8091 (t0) REVERT: C 252 LYS cc_start: 0.8854 (ttmt) cc_final: 0.7936 (tptt) REVERT: C 396 ASP cc_start: 0.8457 (OUTLIER) cc_final: 0.8188 (m-30) REVERT: D 110 SER cc_start: 0.9029 (t) cc_final: 0.8803 (p) REVERT: D 157 GLU cc_start: 0.7415 (mt-10) cc_final: 0.7139 (mp0) REVERT: D 832 ARG cc_start: 0.7905 (ptp90) cc_final: 0.7459 (ptp90) REVERT: D 862 ASP cc_start: 0.8691 (m-30) cc_final: 0.8223 (m-30) REVERT: D 1168 MET cc_start: 0.9027 (mmt) cc_final: 0.8685 (mmt) REVERT: D 1496 GLU cc_start: 0.7342 (tm-30) cc_final: 0.7038 (tm-30) REVERT: E 37 ASN cc_start: 0.8651 (p0) cc_final: 0.8300 (p0) REVERT: F 90 GLN cc_start: 0.7876 (mm110) cc_final: 0.7178 (tt0) REVERT: F 313 GLU cc_start: 0.6027 (tp30) cc_final: 0.5093 (mp0) outliers start: 73 outliers final: 45 residues processed: 305 average time/residue: 0.1736 time to fit residues: 85.9028 Evaluate side-chains 274 residues out of total 2771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 226 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 83 CYS Chi-restraints excluded: chain C residue 179 ASN Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 396 ASP Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 637 LEU Chi-restraints excluded: chain C residue 698 ASP Chi-restraints excluded: chain C residue 792 VAL Chi-restraints excluded: chain C residue 987 ILE Chi-restraints excluded: chain C residue 1010 THR Chi-restraints excluded: chain C residue 1015 LEU Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 386 HIS Chi-restraints excluded: chain D residue 432 TYR Chi-restraints excluded: chain D residue 468 LEU Chi-restraints excluded: chain D residue 537 THR Chi-restraints excluded: chain D residue 538 SER Chi-restraints excluded: chain D residue 694 VAL Chi-restraints excluded: chain D residue 711 LEU Chi-restraints excluded: chain D residue 940 THR Chi-restraints excluded: chain D residue 1099 VAL Chi-restraints excluded: chain D residue 1132 LEU Chi-restraints excluded: chain D residue 1207 TYR Chi-restraints excluded: chain D residue 1234 THR Chi-restraints excluded: chain D residue 1400 VAL Chi-restraints excluded: chain D residue 1422 MET Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 282 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 146 optimal weight: 0.9990 chunk 29 optimal weight: 0.0670 chunk 12 optimal weight: 4.9990 chunk 258 optimal weight: 0.7980 chunk 179 optimal weight: 30.0000 chunk 57 optimal weight: 4.9990 chunk 119 optimal weight: 7.9990 chunk 34 optimal weight: 7.9990 chunk 265 optimal weight: 0.8980 chunk 283 optimal weight: 0.9980 chunk 217 optimal weight: 1.9990 overall best weight: 0.7520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 45 GLN ** C 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 728 HIS ** D 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1465 ASN E 33 HIS ** F 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.117145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.085610 restraints weight = 93551.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.090093 restraints weight = 42972.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.090871 restraints weight = 21954.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.091030 restraints weight = 19132.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.091223 restraints weight = 18060.121| |-----------------------------------------------------------------------------| r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3080 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3080 r_free = 0.3080 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3080 r_free = 0.3080 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3080 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.1202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 27807 Z= 0.107 Angle : 0.515 7.710 37904 Z= 0.272 Chirality : 0.042 0.214 4272 Planarity : 0.004 0.044 4732 Dihedral : 13.570 137.448 4334 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.23 % Allowed : 18.63 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.15), residues: 3246 helix: 1.71 (0.15), residues: 1245 sheet: 0.29 (0.24), residues: 449 loop : 0.44 (0.16), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 154 TYR 0.015 0.001 TYR D 132 PHE 0.011 0.001 PHE B 65 TRP 0.012 0.001 TRP A 200 HIS 0.009 0.001 HIS A 156 Details of bonding type rmsd covalent geometry : bond 0.00239 (27799) covalent geometry : angle 0.51284 (37892) hydrogen bonds : bond 0.03960 ( 1253) hydrogen bonds : angle 4.54276 ( 3451) metal coordination : bond 0.00388 ( 8) metal coordination : angle 2.79746 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6492 Ramachandran restraints generated. 3246 Oldfield, 0 Emsley, 3246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6492 Ramachandran restraints generated. 3246 Oldfield, 0 Emsley, 3246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 270 time to evaluate : 1.082 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 44 ILE cc_start: 0.8910 (pt) cc_final: 0.8507 (mt) REVERT: C 209 ARG cc_start: 0.8500 (ptm-80) cc_final: 0.8170 (ptm160) REVERT: C 252 LYS cc_start: 0.8884 (ttmt) cc_final: 0.7873 (tptt) REVERT: D 57 GLU cc_start: 0.8209 (tm-30) cc_final: 0.7716 (tt0) REVERT: D 110 SER cc_start: 0.8972 (t) cc_final: 0.8729 (p) REVERT: D 157 GLU cc_start: 0.7464 (mt-10) cc_final: 0.7246 (mt-10) REVERT: D 859 ASP cc_start: 0.8780 (m-30) cc_final: 0.8516 (m-30) REVERT: D 862 ASP cc_start: 0.8679 (m-30) cc_final: 0.8219 (m-30) REVERT: D 1168 MET cc_start: 0.8907 (mmt) cc_final: 0.8633 (mmt) REVERT: D 1496 GLU cc_start: 0.7455 (tm-30) cc_final: 0.7140 (tm-30) REVERT: E 37 ASN cc_start: 0.8527 (p0) cc_final: 0.8107 (p0) REVERT: F 90 GLN cc_start: 0.7885 (mm110) cc_final: 0.7252 (tt0) REVERT: F 163 LEU cc_start: 0.7705 (mt) cc_final: 0.7429 (tt) REVERT: F 217 ASN cc_start: 