Starting phenix.real_space_refine on Sat Aug 8 00:40:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8hsg_34996/08_2026/8hsg_34996.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hsg_34996/08_2026/8hsg_34996.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8hsg_34996/08_2026/8hsg_34996.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hsg_34996/08_2026/8hsg_34996.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8hsg_34996/08_2026/8hsg_34996.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8hsg_34996/08_2026/8hsg_34996.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hsg_34996/08_2026/8hsg_34996.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hsg_34996/08_2026/8hsg_34996.map" } resolution = 3.2 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= 0.002 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 1 6.06 5 P 76 5.49 5 Mg 1 5.21 5 S 62 5.16 5 C 15361 2.51 5 N 4366 2.21 5 O 4769 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24636 Number of models: 1 Model: "" Number of chains: 9 Chain: "G" Number of atoms: 1806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1806 Classifications: {'peptide': 229} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 214} Chain: "H" Number of atoms: 1806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1806 Classifications: {'peptide': 229} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 214} Chain: "I" Number of atoms: 8644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1096, 8644 Classifications: {'peptide': 1096} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 69, 'TRANS': 1025} Chain breaks: 1 Chain: "J" Number of atoms: 10078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1278, 10078 Classifications: {'peptide': 1278} Link IDs: {'PTRANS': 62, 'TRANS': 1215} Chain breaks: 3 Chain: "K" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 735 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 5, 'TRANS': 85} Chain: "T" Number of atoms: 764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 764 Classifications: {'DNA': 37} Link IDs: {'rna3p': 36} Chain: "R" Number of atoms: 246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 246 Classifications: {'RNAv2': 12} Modifications used: {'rna3p_pur': 3, 'rna3p_pyr': 9} Link IDs: {'rna3p': 11} Chain: "N" Number of atoms: 555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 555 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain breaks: 1 Chain: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 19413 SG CYS J1112 67.862 89.540 32.227 1.00100.93 S ATOM 20057 SG CYS J1194 67.627 89.462 36.108 1.00 94.30 S ATOM 20113 SG CYS J1201 65.512 87.092 33.975 1.00 92.47 S ATOM 20137 SG CYS J1204 68.990 86.439 34.225 1.00 91.33 S Time building chain proxies: 4.09, per 1000 atoms: 0.17 Number of scatterers: 24636 At special positions: 0 Unit cell: (134.62, 183.38, 140.98, 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 1 29.99 S 62 16.00 P 76 15.00 Mg 1 11.99 O 4769 8.00 N 4366 7.00 C 15361 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: 1.73 Conformation dependent library (CDL) restraints added in 996.4 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1601 " pdb="ZN ZN J1601 " - pdb=" SG CYS J1201 " pdb="ZN ZN J1601 " - pdb=" SG CYS J1204 " pdb="ZN ZN J1601 " - pdb=" SG CYS J1194 " pdb="ZN ZN J1601 " - pdb=" SG CYS J1112 " Number of angles added : 6 5810 Ramachandran restraints generated. 2905 Oldfield, 0 Emsley, 2905 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5396 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 40 sheets defined 39.4% alpha, 17.1% beta 37 base pairs and 53 stacking pairs defined. Time for finding SS restraints: 2.54 Creating SS restraints... Processing helix chain 'G' and resid 31 through 47 removed outlier: 3.809A pdb=" N THR G 35 " --> pdb=" O GLY G 31 " (cutoff:3.500A) Proline residue: G 39 - end of helix Processing helix chain 'G' and resid 74 through 84 removed outlier: 3.857A pdb=" N GLU G 84 " --> pdb=" O LEU G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 114 No H-bonds generated for 'chain 'G' and resid 112 through 114' Processing helix chain 'G' and resid 152 through 157 removed outlier: 3.722A pdb=" N HIS G 156 " --> pdb=" O PRO G 152 " (cutoff:3.500A) Processing helix chain 'G' and resid 206 through 223 Processing helix chain 'G' and resid 224 through 226 No H-bonds generated for 'chain 'G' and resid 224 through 226' Processing helix chain 'H' and resid 31 through 47 removed outlier: 3.663A pdb=" N THR H 35 " --> pdb=" O GLY H 31 " (cutoff:3.500A) Proline residue: H 39 - end of helix Processing helix chain 'H' and resid 74 through 84 removed outlier: 4.020A pdb=" N GLU H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 112 through 114 No H-bonds generated for 'chain 'H' and resid 112 through 114' Processing helix chain 'H' and resid 152 through 157 removed outlier: 4.038A pdb=" N HIS H 156 " --> pdb=" O PRO H 152 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY H 157 " --> pdb=" O ALA H 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 152 through 157' Processing helix chain 'H' and resid 206 through 223 Processing helix chain 'H' and resid 224 through 226 No H-bonds generated for 'chain 'H' and resid 224 through 226' Processing helix chain 'I' and resid 19 through 30 removed outlier: 3.568A pdb=" N VAL I 23 " --> pdb=" O THR I 19 " (cutoff:3.500A) Processing helix chain 'I' and resid 43 through 52 Processing helix chain 'I' and resid 79 through 86 Processing helix chain 'I' and resid 192 through 200 removed outlier: 4.192A pdb=" N LEU I 196 " --> pdb=" O PRO I 192 " (cutoff:3.500A) Processing helix chain 'I' and resid 203 through 211 Processing helix chain 'I' and resid 215 through 217 No H-bonds generated for 'chain 'I' and resid 215 through 217' Processing helix chain 'I' and resid 218 through 223 Processing helix chain 'I' and resid 232 through 242 removed outlier: 3.795A pdb=" N ILE I 236 " --> pdb=" O GLU I 232 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU I 242 " --> pdb=" O LEU I 238 " (cutoff:3.500A) Processing helix chain 'I' and resid 274 through 279 Processing helix chain 'I' and resid 302 through 316 Processing helix chain 'I' and resid 327 through 329 No H-bonds generated for 'chain 'I' and resid 327 through 329' Processing helix chain 'I' and resid 335 through 362 Processing helix chain 'I' and resid 375 through 389 removed outlier: 3.742A pdb=" N SER I 389 " --> pdb=" O PHE I 385 " (cutoff:3.500A) Processing helix chain 'I' and resid 399 through 408 Processing helix chain 'I' and resid 424 through 429 removed outlier: 4.293A pdb=" N ASP I 429 " --> pdb=" O PHE I 425 " (cutoff:3.500A) Processing helix chain 'I' and resid 431 through 435 removed outlier: 3.901A pdb=" N TYR I 435 " --> pdb=" O ARG I 432 " (cutoff:3.500A) Processing helix chain 'I' and resid 487 through 492 Processing helix chain 'I' and resid 525 through 529 Processing helix chain 'I' and resid 535 through 540 Processing helix chain 'I' and resid 543 through 547 Processing helix chain 'I' and resid 549 through 