0.8904 (m110) cc_final: 0.8694 (m-40) REVERT: F 313 GLU cc_start: 0.6022 (tp30) cc_final: 0.4990 (mp0) outliers start: 62 outliers final: 36 residues processed: 317 average time/residue: 0.1759 time to fit residues: 89.6689 Evaluate side-chains 283 residues out of total 2771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 247 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 173 ASP Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 637 LEU Chi-restraints excluded: chain C residue 725 ASP Chi-restraints excluded: chain C residue 792 VAL Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 386 HIS Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 432 TYR Chi-restraints excluded: chain D residue 538 SER Chi-restraints excluded: chain D residue 711 LEU Chi-restraints excluded: chain D residue 940 THR Chi-restraints excluded: chain D residue 971 LEU Chi-restraints excluded: chain D residue 1090 ASP Chi-restraints excluded: chain D residue 1207 TYR Chi-restraints excluded: chain D residue 1234 THR Chi-restraints excluded: chain D residue 1253 THR Chi-restraints excluded: chain D residue 1305 LEU Chi-restraints excluded: chain D residue 1400 VAL Chi-restraints excluded: chain D residue 1422 MET Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain F residue 282 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 292 optimal weight: 4.9990 chunk 91 optimal weight: 7.9990 chunk 211 optimal weight: 5.9990 chunk 276 optimal weight: 0.7980 chunk 237 optimal weight: 8.9990 chunk 178 optimal weight: 8.9990 chunk 208 optimal weight: 0.8980 chunk 131 optimal weight: 4.9990 chunk 325 optimal weight: 10.0000 chunk 65 optimal weight: 2.9990 chunk 156 optimal weight: 0.7980 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 728 HIS F 217 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.114315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.083257 restraints weight = 88766.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.086154 restraints weight = 47601.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.088244 restraints weight = 25477.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.088008 restraints weight = 21717.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.088088 restraints weight = 18778.269| |-----------------------------------------------------------------------------| r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3020 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3020 r_free = 0.3020 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3020 r_free = 0.3020 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3020 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 27807 Z= 0.169 Angle : 0.550 9.124 37904 Z= 0.287 Chirality : 0.043 0.234 4272 Planarity : 0.004 0.046 4732 Dihedral : 13.652 133.584 4334 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 3.06 % Allowed : 18.85 % Favored : 78.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.15), residues: 3246 helix: 1.66 (0.15), residues: 1247 sheet: 0.16 (0.24), residues: 448 loop : 0.36 (0.16), residues: 1551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 154 TYR 0.012 0.001 TYR D 132 PHE 0.011 0.001 PHE B 65 TRP 0.012 0.001 TRP A 200 HIS 0.009 0.001 HIS A 156 Details of bonding type rmsd covalent geometry : bond 0.00403 (27799) covalent geometry : angle 0.54674 (37892) hydrogen bonds : bond 0.04330 ( 1253) hydrogen bonds : angle 4.52778 ( 3451) metal coordination : bond 0.00949 ( 8) metal coordination : angle 3.37737 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6492 Ramachandran restraints generated. 3246 Oldfield, 0 Emsley, 3246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6492 Ramachandran restraints generated. 3246 Oldfield, 0 Emsley, 3246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 242 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 44 ILE cc_start: 0.8926 (pt) cc_final: 0.8666 (mt) REVERT: C 209 ARG cc_start: 0.8521 (ptm-80) cc_final: 0.8208 (ptm160) REVERT: C 222 MET cc_start: 0.7705 (OUTLIER) cc_final: 0.6493 (pmm) REVERT: C 252 LYS cc_start: 0.8929 (ttmt) cc_final: 0.7936 (tptt) REVERT: C 396 ASP cc_start: 0.8554 (OUTLIER) cc_final: 0.8331 (m-30) REVERT: D 57 GLU cc_start: 0.8229 (tm-30) cc_final: 0.7659 (tt0) REVERT: D 110 SER cc_start: 0.9061 (t) cc_final: 0.8820 (p) REVERT: D 142 LEU cc_start: 0.8200 (tm) cc_final: 0.7953 (tp) REVERT: D 157 GLU cc_start: 0.7407 (mt-10) cc_final: 0.7199 (mt-10) REVERT: D 455 ARG cc_start: 0.6960 (OUTLIER) cc_final: 0.6211 (mmm-85) REVERT: D 832 ARG cc_start: 0.8065 (ptp90) cc_final: 0.7497 (ptp90) REVERT: D 862 ASP cc_start: 0.8605 (m-30) cc_final: 0.8173 (m-30) REVERT: D 1168 MET cc_start: 0.8943 (mmt) cc_final: 0.8674 (mmt) REVERT: E 37 ASN cc_start: 0.8708 (p0) cc_final: 0.8300 (p0) REVERT: F 90 GLN cc_start: 0.7922 (mm110) cc_final: 0.7303 (tt0) REVERT: F 163 LEU cc_start: 0.7689 (mt) cc_final: 0.7416 (tt) outliers start: 85 outliers final: 53 residues processed: 311 average time/residue: 0.1738 time to fit residues: 87.1259 Evaluate side-chains 279 residues out of total 2771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 223 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 72 LYS Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 173 ASP Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 222 MET Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 261 ILE Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 396 ASP Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 637 LEU Chi-restraints excluded: chain C residue 725 ASP Chi-restraints excluded: chain C residue 792 VAL Chi-restraints excluded: chain C residue 987 ILE Chi-restraints excluded: chain C residue 1000 MET Chi-restraints excluded: chain C residue 1015 LEU Chi-restraints excluded: chain C residue 1060 ILE Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 386 HIS Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 432 TYR Chi-restraints excluded: chain D residue 455 ARG Chi-restraints excluded: chain D residue 468 LEU Chi-restraints excluded: chain D residue 537 THR Chi-restraints excluded: chain D residue 538 SER Chi-restraints excluded: chain D residue 626 SER Chi-restraints excluded: chain D residue 694 VAL Chi-restraints excluded: chain D residue 711 LEU Chi-restraints excluded: chain D residue 821 VAL Chi-restraints excluded: chain D residue 940 THR Chi-restraints excluded: chain D residue 1038 LEU Chi-restraints excluded: chain D residue 1084 THR Chi-restraints excluded: chain D residue 1099 VAL Chi-restraints excluded: chain D residue 1207 TYR Chi-restraints excluded: chain D residue 1305 LEU Chi-restraints excluded: chain D residue 1400 VAL Chi-restraints excluded: chain D residue 1422 MET Chi-restraints excluded: chain E residue 7 ASP Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain F residue 198 ILE Chi-restraints excluded: chain F residue 262 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 30 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 162 optimal weight: 0.0070 chunk 3 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 325 optimal weight: 10.0000 chunk 11 optimal weight: 0.4980 chunk 203 optimal weight: 4.9990 chunk 24 optimal weight: 0.5980 chunk 44 optimal weight: 8.9990 overall best weight: 0.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 728 HIS F 217 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.116071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.085043 restraints weight = 72599.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.087855 restraints weight = 36294.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.089719 restraints weight = 23098.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.090927 restraints weight = 17388.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.091645 restraints weight = 14596.448| |-----------------------------------------------------------------------------| r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3100 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3100 r_free = 0.3100 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3100 r_free = 0.3100 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3100 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 27807 Z= 0.105 Angle : 0.498 7.449 37904 Z= 0.260 Chirality : 0.042 0.232 4272 Planarity : 0.004 0.049 4732 Dihedral : 13.596 130.132 4334 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.23 % Allowed : 19.89 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.15), residues: 3246 helix: 1.79 (0.15), residues: 1245 sheet: 0.29 (0.24), residues: 454 loop : 0.47 (0.16), residues: 1547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 154 TYR 0.019 0.001 TYR A 57 PHE 0.009 0.001 PHE C 293 TRP 0.011 0.001 TRP A 200 HIS 0.009 0.001 HIS A 156 Details of bonding type rmsd covalent geometry : bond 0.00238 (27799) covalent geometry : angle 0.49583 (37892) hydrogen bonds : bond 0.03721 ( 1253) hydrogen bonds : angle 4.34900 ( 3451) metal coordination : bond 0.00423 ( 8) metal coordination : angle 2.49081 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6492 Ramachandran restraints generated. 3246 Oldfield, 0 Emsley, 3246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6492 Ramachandran restraints generated. 3246 Oldfield, 0 Emsley, 3246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 250 time to evaluate : 1.147 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 46 SER cc_start: 0.9165 (p) cc_final: 0.8904 (p) REVERT: C 55 GLU cc_start: 0.6934 (tm-30) cc_final: 0.6722 (tm-30) REVERT: C 209 ARG cc_start: 0.8454 (ptm-80) cc_final: 0.8181 (ptm160) REVERT: C 222 MET cc_start: 0.7653 (OUTLIER) cc_final: 0.6489 (pmm) REVERT: C 252 LYS cc_start: 0.8846 (ttmt) cc_final: 0.7862 (tptt) REVERT: D 110 SER cc_start: 0.8976 (t) cc_final: 0.8758 (p) REVERT: D 142 LEU cc_start: 0.8141 (tm) cc_final: 0.7931 (tp) REVERT: D 151 GLN cc_start: 0.7812 (tt0) cc_final: 0.7584 (tt0) REVERT: D 455 ARG cc_start: 0.6930 (OUTLIER) cc_final: 0.6303 (mmm-85) REVERT: D 477 LEU cc_start: 0.9350 (OUTLIER) cc_final: 0.9117 (mm) REVERT: D 654 LYS cc_start: 0.8646 (OUTLIER) cc_final: 0.8426 (ttpt) REVERT: D 832 ARG cc_start: 0.7783 (ptp90) cc_final: 0.7421 (ptp90) REVERT: D 859 ASP cc_start: 0.8779 (m-30) cc_final: 0.8519 (m-30) REVERT: D 862 ASP cc_start: 0.8598 (m-30) cc_final: 0.8153 (m-30) REVERT: D 1168 MET cc_start: 0.8885 (mmt) cc_final: 0.8545 (mmt) REVERT: E 37 ASN cc_start: 0.8625 (p0) cc_final: 0.8196 (p0) REVERT: F 90 GLN cc_start: 0.7908 (mm110) cc_final: 0.7338 (tt0) REVERT: F 163 LEU cc_start: 0.7649 (mt) cc_final: 0.7397 (tt) REVERT: F 217 ASN cc_start: 0.8916 (m-40) cc_final: 0.8707 (m-40) outliers start: 62 outliers final: 43 residues processed: 296 average time/residue: 0.1800 time to fit residues: 85.8342 Evaluate side-chains 281 residues out of total 2771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 234 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 83 CYS Chi-restraints excluded: chain C residue 173 ASP Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 222 MET Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 566 THR Chi-restraints excluded: chain C residue 637 LEU Chi-restraints excluded: chain C residue 725 ASP Chi-restraints excluded: chain C residue 792 VAL Chi-restraints excluded: chain C residue 1000 MET Chi-restraints excluded: chain C residue 1015 LEU Chi-restraints excluded: chain C residue 1060 ILE Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain D residue 386 HIS Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 432 TYR Chi-restraints excluded: chain D residue 455 ARG Chi-restraints excluded: chain D residue 456 MET Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 