553 Processing helix chain 'I' and resid 554 through 567 removed outlier: 3.739A pdb=" N THR I 566 " --> pdb=" O SER I 562 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLN I 567 " --> pdb=" O ASN I 563 " (cutoff:3.500A) Processing helix chain 'I' and resid 583 through 591 Processing helix chain 'I' and resid 692 through 697 Processing helix chain 'I' and resid 732 through 736 removed outlier: 3.774A pdb=" N ARG I 735 " --> pdb=" O ALA I 732 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASP I 736 " --> pdb=" O ALA I 733 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 732 through 736' Processing helix chain 'I' and resid 874 through 879 removed outlier: 3.872A pdb=" N SER I 878 " --> pdb=" O LEU I 874 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ARG I 879 " --> pdb=" O GLY I 875 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 874 through 879' Processing helix chain 'I' and resid 882 through 898 removed outlier: 3.699A pdb=" N PHE I 896 " --> pdb=" O LEU I 892 " (cutoff:3.500A) Processing helix chain 'I' and resid 910 through 932 removed outlier: 4.070A pdb=" N GLU I 932 " --> pdb=" O LYS I 928 " (cutoff:3.500A) Processing helix chain 'I' and resid 937 through 950 Processing helix chain 'I' and resid 958 through 969 Processing helix chain 'I' and resid 1000 through 1004 removed outlier: 3.739A pdb=" N ASP I1003 " --> pdb=" O MET I1000 " (cutoff:3.500A) Processing helix chain 'I' and resid 1034 through 1043 Processing helix chain 'I' and resid 1046 through 1054 Processing helix chain 'I' and resid 1059 through 1072 Processing helix chain 'I' and resid 1082 through 1095 removed outlier: 3.634A pdb=" N LEU I1095 " --> pdb=" O GLU I1091 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 21 Processing helix chain 'J' and resid 46 through 51 Processing helix chain 'J' and resid 83 through 89 removed outlier: 3.618A pdb=" N ARG J 87 " --> pdb=" O SER J 83 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR J 88 " --> pdb=" O ILE J 84 " (cutoff:3.500A) Processing helix chain 'J' and resid 102 through 107 Processing helix chain 'J' and resid 110 through 116 Processing helix chain 'J' and resid 122 through 129 Processing helix chain 'J' and resid 155 through 163 removed outlier: 4.162A pdb=" N TYR J 163 " --> pdb=" O ARG J 159 " (cutoff:3.500A) Processing helix chain 'J' and resid 423 through 426 Processing helix chain 'J' and resid 456 through 468 removed outlier: 3.691A pdb=" N ALA J 460 " --> pdb=" O MET J 456 " (cutoff:3.500A) Processing helix chain 'J' and resid 469 through 483 removed outlier: 3.536A pdb=" N LEU J 473 " --> pdb=" O ASP J 469 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N HIS J 483 " --> pdb=" O GLU J 479 " (cutoff:3.500A) Processing helix chain 'J' and resid 485 through 505 removed outlier: 4.404A pdb=" N LYS J 491 " --> pdb=" O ALA J 487 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N VAL J 498 " --> pdb=" O LYS J 494 " (cutoff:3.500A) Processing helix chain 'J' and resid 508 through 511 removed outlier: 3.922A pdb=" N TRP J 511 " --> pdb=" O ARG J 508 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 508 through 511' Processing helix chain 'J' and resid 521 through 525 Processing helix chain 'J' and resid 538 through 561 removed outlier: 3.825A pdb=" N ASP J 542 " --> pdb=" O SER J 538 " (cutoff:3.500A) Processing helix chain 'J' and resid 563 through 583 Processing helix chain 'J' and resid 602 through 608 Processing helix chain 'J' and resid 613 through 618 Processing helix chain 'J' and resid 646 through 653 Processing helix chain 'J' and resid 653 through 664 Processing helix chain 'J' and resid 669 through 678 Processing helix chain 'J' and resid 679 through 683 Processing helix chain 'J' and resid 684 through 695 Processing helix chain 'J' and resid 709 through 711 No H-bonds generated for 'chain 'J' and resid 709 through 711' Processing helix chain 'J' and resid 729 through 734 removed outlier: 4.272A pdb=" N GLU J 734 " --> pdb=" O LEU J 731 " (cutoff:3.500A) Processing helix chain 'J' and resid 752 through 763 Processing helix chain 'J' and resid 764 through 768 Processing helix chain 'J' and resid 782 through 793 Processing helix chain 'J' and resid 811 through 822 removed outlier: 3.696A pdb=" N ALA J 815 " --> pdb=" O GLU J 811 " (cutoff:3.500A) Processing helix chain 'J' and resid 835 through 841 Processing helix chain 'J' and resid 845 through 855 Processing helix chain 'J' and resid 876 through 890 Processing helix chain 'J' and resid 892 through 899 removed outlier: 3.949A pdb=" N ALA J 896 " --> pdb=" O ASP J 892 " (cutoff:3.500A) Processing helix chain 'J' and resid 907 through 922 Processing helix chain 'J' and resid 924 through 946 removed outlier: 3.601A pdb=" N GLY J 946 " --> pdb=" O SER J 942 " (cutoff:3.500A) Processing helix chain 'J' and resid 950 through 954 Processing helix chain 'J' and resid 957 through 980 removed outlier: 4.203A pdb=" N LYS J 961 " --> pdb=" O PRO J 957 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLN J 962 " --> pdb=" O GLU J 958 " (cutoff:3.500A) Processing helix chain 'J' and resid 984 through 1014 removed outlier: 3.597A pdb=" N GLU J1001 " --> pdb=" O THR J 997 " (cutoff:3.500A) Processing helix chain 'J' and resid 1018 through 1026 Processing helix chain 'J' and resid 1031 through 1040 Processing helix chain 'J' and resid 1066 through 1103 removed outlier: 3.800A pdb=" N HIS J1075 " --> pdb=" O PHE J1071 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLY J1076 " --> pdb=" O ILE J1072 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ALA J1089 " --> pdb=" O ALA J1085 " (cutoff:3.500A) Processing helix chain 'J' and resid 1136 through 1145 Processing helix chain 'J' and resid 1167 through 1181 Processing helix chain 'J' and resid 1190 through 1194 Processing helix chain 'J' and resid 1201 through 1206 Processing helix chain 'J' and resid 1220 through 1235 removed outlier: 3.663A pdb=" N VAL J1224 " --> pdb=" O ALA J1220 " (cutoff:3.500A) Proline residue: J1232 - end of helix removed outlier: 4.260A pdb=" N GLN J1235 " --> pdb=" O GLU J1231 " (cutoff:3.500A) Processing helix chain 'J' and resid 1256 through 1264 Processing helix chain 'J' and resid 1331 through 1339 Processing helix chain 'J' and resid 1340 through 1359 removed outlier: 3.716A pdb=" N VAL J1355 " --> pdb=" O GLU J1351 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TYR J1356 " --> pdb=" O ILE J1352 " (cutoff:3.500A) Processing helix chain 'J' and resid 1364 through 1376 removed outlier: 4.461A pdb=" N ILE J1368 " --> pdb=" O HIS J1364 " (cutoff:3.500A) Processing helix chain 'J' and resid 1395 through 1407 Processing helix chain 'J' and resid 1423 through 1430 Processing helix chain 'J' and resid 1433 through 1441 removed outlier: 3.902A pdb=" N ALA J1437 " --> pdb=" O SER J1433 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN J1441 " --> pdb=" O ALA J1437 " (cutoff:3.500A) Processing helix chain 'J' and resid 1442 through 1453 removed outlier: 3.566A pdb=" N VAL J1446 " --> pdb=" O ASN J1442 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA J1453 " --> pdb=" O GLU J1449 " (cutoff:3.500A) Processing helix chain 'J' and resid 1461 through 1469 removed outlier: 3.727A pdb=" N ASN J1465 " --> pdb=" O GLY J1461 " (cutoff:3.500A) Processing helix chain 'J' and resid 1474 through 1478 Processing helix chain 'J' and resid 1489 through 1503 Processing helix chain 'K' and resid 5 through 12 Processing helix chain 'K' and resid 15 through 34 Processing helix chain 'K' and resid 52 through 56 Processing helix chain 'K' and resid 59 through 70 removed outlier: 3.869A pdb=" N TRP K 63 " --> pdb=" O ASN K 59 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N THR K 70 " --> pdb=" O LYS K 66 " (cutoff:3.500A) Processing helix chain 'K' and resid 81 through 91 removed outlier: 3.921A pdb=" N LEU K 85 " --> pdb=" O PRO K 81 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU K 90 " --> pdb=" O GLN K 86 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG K 91 " --> pdb=" O LYS K 87 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 10 through 16 removed outlier: 3.611A pdb=" N TYR G 20 " --> pdb=" O GLN G 16 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N TYR G 20 " --> pdb=" O THR G 201 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N THR G 201 " --> pdb=" O TYR G 20 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N GLU G 22 " --> pdb=" O ILE G 199 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ILE G 199 " --> pdb=" O GLU G 22 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N VAL G 24 " --> pdb=" O LEU G 197 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N LEU G 197 " --> pdb=" O VAL G 24 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N GLU G 26 " --> pdb=" O LEU G 195 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N LEU G 195 " --> pdb=" O GLU G 26 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 96 through 103 removed outlier: 7.468A pdb=" N ASN G 139 " --> pdb=" O ILE G 58 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N ILE G 58 " --> pdb=" O ASN G 139 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N GLU G 141 " --> pdb=" O VAL G 56 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N VAL G 56 " --> pdb=" O GLU G 141 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ARG G 143 " --> pdb=" O THR G 54 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 87 through 89 Processing sheet with id=AA4, first strand: chain 'G' and resid 107 through 110 Processing sheet with id=AA5, first strand: chain 'G' and resid 150 through 151 Processing sheet with id=AA6, first strand: chain 'H' and resid 10 through 16 removed outlier: 3.683A pdb=" N TYR H 20 " --> pdb=" O GLN H 16 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N TYR H 20 " --> pdb=" O THR H 201 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N THR H 201 " --> pdb=" O TYR H 20 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N GLU H 22 " --> pdb=" O ILE H 199 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N ILE H 199 " --> pdb=" O GLU H 22 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N VAL H 24 " --> pdb=" O LEU H 197 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N LEU H 197 " --> pdb=" O VAL H 24 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N GLU H 26 " --> pdb=" O LEU H 195 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N LEU H 195 " --> pdb=" O GLU H 26 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 96 through 103 removed outlier: 7.843A pdb=" N ASN H 139 " --> pdb=" O ILE H 58 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N ILE H 58 " --> pdb=" O ASN H 139 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N GLU H 141 " --> pdb=" O VAL H 56 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N VAL H 56 " --> pdb=" O GLU H 141 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ARG H 143 " --> pdb=" O THR H 54 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 87 through 89 Processing sheet with id=AA9, first strand: chain 'H' and resid 108 through 110 Processing sheet with id=AB1, first strand: chain 'H' and resid 150 through 151 Processing sheet with id=AB2, first strand: chain 'I' and resid 3 through 5 removed outlier: 6.363A pdb=" N LYS I 4 " --> pdb=" O ILE I 902 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 65 through 72 removed outlier: 5.250A pdb=" N LEU I 66 " --> pdb=" O ILE I 101 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N ILE I 101 " --> pdb=" O LEU I 66 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N PHE I 68 " --> pdb=" O GLN I 99 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N GLN I 99 " --> pdb=" O PHE I 68 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLU I 70 " --> pdb=" O ARG I 97 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N GLY I 116 " --> pdb=" O LEU I 94 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ALA I 96 " --> pdb=" O PHE I 114 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N PHE I 114 " --> pdb=" O ALA I 96 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N LEU I 98 " --> pdb=" O GLU I 112 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N GLU I 112 " --> pdb=" O LEU I 98 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N LEU I 100 " --> pdb=" O GLU I 110 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N GLU I 110 " --> pdb=" O LEU I 100 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 127 through 128 Processing sheet with id=AB5, first strand: chain 'I' and resid 331 through 334 removed outlier: 6.431A pdb=" N SER I 138 " --> pdb=" O SER I 411 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 145 through 150 removed outlier: 3.668A pdb=" N GLY I 145 " --> pdb=" O ILE I 163 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N TYR I 158 " --> pdb=" O VAL I 176 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N VAL I 176 " --> pdb=" O TYR I 158 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 460 through 461 removed outlier: 5.492A pdb=" N GLU I 482 " --> pdb=" O ARG I 473 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N VAL I 475 " --> pdb=" O THR I 480 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N THR I 480 " --> pdb=" O VAL I 475 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 460 through 461 Processing sheet with id=AB9, first strand: chain 'I' and resid 496 through 497 Processing sheet with id=AC1, first strand: chain 'I' and resid 595 through 596 removed outlier: 6.534A pdb=" N LEU I 595 " --> pdb=" O LEU I 655 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 620 through 624 removed outlier: 7.093A pdb=" N ARG I 610 " --> pdb=" O VAL I 606 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N VAL I 606 " --> pdb=" O ARG I 610 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N VAL I 612 " --> pdb=" O ALA I 604 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 629 through 630 Processing sheet with id=AC4, first strand: chain 'I' and resid 971 through 972 removed outlier: 7.362A pdb=" N ILE I 688 " --> pdb=" O ALA I 850 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ILE I 852 " --> pdb=" O ILE I 