538 SER Chi-restraints excluded: chain D residue 654 LYS Chi-restraints excluded: chain D residue 694 VAL Chi-restraints excluded: chain D residue 711 LEU Chi-restraints excluded: chain D residue 940 THR Chi-restraints excluded: chain D residue 1038 LEU Chi-restraints excluded: chain D residue 1084 THR Chi-restraints excluded: chain D residue 1207 TYR Chi-restraints excluded: chain D residue 1234 THR Chi-restraints excluded: chain D residue 1305 LEU Chi-restraints excluded: chain D residue 1382 THR Chi-restraints excluded: chain D residue 1400 VAL Chi-restraints excluded: chain E residue 7 ASP Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain F residue 196 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 230 optimal weight: 1.9990 chunk 168 optimal weight: 3.9990 chunk 314 optimal weight: 10.0000 chunk 317 optimal weight: 6.9990 chunk 311 optimal weight: 5.9990 chunk 131 optimal weight: 3.9990 chunk 154 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 253 optimal weight: 0.5980 chunk 123 optimal weight: 8.9990 chunk 271 optimal weight: 0.0770 overall best weight: 1.7344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 128 HIS C 728 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.114819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.083764 restraints weight = 89095.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.086773 restraints weight = 46517.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.089375 restraints weight = 25013.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.089103 restraints weight = 20208.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.088977 restraints weight = 17449.424| |-----------------------------------------------------------------------------| r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3029 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3029 r_free = 0.3029 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3029 r_free = 0.3029 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3029 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 27807 Z= 0.146 Angle : 0.519 7.512 37904 Z= 0.271 Chirality : 0.042 0.195 4272 Planarity : 0.004 0.055 4732 Dihedral : 13.606 127.468 4334 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.38 % Allowed : 20.14 % Favored : 77.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.15), residues: 3246 helix: 1.78 (0.15), residues: 1246 sheet: 0.15 (0.24), residues: 448 loop : 0.42 (0.16), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 154 TYR 0.020 0.001 TYR A 57 PHE 0.009 0.001 PHE C 679 TRP 0.011 0.001 TRP A 200 HIS 0.008 0.001 HIS A 156 Details of bonding type rmsd covalent geometry : bond 0.00344 (27799) covalent geometry : angle 0.51658 (37892) hydrogen bonds : bond 0.03990 ( 1253) hydrogen bonds : angle 4.39960 ( 3451) metal coordination : bond 0.00791 ( 8) metal coordination : angle 2.88085 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6492 Ramachandran restraints generated. 3246 Oldfield, 0 Emsley, 3246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6492 Ramachandran restraints generated. 3246 Oldfield, 0 Emsley, 3246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 231 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 TYR cc_start: 0.8420 (t80) cc_final: 0.8129 (t80) REVERT: C 222 MET cc_start: 0.7642 (OUTLIER) cc_final: 0.6386 (pmm) REVERT: C 252 LYS cc_start: 0.8903 (ttmt) cc_final: 0.7880 (tptt) REVERT: D 57 GLU cc_start: 0.8317 (tm-30) cc_final: 0.7618 (tt0) REVERT: D 110 SER cc_start: 0.9031 (t) cc_final: 0.8811 (p) REVERT: D 142 LEU cc_start: 0.8150 (OUTLIER) cc_final: 0.7932 (tp) REVERT: D 151 GLN cc_start: 0.7861 (tt0) cc_final: 0.7589 (tt0) REVERT: D 157 GLU cc_start: 0.7536 (mt-10) cc_final: 0.7275 (mp0) REVERT: D 455 ARG cc_start: 0.6913 (OUTLIER) cc_final: 0.6299 (mmm-85) REVERT: D 477 LEU cc_start: 0.9379 (OUTLIER) cc_final: 0.9143 (mm) REVERT: D 654 LYS cc_start: 0.8654 (OUTLIER) cc_final: 0.8452 (ttpt) REVERT: D 754 PHE cc_start: 0.8746 (OUTLIER) cc_final: 0.8253 (t80) REVERT: D 832 ARG cc_start: 0.7932 (ptp90) cc_final: 0.7538 (ptp90) REVERT: D 859 ASP cc_start: 0.8805 (m-30) cc_final: 0.8535 (m-30) REVERT: D 862 ASP cc_start: 0.8592 (m-30) cc_final: 0.8157 (m-30) REVERT: D 1168 MET cc_start: 0.8919 (mmt) cc_final: 0.8638 (mmt) REVERT: E 37 ASN cc_start: 0.8767 (p0) cc_final: 0.8311 (p0) REVERT: F 90 GLN cc_start: 0.7899 (mm110) cc_final: 0.7346 (tt0) REVERT: F 93 LEU cc_start: 0.7022 (OUTLIER) cc_final: 0.6788 (tt) REVERT: F 163 LEU cc_start: 0.7687 (mt) cc_final: 0.7429 (tt) outliers start: 66 outliers final: 47 residues processed: 281 average time/residue: 0.1769 time to fit residues: 80.5440 Evaluate side-chains 278 residues out of total 2771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 224 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 83 CYS Chi-restraints excluded: chain C residue 173 ASP Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 222 MET Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 403 SER Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 566 THR Chi-restraints excluded: chain C residue 637 LEU Chi-restraints excluded: chain C residue 725 ASP Chi-restraints excluded: chain C residue 792 VAL Chi-restraints excluded: chain C residue 1000 MET Chi-restraints excluded: chain C residue 1015 LEU Chi-restraints excluded: chain C residue 1060 ILE Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 386 HIS Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 432 TYR Chi-restraints excluded: chain D residue 455 ARG Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 537 THR Chi-restraints excluded: chain D residue 538 SER Chi-restraints excluded: chain D residue 654 LYS Chi-restraints excluded: chain D residue 694 VAL Chi-restraints excluded: chain D residue 711 LEU Chi-restraints excluded: chain D residue 754 PHE Chi-restraints excluded: chain D residue 940 THR Chi-restraints excluded: chain D residue 1038 LEU Chi-restraints excluded: chain D residue 1084 THR Chi-restraints excluded: chain D residue 1207 TYR Chi-restraints excluded: chain D residue 1305 LEU Chi-restraints excluded: chain D residue 1382 THR Chi-restraints excluded: chain D residue 1400 VAL Chi-restraints excluded: chain D residue 1422 MET Chi-restraints excluded: chain E residue 7 ASP Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain F residue 262 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 191 optimal weight: 0.9990 chunk 80 optimal weight: 4.9990 chunk 164 optimal weight: 1.9990 chunk 267 optimal weight: 0.9990 chunk 87 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 174 optimal weight: 4.9990 chunk 124 optimal weight: 0.9990 chunk 281 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 40 optimal weight: 7.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 728 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.116263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.085119 restraints weight = 90658.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.088991 restraints weight = 41948.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.090393 restraints weight = 22137.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.090548 restraints weight = 19550.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.090435 restraints weight = 16909.076| |-----------------------------------------------------------------------------| r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3068 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3068 r_free = 0.3068 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3068 r_free = 0.3068 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3068 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 27807 Z= 0.104 Angle : 0.493 7.827 37904 Z= 0.257 Chirality : 0.041 0.155 4272 Planarity : 0.004 0.057 4732 Dihedral : 13.516 125.071 4334 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.23 % Allowed : 20.36 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.15), residues: 3246 helix: 1.84 (0.15), residues: 1251 sheet: 0.29 (0.24), residues: 458 loop : 0.49 (0.16), residues: 1537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 154 TYR 0.012 0.001 TYR D 450 PHE 0.011 0.001 PHE C 293 TRP 0.011 0.001 TRP A 200 HIS 0.009 0.001 HIS A 156 Details of bonding type rmsd covalent geometry : bond 0.00238 (27799) covalent geometry : angle 0.49121 (37892) hydrogen bonds : bond 0.03575 ( 1253) hydrogen bonds : angle 4.27382 ( 3451) metal coordination : bond 0.00447 ( 8) metal coordination : angle 2.34455 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6492 Ramachandran restraints generated. 3246 Oldfield, 0 Emsley, 3246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6492 Ramachandran restraints generated. 3246 Oldfield, 0 Emsley, 3246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 246 time to evaluate : 0.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 222 MET cc_start: 0.7563 (OUTLIER) cc_final: 0.6258 (pmm) REVERT: C 252 LYS cc_start: 0.8876 (ttmt) cc_final: 0.7846 (tptt) REVERT: D 110 SER cc_start: 0.8942 (t) cc_final: 0.8720 (p) REVERT: D 142 LEU cc_start: 0.8117 (OUTLIER) cc_final: 0.7893 (tp) REVERT: D 151 GLN cc_start: 0.7774 (tt0) cc_final: 0.7527 (tt0) REVERT: D 455 ARG cc_start: 0.6932 (OUTLIER) cc_final: 0.6243 (mmm-85) REVERT: D 477 LEU cc_start: 0.9332 (OUTLIER) cc_final: 0.9098 (mm) REVERT: D 754 PHE cc_start: 0.8639 (OUTLIER) cc_final: 0.8214 (t80) REVERT: D 832 ARG cc_start: 0.7855 (ptp90) cc_final: 0.7519 (ptp90) REVERT: D 859 ASP cc_start: 0.8790 (m-30) cc_final: 0.8526 (m-30) REVERT: D 862 ASP cc_start: 0.8586 (m-30) cc_final: 0.8153 (m-30) REVERT: D 924 MET cc_start: 0.7232 (mtm) cc_final: 0.7018 (mtp) REVERT: D 1318 TYR cc_start: 0.6242 (t80) cc_final: 0.6040 (t80) REVERT: E 37 ASN cc_start: 0.8714 (p0) cc_final: 0.8282 (p0) REVERT: F 90 GLN cc_start: 0.7912 (mm110) cc_final: 0.7372 (tt0) REVERT: F 93 LEU cc_start: 0.6987 (OUTLIER) cc_final: 0.6758 (tt) outliers start: 62 outliers final: 46 residues processed: 291 average time/residue: 0.1650 time to fit residues: 77.8944 Evaluate side-chains 273 residues out of total 2771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 221 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 83 CYS Chi-restraints excluded: chain C residue 173 ASP Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 222 MET Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 403 SER Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 566 THR Chi-restraints excluded: chain C residue 637 LEU Chi-restraints excluded: chain C residue 725 ASP Chi-restraints excluded: chain C residue 792 VAL Chi-restraints excluded: chain C residue 1000 MET Chi-restraints excluded: chain C residue 1015 LEU Chi-restraints excluded: chain C residue 1060 ILE Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 386 HIS Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 432 TYR Chi-restraints excluded: chain D residue 455 ARG Chi-restraints excluded: chain D residue 456 MET Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 538 SER Chi-restraints excluded: chain D residue 694 VAL Chi-restraints excluded: chain D residue 711 LEU Chi-restraints excluded: chain D residue 754 PHE Chi-restraints excluded: chain D residue 848 GLU Chi-restraints excluded: chain D residue 940 THR Chi-restraints excluded: chain D residue 962 GLN Chi-restraints excluded: chain D residue 1038 LEU Chi-restraints excluded: chain D residue 1207 TYR Chi-restraints excluded: chain D residue 1305 LEU Chi-restraints excluded: chain D residue 1382 THR Chi-restraints excluded: chain D residue 1400 VAL Chi-restraints excluded: chain D residue 1422 MET Chi-restraints excluded: chain E residue 7 ASP Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 196 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 305 optimal weight: 10.0000 chunk 120 optimal weight: 0.0060 chunk 155 optimal weight: 0.6980 chunk 221 optimal weight: 0.0010 chunk 89 optimal weight: 5.9990 chunk 139 optimal weight: 0.6980 chunk 292 optimal weight: 0.0570 chunk 32 optimal weight: 9.9990 chunk 122 optimal weight: 5.9990 chunk 109 optimal weight: 0.0070 chunk 242 optimal weight: 0.9980 overall best weight: 0.1538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 728 HIS C 991 GLN D 166 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.118214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.086559 restraints weight = 83533.