688 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ILE I 690 " --> pdb=" O ILE I 852 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL I 689 " --> pdb=" O ILE I 870 " (cutoff:3.500A) removed outlier: 8.828A pdb=" N VAL I 869 " --> pdb=" O ASN I 671 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N LEU I 673 " --> pdb=" O VAL I 869 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N LEU I 871 " --> pdb=" O LEU I 673 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ALA I 675 " --> pdb=" O LEU I 871 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N VAL I 988 " --> pdb=" O ILE I 676 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 718 through 719 removed outlier: 3.697A pdb=" N THR I 715 " --> pdb=" O GLY I 718 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N ASP I 714 " --> pdb=" O VAL I 819 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N VAL I 819 " --> pdb=" O ASP I 714 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N VAL I 822 " --> pdb=" O ARG I 805 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ARG I 805 " --> pdb=" O VAL I 822 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ARG I 824 " --> pdb=" O THR I 803 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N THR I 803 " --> pdb=" O ARG I 824 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N TYR I 826 " --> pdb=" O VAL I 801 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 721 through 722 Processing sheet with id=AC7, first strand: chain 'I' and resid 754 through 756 removed outlier: 6.748A pdb=" N LEU I 790 " --> pdb=" O LEU I 755 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 1108 through 1109 removed outlier: 4.210A pdb=" N THR I1101 " --> pdb=" O VAL I1109 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'J' and resid 22 through 25 removed outlier: 6.599A pdb=" N HIS J 92 " --> pdb=" O TYR J 23 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N GLU J 25 " --> pdb=" O HIS J 92 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N GLU J 94 " --> pdb=" O GLU J 25 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N GLU J 515 " --> pdb=" O LEU J 95 " (cutoff:3.500A) removed outlier: 11.389A pdb=" N THR J 97 " --> pdb=" O ILE J 513 " (cutoff:3.500A) removed outlier: 10.647A pdb=" N ILE J 513 " --> pdb=" O THR J 97 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 132 through 134 Processing sheet with id=AD2, first strand: chain 'J' and resid 166 through 170 removed outlier: 3.601A pdb=" N GLU J 183 " --> pdb=" O ALA J 203 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 398 through 402 removed outlier: 3.893A pdb=" N ARG J 434 " --> pdb=" O VAL J 447 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'J' and resid 420 through 422 removed outlier: 7.540A pdb=" N VAL J 427 " --> pdb=" O LEU J 421 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 527 through 529 Processing sheet with id=AD6, first strand: chain 'J' and resid 626 through 633 removed outlier: 7.829A pdb=" N ILE J 726 " --> pdb=" O ARG J 628 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL J 630 " --> pdb=" O ILE J 726 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N LEU J 728 " --> pdb=" O VAL J 630 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N VAL J 632 " --> pdb=" O LEU J 728 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 842 through 843 removed outlier: 7.031A pdb=" N PHE J 843 " --> pdb=" O ARG J 867 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 1118 through 1121 Processing sheet with id=AD9, first strand: chain 'J' and resid 1123 through 1124 removed outlier: 3.669A pdb=" N ARG J1133 " --> pdb=" O GLN J1124 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 1153 through 1154 Processing sheet with id=AE2, first strand: chain 'J' and resid 1300 through 1305 Processing sheet with id=AE3, first strand: chain 'J' and resid 1392 through 1394 removed outlier: 4.453A pdb=" N TYR J1378 " --> pdb=" O LEU J1420 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 1485 through 1488 removed outlier: 3.536A pdb=" N VAL J1487 " --> pdb=" O VAL K 74 " (cutoff:3.500A) 945 hydrogen bonds defined for protein. 2634 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 88 hydrogen bonds 152 hydrogen bond angles 0 basepair planarities 37 basepair parallelities 53 stacking parallelities Total time for adding SS restraints: 6.74 Time building geometry restraints manager: 2.39 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: 7917 1.34 - 1.46: 3443 1.46 - 1.57: 13604 1.57 - 1.69: 148 1.69 - 1.81: 115 Bond restraints: 25227 Sorted by residual: bond pdb=" C1' DC T 21 " pdb=" N1 DC T 21 " ideal model delta sigma weight residual 1.468 1.515 -0.047 1.40e-02 5.10e+03 1.14e+01 bond pdb=" C3' DC N 26 " pdb=" C2' DC N 26 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.98e+00 bond pdb=" C3' DT N 28 " pdb=" C2' DT N 28 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.17e+00 bond pdb=" C3' DT T 29 " pdb=" C2' DT T 29 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.37e+00 bond pdb=" C3' DG T 30 " pdb=" C2' DG T 30 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.03e+00 ... (remaining 25222 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 33788 2.05 - 4.09: 593 4.09 - 6.14: 55 6.14 - 8.19: 9 8.19 - 10.23: 5 Bond angle restraints: 34450 Sorted by residual: angle pdb=" O4' DG T 24 " pdb=" C4' DG T 24 " pdb=" C3' DG T 24 " ideal model delta sigma weight residual 106.00 103.12 2.88 6.00e-01 2.78e+00 2.30e+01 angle pdb=" O4' DG T 23 " pdb=" C4' DG T 23 " pdb=" C3' DG T 23 " ideal model delta sigma weight residual 106.00 103.21 2.79 6.00e-01 2.78e+00 2.17e+01 angle pdb=" N3 DT T 31 " pdb=" C4 DT T 31 " pdb=" O4 DT T 31 " ideal model delta sigma weight residual 119.90 122.55 -2.65 6.00e-01 2.78e+00 1.95e+01 angle pdb=" N3 DT N 6 " pdb=" C4 DT N 6 " pdb=" O4 DT N 6 " ideal model delta sigma weight residual 119.90 122.53 -2.63 6.00e-01 2.78e+00 1.92e+01 angle pdb=" N3 DT N 24 " pdb=" C4 DT N 24 " pdb=" O4 DT N 24 " ideal model delta sigma weight residual 119.90 122.49 -2.59 6.00e-01 2.78e+00 1.86e+01 ... (remaining 34445 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.39: 14593 30.39 - 60.77: 664 60.77 - 91.16: 30 91.16 - 121.54: 0 121.54 - 151.93: 1 Dihedral angle restraints: 15288 sinusoidal: 6896 harmonic: 8392 Sorted by residual: dihedral pdb=" CA GLU J1109 " pdb=" C GLU J1109 " pdb=" N ALA J1110 " pdb=" CA ALA J1110 " ideal model delta harmonic sigma weight residual 180.00 141.25 38.75 0 5.00e+00 4.00e-02 6.01e+01 dihedral pdb=" O5' C R 19 " pdb=" C5' C R 19 " pdb=" C4' C R 19 " pdb=" C3' C R 19 " ideal model delta sinusoidal sigma weight residual 180.00 146.93 33.07 3 6.40e+00 2.44e-02 3.02e+01 dihedral pdb=" CA PRO G 9 " pdb=" C PRO G 9 " pdb=" N VAL G 10 " pdb=" CA VAL G 10 " ideal model delta harmonic sigma weight residual 180.00 154.00 26.00 0 5.00e+00 4.00e-02 2.70e+01 ... (remaining 15285 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 3041 0.050 - 0.099: 696 0.099 - 0.149: 153 0.149 - 0.198: 4 0.198 - 0.248: 12 Chirality restraints: 3906 Sorted by residual: chirality pdb=" P C R 19 " pdb=" OP1 C R 19 " pdb=" OP2 C R 19 " pdb=" O5' C R 19 " both_signs ideal model delta sigma weight residual True 2.17 -2.42 -0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" P C R 21 " pdb=" OP1 C R 21 " pdb=" OP2 C R 21 " pdb=" O5' C R 21 " both_signs ideal model delta sigma weight residual True 2.17 -2.41 -0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" P A R 22 " pdb=" OP1 A R 22 " pdb=" OP2 A R 22 " pdb=" O5' A R 22 " both_signs ideal model delta sigma weight residual True 2.17 -2.41 -0.23 2.00e-01 2.50e+01 1.37e+00 ... (remaining 3903 not shown) Planarity restraints: 4246 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL J 108 " 0.042 5.00e-02 4.00e+02 6.41e-02 6.58e+00 pdb=" N PRO J 109 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO J 109 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO J 109 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR I 368 " -0.037 5.00e-02 4.00e+02 5.60e-02 5.02e+00 pdb=" N PRO I 369 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO I 369 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO I 369 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP K 57 " -0.037 5.00e-02 4.00e+02 5.54e-02 4.91e+00 pdb=" N PRO K 58 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO K 58 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO K 58 " -0.031 5.00e-02 4.00e+02 ... (remaining 4243 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 325 2.63 - 3.20: 21761 3.20 - 3.76: 39301 3.76 - 4.33: 53106 4.33 - 4.90: 85791 Nonbonded interactions: 200284 Sorted by model distance: nonbonded pdb=" OD1 ASP J 739 " pdb="MG MG J1602 " model vdw 2.059 2.170 nonbonded pdb=" O3' C R 28 " pdb="MG MG J1602 " model vdw 2.083 2.170 nonbonded pdb=" OP1 U R 29 " pdb="MG MG J1602 " model vdw 2.112 2.170 nonbonded pdb=" O THR I 240 " pdb=" NH2 ARG I 243 " model vdw 2.113 3.120 nonbonded pdb=" OG1 THR J 121 " pdb=" OE1 GLU J 122 " model vdw 2.136 3.040 ... (remaining 200279 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 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 2.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.400 Check model and map are aligned: 0.090 Set scattering table: 0.050 Process input model: 26.170 Find NCS groups from input model: 0.210 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 25231 Z= 0.198 Angle : 0.621 10.235 34456 Z= 0.367 Chirality : 0.045 0.248 3906 Planarity : 0.005 0.064 4246 Dihedral : 15.495 151.927 9892 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.30 (0.16), residues: 2905 helix: 0.92 (0.17), residues: 992 sheet: -0.28 (0.26), residues: 397 loop : -0.92 (0.16), residues: 1516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG K 32 TYR 0.022 0.001 TYR J1207 PHE 0.014 0.001 PHE I 148 TRP 0.028 0.001 TRP K 63 HIS 0.005 0.001 HIS K 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.20 (25227) covalent geometry : angle 0.61833 / 0.37 (34450) hydrogen bonds : bond 0.14710 / 9.72 ( 1031) hydrogen bonds : angle 5.86651 / 4.15 ( 2786) metal coordination : bond 0.00734 / 0.37 ( 4) metal coordination : angle 4.40994 / 2.23 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5810 Ramachandran restraints generated. 2905 Oldfield, 0 Emsley, 2905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5810 Ramachandran restraints generated. 2905 Oldfield, 0 Emsley, 2905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 229 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 4 SER cc_start: 0.6430 (m) cc_final: 0.5852 (p) REVERT: H 84 GLU cc_start: 0.7836 (mp0) cc_final: 0.7598 (mp0) REVERT: I 184 MET cc_start: 0.7173 (tmm) cc_final: 0.6539 (tmm) REVERT: I 338 GLU cc_start: 0.7558 (tp30) cc_final: 0.7201 (tp30) REVERT: I 711 GLU cc_start: 0.8650 (pm20) cc_final: 0.8229 (pm20) REVERT: J 481 MET cc_start: 0.8791 (tmm) cc_final: 0.8448 (ttt) REVERT: J 1045 MET cc_start: 0.8462 (mmt) cc_final: 0.8247 (mmt) REVERT: J 1307 LYS cc_start: 0.6935 (mmmt) cc_final: 0.6112 (mmmt) REVERT: K 59 ASN cc_start: 0.7729 (t0) cc_final: 0.7338 (t0) REVERT: K 72 ARG cc_start: 0.8332 (mpt-90) cc_final: 0.7723 (mpt-90) outliers start: 0 outliers final: 0 residues processed: 229 average time/residue: 0.1596 time to fit residues: 57.5935 Evaluate side-chains 181 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.5980 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 0.0870 chunk 183 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 overall best weight: 0.8560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.095253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.066270 restraints weight = 67763.389| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 3.62 r_work: 0.2988 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.0831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25231 Z= 0.134 Angle : 0.623 11.777 34456 Z= 0.313 Chirality : 0.045 0.332 3906 Planarity : 0.005 0.049 4246 Dihedral : 14.354 151.445 4065 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 0.52 % Allowed : 7.97 % Favored : 91.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.25 (0.16), residues: 2905 helix: 0.93 (0.17), residues: 1002 sheet: -0.28 (0.26), residues: 386 loop : -0.86 (0.16), residues: 1517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 32 TYR 0.022 0.001 TYR J 158 PHE 0.016 0.001 PHE I 114 TRP 0.011 0.001 TRP K 63 HIS 0.005 0.001 HIS G 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (25227) covalent geometry : angle 0.62143 / 0.31 (34450) hydrogen bonds : bond 0.06040 / 4.26 ( 1031) hydrogen bonds : angle 4.85845 / 3.42 ( 2786) metal coordination : bond 0.00777 / 0.39 ( 4) metal coordination : angle 3.34631 / 1.64 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5810 Ramachandran restraints generated. 2905 Oldfield, 0 Emsley, 2905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5810 Ramachandran restraints generated. 2905 Oldfield, 0 Emsley, 2905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 197 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 102 LYS cc_start: 0.9175 (mmpt) cc_final: 0.8818 (mmmt) REVERT: G 155 LYS cc_start: 0.9501 (OUTLIER) cc_final: 0.9231 (ttpt) REVERT: H 4 SER cc_start: 0.6759 (m) cc_final: 0.6428 (p) REVERT: H 84 GLU cc_start: 0.8301 (mp0) cc_final: 0.8100 (mp0) REVERT: I 219 GLN cc_start: 0.8987 (mp10) cc_final: 0.8458 (mp10) REVERT: I 275 TYR cc_start: 0.8705 (OUTLIER) cc_final: 0.8204 (m-80) REVERT: I 338 GLU cc_start: 0.8309 (tp30) cc_final: 0.7879 (tp30) REVERT: I 698 ASP cc_start: 0.8517 (m-30) cc_final: 0.8308 (m-30) REVERT: I 711 GLU cc_start: 0.9074 (pm20) cc_final: 0.8643 (pm20) REVERT: J 127 LEU cc_start: 0.9194 (OUTLIER) cc_final: 0.8901 (tt) REVERT: J 481 MET cc_start: 0.8848 (tmm) cc_final: 0.8599 (ttt) REVERT: K 29 GLN cc_start: 0.8175 (mt0) cc_final: 0.7943 (mt0) REVERT: K 59 ASN cc_start: 0.7709 (t0) cc_final: 0.7216 (t0) REVERT: K 89 MET cc_start: 0.5872 (tpt) cc_final: 0.5296 (mtt) outliers start: 13 outliers final: 10 residues processed: 201 average time/residue: 0.1679 time to fit residues: 51.7892 Evaluate side-chains 194 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 181 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 155 LYS Chi-restraints excluded: chain H residue 172 SER Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain I residue 193 LEU Chi-restraints excluded: chain I residue 275 TYR Chi-restraints excluded: chain I residue 307 LEU Chi-restraints excluded: chain I residue 464 LEU Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain J residue 125 GLN Chi-restraints excluded: chain J residue 127 LEU Chi-restraints excluded: chain K residue 31 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 179 optimal weight: 5.9990 chunk 186 optimal weight: 3.9990 chunk 86 optimal weight: 7.9990 chunk 93 optimal weight: 2.9990 chunk 148 optimal weight: 6.9990 chunk 65 optimal weight: 10.0000 chunk 164 optimal weight: 10.0000 chunk 17 optimal weight: 0.9980 chunk 243 optimal weight: 7.9990 chunk 33 optimal weight: 7.9990 chunk 192 optimal weight: 6.