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.089588 restraints weight = 40202.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.091593 restraints weight = 24826.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.092904 restraints weight = 18340.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.093695 restraints weight = 15215.591| |-----------------------------------------------------------------------------| r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3135 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3135 r_free = 0.3135 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3135 r_free = 0.3135 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3135 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 27807 Z= 0.094 Angle : 0.486 8.058 37904 Z= 0.252 Chirality : 0.041 0.149 4272 Planarity : 0.004 0.045 4732 Dihedral : 13.418 123.391 4334 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.91 % Allowed : 21.23 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.15), residues: 3246 helix: 1.93 (0.15), residues: 1246 sheet: 0.44 (0.24), residues: 445 loop : 0.53 (0.16), residues: 1555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 154 TYR 0.017 0.001 TYR A 57 PHE 0.008 0.001 PHE B 65 TRP 0.009 0.001 TRP A 200 HIS 0.010 0.000 HIS A 156 Details of bonding type rmsd covalent geometry : bond 0.00202 (27799) covalent geometry : angle 0.48494 (37892) hydrogen bonds : bond 0.03246 ( 1253) hydrogen bonds : angle 4.16786 ( 3451) metal coordination : bond 0.00307 ( 8) metal coordination : angle 2.10430 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6492 Ramachandran restraints generated. 3246 Oldfield, 0 Emsley, 3246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6492 Ramachandran restraints generated. 3246 Oldfield, 0 Emsley, 3246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 264 time to evaluate : 1.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 74 ASP cc_start: 0.8119 (p0) cc_final: 0.7802 (p0) REVERT: C 209 ARG cc_start: 0.8431 (ptm-80) cc_final: 0.8118 (ptm160) REVERT: C 252 LYS cc_start: 0.8877 (ttmt) cc_final: 0.7894 (tptt) REVERT: C 657 ASP cc_start: 0.7338 (t0) cc_final: 0.7064 (t0) REVERT: D 110 SER cc_start: 0.8869 (t) cc_final: 0.8637 (p) REVERT: D 157 GLU cc_start: 0.7387 (mt-10) cc_final: 0.7115 (mp0) REVERT: D 455 ARG cc_start: 0.6879 (OUTLIER) cc_final: 0.6217 (mmm-85) REVERT: D 477 LEU cc_start: 0.9303 (OUTLIER) cc_final: 0.9066 (mm) REVERT: D 754 PHE cc_start: 0.8567 (OUTLIER) cc_final: 0.8224 (t80) REVERT: D 859 ASP cc_start: 0.8760 (m-30) cc_final: 0.8485 (m-30) REVERT: D 862 ASP cc_start: 0.8524 (m-30) cc_final: 0.8091 (m-30) REVERT: D 1318 TYR cc_start: 0.6114 (t80) cc_final: 0.5895 (t80) REVERT: E 37 ASN cc_start: 0.8674 (p0) cc_final: 0.8229 (p0) REVERT: F 90 GLN cc_start: 0.7898 (mm110) cc_final: 0.7340 (tt0) REVERT: F 93 LEU cc_start: 0.6941 (OUTLIER) cc_final: 0.6711 (tt) REVERT: F 163 LEU cc_start: 0.7680 (mt) cc_final: 0.7431 (tt) outliers start: 53 outliers final: 39 residues processed: 301 average time/residue: 0.1717 time to fit residues: 84.2945 Evaluate side-chains 273 residues out of total 2771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 230 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 173 ASP Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 403 SER Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 566 THR Chi-restraints excluded: chain C residue 637 LEU Chi-restraints excluded: chain C residue 792 VAL Chi-restraints excluded: chain C residue 1000 MET Chi-restraints excluded: chain C residue 1015 LEU Chi-restraints excluded: chain C residue 1060 ILE Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain D residue 386 HIS Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 432 TYR Chi-restraints excluded: chain D residue 455 ARG Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 538 SER Chi-restraints excluded: chain D residue 694 VAL Chi-restraints excluded: chain D residue 754 PHE Chi-restraints excluded: chain D residue 848 GLU Chi-restraints excluded: chain D residue 904 VAL Chi-restraints excluded: chain D residue 940 THR Chi-restraints excluded: chain D residue 1207 TYR Chi-restraints excluded: chain D residue 1305 LEU Chi-restraints excluded: chain D residue 1382 THR Chi-restraints excluded: chain D residue 1400 VAL Chi-restraints excluded: chain E residue 7 ASP Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 264 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 297 optimal weight: 6.9990 chunk 265 optimal weight: 2.9990 chunk 230 optimal weight: 0.8980 chunk 176 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 52 optimal weight: 6.9990 chunk 324 optimal weight: 10.0000 chunk 207 optimal weight: 0.2980 chunk 40 optimal weight: 8.9990 chunk 172 optimal weight: 2.9990 chunk 312 optimal weight: 10.0000 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 545 ASN C 728 HIS D 151 GLN F 218 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.118172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.087319 restraints weight = 78080.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.090188 restraints weight = 39762.