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 229 GLN H 229 GLN I 45 GLN I 99 GLN J 762 GLN J1103 HIS ** J1364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.089635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.060199 restraints weight = 68153.801| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 3.56 r_work: 0.2840 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.129 25231 Z= 0.352 Angle : 0.772 10.926 34456 Z= 0.393 Chirality : 0.050 0.512 3906 Planarity : 0.006 0.077 4246 Dihedral : 14.554 132.093 4065 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 1.45 % Allowed : 10.99 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.65 (0.15), residues: 2905 helix: 0.56 (0.17), residues: 1014 sheet: -0.47 (0.25), residues: 395 loop : -1.09 (0.16), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 420 TYR 0.036 0.002 TYR J1207 PHE 0.022 0.002 PHE I1112 TRP 0.023 0.002 TRP J 511 HIS 0.012 0.002 HIS I 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00804 / 0.35 (25227) covalent geometry : angle 0.77012 / 0.39 (34450) hydrogen bonds : bond 0.06345 / 4.43 ( 1031) hydrogen bonds : angle 4.90758 / 3.44 ( 2786) metal coordination : bond 0.02575 / 1.29 ( 4) metal coordination : angle 3.72133 / 1.93 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5810 Ramachandran restraints generated. 2905 Oldfield, 0 Emsley, 2905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5810 Ramachandran restraints generated. 2905 Oldfield, 0 Emsley, 2905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 174 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 102 LYS cc_start: 0.9081 (mmpt) cc_final: 0.8651 (mmmt) REVERT: H 4 SER cc_start: 0.6707 (m) cc_final: 0.6373 (p) REVERT: H 84 GLU cc_start: 0.8487 (mp0) cc_final: 0.8163 (mp0) REVERT: I 209 ARG cc_start: 0.9214 (ptm160) cc_final: 0.8908 (ptm-80) REVERT: I 219 GLN cc_start: 0.8980 (mp10) cc_final: 0.8457 (mp10) REVERT: I 420 ARG cc_start: 0.7516 (ttp-170) cc_final: 0.7067 (tmm160) REVERT: J 54 LYS cc_start: 0.7798 (tmmt) cc_final: 0.7518 (tmtt) REVERT: J 123 LEU cc_start: 0.9187 (mp) cc_final: 0.8895 (mp) REVERT: J 481 MET cc_start: 0.8880 (tmm) cc_final: 0.8666 (ttt) REVERT: K 59 ASN cc_start: 0.7829 (t0) cc_final: 0.7324 (t0) REVERT: K 89 MET cc_start: 0.5952 (tpt) cc_final: 0.5511 (mtt) outliers start: 36 outliers final: 27 residues processed: 198 average time/residue: 0.1726 time to fit residues: 53.0706 Evaluate side-chains 191 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 164 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 74 ASP Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain G residue 229 GLN Chi-restraints excluded: chain H residue 172 SER Chi-restraints excluded: chain H residue 229 GLN Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 83 CYS Chi-restraints excluded: chain I residue 193 LEU Chi-restraints excluded: chain I residue 261 ILE Chi-restraints excluded: chain I residue 290 LEU Chi-restraints excluded: chain I residue 307 LEU Chi-restraints excluded: chain I residue 360 LEU Chi-restraints excluded: chain I residue 367 LEU Chi-restraints excluded: chain I residue 464 LEU Chi-restraints excluded: chain I residue 560 MET Chi-restraints excluded: chain I residue 865 THR Chi-restraints excluded: chain I residue 988 VAL Chi-restraints excluded: chain I residue 995 MET Chi-restraints excluded: chain I residue 1005 MET Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain J residue 125 GLN Chi-restraints excluded: chain J residue 127 LEU Chi-restraints excluded: chain J residue 762 GLN Chi-restraints excluded: chain J residue 1420 LEU Chi-restraints excluded: chain K residue 31 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 116 optimal weight: 2.9990 chunk 192 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 211 optimal weight: 1.9990 chunk 162 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 185 optimal weight: 0.0870 chunk 108 optimal weight: 0.7980 chunk 103 optimal weight: 0.9990 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 567 GLN J 680 GLN J 762 GLN J1334 GLN ** J1364 HIS ** 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 = 0.3715 r_free = 0.3715 target = 0.092710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.063332 restraints weight = 66959.228| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 3.58 r_work: 0.2912 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 25231 Z= 0.132 Angle : 0.623 9.517 34456 Z= 0.313 Chirality : 0.045 0.354 3906 Planarity : 0.004 0.045 4246 Dihedral : 14.462 142.092 4065 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 1.13 % Allowed : 12.96 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.37 (0.16), residues: 2905 helix: 0.85 (0.17), residues: 1005 sheet: -0.47 (0.26), residues: 395 loop : -0.92 (0.16), residues: 1505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG I 243 TYR 0.026 0.001 TYR J1207 PHE 0.012 0.001 PHE J 806 TRP 0.009 0.001 TRP G 200 HIS 0.005 0.001 HIS J1075 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (25227) covalent geometry : angle 0.62159 / 0.31 (34450) hydrogen bonds : bond 0.05493 / 3.88 ( 1031) hydrogen bonds : angle 4.66103 / 3.26 ( 2786) metal coordination : bond 0.00515 / 0.26 ( 4) metal coordination : angle 3.52588 / 1.75 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5810 Ramachandran restraints generated. 2905 Oldfield, 0 Emsley, 2905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5810 Ramachandran restraints generated. 2905 Oldfield, 0 Emsley, 2905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 181 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 102 LYS cc_start: 0.9123 (mmpt) cc_final: 0.8720 (mmmt) REVERT: G 229 GLN cc_start: 0.8444 (OUTLIER) cc_final: 0.8192 (pm20) REVERT: H 4 SER cc_start: 0.6491 (m) cc_final: 0.6222 (p) REVERT: H 84 GLU cc_start: 0.8434 (mp0) cc_final: 0.8115 (mp0) REVERT: H 229 GLN cc_start: 0.8252 (mm-40) cc_final: 0.7796 (mm110) REVERT: I 209 ARG cc_start: 0.9230 (ptm160) cc_final: 0.8903 (ptm-80) REVERT: I 219 GLN cc_start: 0.9040 (mp10) cc_final: 0.8491 (mp10) REVERT: I 229 MET cc_start: 0.7544 (mmp) cc_final: 0.7096 (mpp) REVERT: I 275 TYR cc_start: 0.8743 (t80) cc_final: 0.8331 (m-10) REVERT: I 711 GLU cc_start: 0.9015 (pm20) cc_final: 0.8634 (pm20) REVERT: J 49 ILE cc_start: 0.8730 (OUTLIER) cc_final: 0.8468 (tt) REVERT: J 54 LYS cc_start: 0.7727 (tmmt) cc_final: 0.7466 (tmtt) REVERT: J 123 LEU cc_start: 0.9101 (mp) cc_final: 0.8779 (mp) REVERT: J 481 MET cc_start: 0.8815 (tmm) cc_final: 0.8556 (ttt) REVERT: J 1482 ARG cc_start: 0.8477 (ttp80) cc_final: 0.8275 (ttm-80) REVERT: K 59 ASN cc_start: 0.7429 (t0) cc_final: 0.6987 (t0) REVERT: K 89 MET cc_start: 0.5693 (tpt) cc_final: 0.5417 (mtt) outliers start: 28 outliers final: 17 residues processed: 201 average time/residue: 0.1679 time to fit residues: 52.4475 Evaluate side-chains 186 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 167 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 229 GLN Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain H residue 226 SER Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 102 HIS Chi-restraints excluded: chain I residue 290 LEU Chi-restraints excluded: chain I residue 307 LEU Chi-restraints excluded: chain I residue 464 LEU Chi-restraints excluded: chain I residue 513 VAL Chi-restraints excluded: chain I residue 865 THR Chi-restraints excluded: chain I residue 995 MET Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain J residue 49 ILE Chi-restraints excluded: chain J residue 125 GLN Chi-restraints excluded: chain J residue 127 LEU Chi-restraints excluded: chain J residue 1424 VAL Chi-restraints excluded: chain K residue 31 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 243 optimal weight: 0.7980 chunk 211 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 chunk 280 optimal weight: 0.6980 chunk 285 optimal weight: 0.0020 chunk 141 optimal weight: 3.9990 chunk 154 optimal weight: 6.9990 chunk 111 optimal weight: 4.9990 chunk 267 optimal weight: 0.8980 chunk 137 optimal weight: 0.9990 chunk 153 optimal weight: 5.9990 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** J1364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.093197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.063904 restraints weight = 66840.345| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 3.59 r_work: 0.2928 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25231 Z= 0.120 Angle : 0.598 9.338 34456 Z= 0.300 Chirality : 0.044 0.350 3906 Planarity : 0.004 0.050 4246 Dihedral : 14.390 144.379 4065 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 1.53 % Allowed : 14.17 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.16), residues: 2905 helix: 0.96 (0.17), residues: 1007 sheet: -0.38 (0.26), residues: 389 loop : -0.87 (0.16), residues: 1509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 284 TYR 0.025 0.001 TYR J1207 PHE 0.012 0.001 PHE J 806 TRP 0.011 0.001 TRP J1398 HIS 0.005 0.001 HIS J1075 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (25227) covalent geometry : angle 0.59648 / 0.30 (34450) hydrogen bonds : bond 0.05226 / 3.74 ( 1031) hydrogen bonds : angle 4.54666 / 3.18 ( 2786) metal coordination : bond 0.00446 / 0.22 ( 4) metal coordination : angle 3.59247 / 1.82 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5810 Ramachandran restraints generated. 2905 Oldfield, 0 Emsley, 2905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5810 Ramachandran restraints generated. 2905 Oldfield, 0 Emsley, 2905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 176 time to evaluate : 0.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 84 GLU cc_start: 0.9169 (mt-10) cc_final: 0.8909 (mp0) REVERT: G 102 LYS cc_start: 0.9092 (mmpt) cc_final: 0.8673 (mmmt) REVERT: H 84 GLU cc_start: 0.8401 (mp0) cc_final: 0.8011 (mp0) REVERT: I 82 GLU cc_start: 0.9203 (OUTLIER) cc_final: 0.8847 (pm20) REVERT: I 209 ARG cc_start: 0.9226 (ptm160) cc_final: 0.8874 (ptm-80) REVERT: I 219 GLN cc_start: 0.9035 (mp10) cc_final: 0.8694 (mp10) REVERT: I 229 MET cc_start: 0.7636 (mmp) cc_final: 0.7236 (mpp) REVERT: I 275 TYR cc_start: 0.8694 (t80) cc_final: 0.8367 (m-10) REVERT: I 711 GLU cc_start: 0.9048 (pm20) cc_final: 0.8676 (pm20) REVERT: I 1003 ASP cc_start: 0.4953 (OUTLIER) cc_final: 0.0739 (t70) REVERT: J 49 ILE cc_start: 0.8727 (OUTLIER) cc_final: 0.8460 (tt) REVERT: J 54 LYS cc_start: 0.7714 (tmmt) cc_final: 0.7459 (tmtt) REVERT: J 123 LEU cc_start: 0.9120 (mp) cc_final: 0.8791 (mp) REVERT: J 456 MET cc_start: 0.5791 (ttp) cc_final: 0.4770 (ttt) REVERT: J 481 MET cc_start: 0.8823 (tmm) cc_final: 0.8530 (ttt) REVERT: J 1482 ARG cc_start: 0.8472 (ttp80) cc_final: 0.8249 (ttm-80) REVERT: K 59 ASN cc_start: 0.7459 (t0) cc_final: 0.7058 (t0) REVERT: K 89 MET cc_start: 0.5664 (tpt) cc_final: 0.5382 (mtt) outliers start: 38 outliers final: 23 residues processed: 204 average time/residue: 0.1893 time to fit residues: 60.0207 Evaluate side-chains 193 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 167 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 74 ASP Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 82 GLU Chi-restraints excluded: chain I residue 102 HIS Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain I residue 307 LEU Chi-restraints excluded: chain I residue 464 LEU Chi-restraints excluded: chain I residue 513 VAL Chi-restraints excluded: chain I residue 560 MET Chi-restraints excluded: chain I residue 865 THR Chi-restraints excluded: chain I residue 1003 ASP Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain J residue 49 ILE Chi-restraints excluded: chain J residue 125 GLN Chi-restraints excluded: chain J residue 127 LEU Chi-restraints excluded: chain J residue 778 LEU Chi-restraints excluded: chain J residue 1099 VAL Chi-restraints excluded: chain J residue 1424 VAL Chi-restraints excluded: chain J residue 1483 PHE Chi-restraints excluded: chain K residue 31 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 198 optimal weight: 2.9990 chunk 76 optimal weight: 6.9990 chunk 200 optimal weight: 3.9990 chunk 28 optimal weight: 8.9990 chunk 190 optimal weight: 6.9990 chunk 176 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 192 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 chunk 275 optimal weight: 0.9990 chunk 285 optimal weight: 0.0270 overall best weight: 1.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 567 GLN J1103 HIS ** J1364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.091972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.062620 restraints weight = 67107.063| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 3.56 r_work: 0.2899 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 25231 Z= 0.173 Angle : 0.617 9.394 34456 Z= 0.309 Chirality : 0.045 0.390 3906 Planarity : 0.005 0.098 4246 Dihedral : 14.395 139.569 4065 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 1.73 % Allowed : 14.94 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.16), residues: 2905 helix: 0.96 (0.17), residues: 1006 sheet: -0.39 (0.25), residues: 408 loop : -0.89 (0.16), residues: 1491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG J1388 TYR 0.028 0.001 TYR J1207 PHE 0.014 0.001 PHE J 806 TRP 0.011 0.001 TRP J 511 HIS 0.005 0.001 HIS K 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.17 (25227) covalent geometry : angle 0.61554 / 0.31 (34450) hydrogen bonds : bond 0.05258 / 3.74 ( 1031) hydrogen bonds : angle 4.52489 / 3.16 ( 2786) metal coordination : bond 0.00947 / 0.48 ( 4) metal coordination : angle 3.56934 / 1.84 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5810 Ramachandran restraints generated. 