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.092038 restraints weight = 25347.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.093264 restraints weight = 19181.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.093983 restraints weight = 16118.405| |-----------------------------------------------------------------------------| r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3127 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3127 r_free = 0.3127 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3127 r_free = 0.3127 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3127 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 27807 Z= 0.119 Angle : 0.500 8.388 37904 Z= 0.259 Chirality : 0.042 0.255 4272 Planarity : 0.004 0.043 4732 Dihedral : 13.441 122.117 4334 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.91 % Allowed : 21.55 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.15), residues: 3246 helix: 1.93 (0.15), residues: 1247 sheet: 0.36 (0.24), residues: 461 loop : 0.53 (0.16), residues: 1538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 154 TYR 0.013 0.001 TYR B 57 PHE 0.020 0.001 PHE D 740 TRP 0.010 0.001 TRP A 200 HIS 0.009 0.001 HIS A 156 Details of bonding type rmsd covalent geometry : bond 0.00278 (27799) covalent geometry : angle 0.49770 (37892) hydrogen bonds : bond 0.03545 ( 1253) hydrogen bonds : angle 4.20295 ( 3451) metal coordination : bond 0.00598 ( 8) metal coordination : angle 2.57805 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6492 Ramachandran restraints generated. 3246 Oldfield, 0 Emsley, 3246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6492 Ramachandran restraints generated. 3246 Oldfield, 0 Emsley, 3246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 221 time to evaluate : 1.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 209 ARG cc_start: 0.8478 (ptm-80) cc_final: 0.8153 (ptm160) REVERT: C 222 MET cc_start: 0.7549 (OUTLIER) cc_final: 0.6233 (pmm) REVERT: C 252 LYS cc_start: 0.8890 (ttmt) cc_final: 0.7877 (tptt) REVERT: C 657 ASP cc_start: 0.7379 (t0) cc_final: 0.7077 (t0) REVERT: D 110 SER cc_start: 0.8925 (t) cc_final: 0.8697 (p) REVERT: D 157 GLU cc_start: 0.7427 (mt-10) cc_final: 0.7099 (mp0) REVERT: D 455 ARG cc_start: 0.6873 (OUTLIER) cc_final: 0.6121 (mmm-85) REVERT: D 477 LEU cc_start: 0.9342 (OUTLIER) cc_final: 0.9112 (mm) REVERT: D 754 PHE cc_start: 0.8715 (OUTLIER) cc_final: 0.8319 (t80) REVERT: D 859 ASP cc_start: 0.8791 (m-30) cc_final: 0.8516 (m-30) REVERT: D 862 ASP cc_start: 0.8519 (m-30) cc_final: 0.8083 (m-30) REVERT: D 1318 TYR cc_start: 0.6146 (t80) cc_final: 0.5936 (t80) REVERT: E 37 ASN cc_start: 0.8722 (p0) cc_final: 0.8259 (p0) REVERT: F 90 GLN cc_start: 0.7872 (mm110) cc_final: 0.7363 (tt0) outliers start: 53 outliers final: 43 residues processed: 259 average time/residue: 0.1659 time to fit residues: 70.9615 Evaluate side-chains 264 residues out of total 2771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 217 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 72 LYS Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 173 ASP Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 222 MET Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 403 SER Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 566 THR Chi-restraints excluded: chain C residue 637 LEU Chi-restraints excluded: chain C residue 792 VAL Chi-restraints excluded: chain C residue 1000 MET Chi-restraints excluded: chain C residue 1015 LEU Chi-restraints excluded: chain C residue 1060 ILE Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 386 HIS Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 432 TYR Chi-restraints excluded: chain D residue 455 ARG Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 538 SER Chi-restraints excluded: chain D residue 694 VAL Chi-restraints excluded: chain D residue 754 PHE Chi-restraints excluded: chain D residue 848 GLU Chi-restraints excluded: chain D residue 904 VAL Chi-restraints excluded: chain D residue 940 THR Chi-restraints excluded: chain D residue 1207 TYR Chi-restraints excluded: chain D residue 1305 LEU Chi-restraints excluded: chain D residue 1382 THR Chi-restraints excluded: chain D residue 1400 VAL Chi-restraints excluded: chain E residue 7 ASP Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain F residue 196 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 2 optimal weight: 5.9990 chunk 116 optimal weight: 0.0030 chunk 204 optimal weight: 1.9990 chunk 329 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 chunk 0 optimal weight: 6.9990 chunk 166 optimal weight: 6.9990 chunk 321 optimal weight: 10.0000 chunk 235 optimal weight: 4.9990 chunk 307 optimal weight: 10.0000 chunk 144 optimal weight: 4.9990 overall best weight: 3.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 728 HIS D 166 GLN F 218 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.113636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.083295 restraints weight = 91499.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.086921 restraints weight = 44824.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.087447 restraints weight = 24712.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.087607 restraints weight = 22337.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.087678 restraints weight = 20812.591| |-----------------------------------------------------------------------------| r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2934 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2934 r_free = 0.2934 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2934 r_free = 0.2934 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2934 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 27807 Z= 0.258 Angle : 0.626 13.377 37904 Z= 0.324 Chirality : 0.045 0.215 4272 Planarity : 0.005 0.047 4732 Dihedral : 13.694 116.945 4334 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.91 % Allowed : 21.77 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.15), residues: 3246 helix: 1.60 (0.15), residues: 1239 sheet: 0.09 (0.24), residues: 468 loop : 0.23 (0.16), residues: 1539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 250 TYR 0.017 0.002 TYR C 90 PHE 0.025 0.002 PHE D 740 TRP 0.014 0.002 TRP A 200 HIS 0.009 0.001 HIS A 156 Details of bonding type rmsd covalent geometry : bond 0.00617 (27799) covalent geometry : angle 0.62309 (37892) hydrogen bonds : bond 0.04817 ( 1253) hydrogen bonds : angle 4.62940 ( 3451) metal coordination : bond 0.01551 ( 8) metal coordination : angle 3.57471 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6492 Ramachandran restraints generated. 3246 Oldfield, 0 Emsley, 3246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6492 Ramachandran restraints generated. 3246 Oldfield, 0 Emsley, 3246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 213 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 222 MET cc_start: 0.7727 (OUTLIER) cc_final: 0.6508 (pmm) REVERT: C 252 LYS cc_start: 0.8962 (ttmt) cc_final: 0.7997 (tptt) REVERT: C 868 ASP cc_start: 0.8405 (m-30) cc_final: 0.8128 (m-30) REVERT: D 110 SER cc_start: 0.9081 (t) cc_final: 0.8870 (p) REVERT: D 157 GLU cc_start: 0.7511 (mt-10) cc_final: 0.7132 (mp0) REVERT: D 455 ARG cc_start: 0.6789 (OUTLIER) cc_final: 0.6072 (mmm-85) REVERT: D 477 LEU cc_start: 0.9421 (OUTLIER) cc_final: 0.9209 (mm) REVERT: D 754 PHE cc_start: 0.8885 (OUTLIER) cc_final: 0.8381 (t80) REVERT: D 862 ASP cc_start: 0.8418 (m-30) cc_final: 0.8045 (m-30) REVERT: D 1168 MET cc_start: 0.9017 (mmt) cc_final: 0.8691 (mmt) REVERT: E 37 ASN cc_start: 0.8911 (p0) cc_final: 0.8452 (p0) REVERT: F 90 GLN cc_start: 0.7793 (mm110) cc_final: 0.7413 (tt0) outliers start: 53 outliers final: 41 residues processed: 252 average time/residue: 0.1696 time to fit residues: 70.4952 Evaluate side-chains 247 residues out of total 2771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 202 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 72 LYS Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 83 CYS Chi-restraints excluded: chain C residue 173 ASP Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 222 MET Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 403 SER Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 566 THR Chi-restraints excluded: chain C residue 637 LEU Chi-restraints excluded: chain C residue 979 THR Chi-restraints excluded: chain C residue 1000 MET Chi-restraints excluded: chain C residue 1015 LEU Chi-restraints excluded: chain C residue 1060 ILE Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain D residue 386 HIS Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 432 TYR Chi-restraints excluded: chain D residue 455 ARG Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 538 SER Chi-restraints excluded: chain D residue 694 VAL Chi-restraints excluded: chain D residue 752 SER Chi-restraints excluded: chain D residue 754 PHE Chi-restraints excluded: chain D residue 904 VAL Chi-restraints excluded: chain D residue 940 THR Chi-restraints excluded: chain D residue 962 GLN Chi-restraints excluded: chain D residue 1207 TYR Chi-restraints excluded: chain D residue 1305 LEU Chi-restraints excluded: chain D residue 1382 THR Chi-restraints excluded: chain E residue 7 ASP Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain F residue 218 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 118 optimal weight: 0.6980 chunk 94 optimal weight: 0.9980 chunk 137 optimal weight: 0.5980 chunk 226 optimal weight: 2.9990 chunk 253 optimal weight: 0.0570 chunk 144 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 53 optimal weight: 10.0000 chunk 197 optimal weight: 4.9990 chunk 103 optimal weight: 10.0000 overall best weight: 0.8700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 728 HIS F 280 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.117105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.086757 restraints weight = 80954.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.090883 restraints weight = 40060.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.091160 restraints weight = 23594.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.091269 restraints weight = 20614.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.091410 restraints weight = 18951.453| |-----------------------------------------------------------------------------| r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3037 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3037 r_free = 0.3037 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3037 r_free = 0.3037 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3037 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 27807 Z= 0.114 Angle : 0.524 11.199 37904 Z= 0.272 Chirality : 0.042 0.210 4272 Planarity : 0.004 0.044 4732 Dihedral : 13.538 111.536 4334 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.37 % Allowed : 22.27 % Favored : 76.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.15), residues: 3246 helix: 1.76 (0.15), residues: 1237 sheet: 0.16 (0.24), residues: 461 loop : 0.32 (0.16), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 154 TYR 0.012 0.001 TYR D 450 PHE 0.014 0.001 PHE D 740 TRP 0.012 0.001 TRP A 200 HIS 0.010 0.001 HIS A 156 Details of bonding type rmsd covalent geometry : bond 0.00262 (27799) covalent geometry : angle 0.52196 (37892) hydrogen bonds : bond 0.03836 ( 1253) hydrogen bonds : angle 4.35034 ( 3451) metal coordination : bond 0.00492 ( 8) metal coordination : angle 2.37632 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4410.98 seconds wall clock time: 76 minutes 52.00 seconds (4612.00 seconds total)