2905 Oldfield, 0 Emsley, 2905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5810 Ramachandran restraints generated. 2905 Oldfield, 0 Emsley, 2905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 169 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 1 MET cc_start: 0.7229 (tpt) cc_final: 0.7010 (tpt) REVERT: G 84 GLU cc_start: 0.9194 (mt-10) cc_final: 0.8908 (mp0) REVERT: G 102 LYS cc_start: 0.9036 (mmpt) cc_final: 0.8642 (mmmt) REVERT: I 82 GLU cc_start: 0.9209 (OUTLIER) cc_final: 0.8884 (pm20) REVERT: I 219 GLN cc_start: 0.9002 (mp10) cc_final: 0.8677 (mp10) REVERT: I 275 TYR cc_start: 0.8708 (t80) cc_final: 0.8286 (m-10) REVERT: I 1003 ASP cc_start: 0.4938 (OUTLIER) cc_final: 0.0882 (t70) REVERT: J 49 ILE cc_start: 0.8774 (OUTLIER) cc_final: 0.8517 (tt) REVERT: J 54 LYS cc_start: 0.7725 (tmmt) cc_final: 0.7471 (tmtt) REVERT: J 123 LEU cc_start: 0.9124 (mp) cc_final: 0.8846 (mp) REVERT: J 481 MET cc_start: 0.8825 (tmm) cc_final: 0.8566 (ttt) REVERT: J 619 LEU cc_start: 0.7320 (mp) cc_final: 0.7064 (mp) REVERT: K 59 ASN cc_start: 0.7479 (t0) cc_final: 0.7084 (t0) REVERT: K 89 MET cc_start: 0.5786 (tpt) cc_final: 0.5472 (mtt) outliers start: 43 outliers final: 30 residues processed: 202 average time/residue: 0.1765 time to fit residues: 55.3418 Evaluate side-chains 193 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 160 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 74 ASP Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 82 GLU Chi-restraints excluded: chain I residue 102 HIS Chi-restraints excluded: chain I residue 158 TYR Chi-restraints excluded: chain I residue 290 LEU Chi-restraints excluded: chain I residue 307 LEU Chi-restraints excluded: chain I residue 464 LEU Chi-restraints excluded: chain I residue 513 VAL Chi-restraints excluded: chain I residue 514 VAL Chi-restraints excluded: chain I residue 560 MET Chi-restraints excluded: chain I residue 865 THR Chi-restraints excluded: chain I residue 995 MET Chi-restraints excluded: chain I residue 1003 ASP Chi-restraints excluded: chain I residue 1005 MET Chi-restraints excluded: chain I residue 1006 HIS Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain J residue 49 ILE Chi-restraints excluded: chain J residue 125 GLN Chi-restraints excluded: chain J residue 127 LEU Chi-restraints excluded: chain J residue 747 VAL Chi-restraints excluded: chain J residue 778 LEU Chi-restraints excluded: chain J residue 1415 VAL Chi-restraints excluded: chain J residue 1424 VAL Chi-restraints excluded: chain J residue 1466 VAL Chi-restraints excluded: chain J residue 1483 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 119 optimal weight: 6.9990 chunk 70 optimal weight: 4.9990 chunk 217 optimal weight: 0.0470 chunk 174 optimal weight: 9.9990 chunk 18 optimal weight: 9.9990 chunk 161 optimal weight: 0.0770 chunk 247 optimal weight: 9.9990 chunk 10 optimal weight: 5.9990 chunk 267 optimal weight: 0.8980 chunk 154 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 overall best weight: 1.6040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 845 ASN ** J1364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.091962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.062726 restraints weight = 66972.303| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 3.55 r_work: 0.2902 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 25231 Z= 0.159 Angle : 0.618 18.769 34456 Z= 0.307 Chirality : 0.045 0.354 3906 Planarity : 0.004 0.057 4246 Dihedral : 14.381 139.343 4065 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 1.77 % Allowed : 15.30 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.25 (0.16), residues: 2905 helix: 0.98 (0.17), residues: 1006 sheet: -0.37 (0.25), residues: 409 loop : -0.88 (0.16), residues: 1490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I1031 TYR 0.027 0.001 TYR J1207 PHE 0.013 0.001 PHE J 806 TRP 0.009 0.001 TRP K 63 HIS 0.005 0.001 HIS J1075 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 (25227) covalent geometry : angle 0.61634 / 0.31 (34450) hydrogen bonds : bond 0.05178 / 3.68 ( 1031) hydrogen bonds : angle 4.49783 / 3.14 ( 2786) metal coordination : bond 0.00811 / 0.41 ( 4) metal coordination : angle 3.51426 / 1.77 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5810 Ramachandran restraints generated. 2905 Oldfield, 0 Emsley, 2905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5810 Ramachandran restraints generated. 2905 Oldfield, 0 Emsley, 2905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 168 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 84 GLU cc_start: 0.9197 (mt-10) cc_final: 0.8914 (mp0) REVERT: I 82 GLU cc_start: 0.9190 (OUTLIER) cc_final: 0.8886 (pm20) REVERT: I 219 GLN cc_start: 0.9010 (mp10) cc_final: 0.8670 (mp10) REVERT: I 275 TYR cc_start: 0.8719 (t80) cc_final: 0.8378 (m-10) REVERT: I 711 GLU cc_start: 0.9058 (pm20) cc_final: 0.8658 (pm20) REVERT: I 1003 ASP cc_start: 0.4951 (OUTLIER) cc_final: 0.0815 (t70) REVERT: J 49 ILE cc_start: 0.8753 (OUTLIER) cc_final: 0.8501 (tt) REVERT: J 54 LYS cc_start: 0.7678 (tmmt) cc_final: 0.7425 (tmtt) REVERT: J 123 LEU cc_start: 0.9178 (mp) cc_final: 0.8835 (mp) REVERT: J 481 MET cc_start: 0.8845 (tmm) cc_final: 0.8559 (ttt) REVERT: K 59 ASN cc_start: 0.7435 (t0) cc_final: 0.7040 (t0) REVERT: K 89 MET cc_start: 0.5793 (tpt) cc_final: 0.5165 (tpp) outliers start: 44 outliers final: 32 residues processed: 201 average time/residue: 0.1778 time to fit residues: 55.8912 Evaluate side-chains 200 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 165 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 82 GLU Chi-restraints excluded: chain I residue 83 CYS Chi-restraints excluded: chain I residue 102 HIS Chi-restraints excluded: chain I residue 158 TYR Chi-restraints excluded: chain I residue 290 LEU Chi-restraints excluded: chain I residue 307 LEU Chi-restraints excluded: chain I residue 464 LEU Chi-restraints excluded: chain I residue 513 VAL Chi-restraints excluded: chain I residue 514 VAL Chi-restraints excluded: chain I residue 560 MET Chi-restraints excluded: chain I residue 865 THR Chi-restraints excluded: chain I residue 995 MET Chi-restraints excluded: chain I residue 1003 ASP Chi-restraints excluded: chain I residue 1005 MET Chi-restraints excluded: chain I residue 1006 HIS Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain J residue 49 ILE Chi-restraints excluded: chain J residue 125 GLN Chi-restraints excluded: chain J residue 126 VAL Chi-restraints excluded: chain J residue 127 LEU Chi-restraints excluded: chain J residue 747 VAL Chi-restraints excluded: chain J residue 778 LEU Chi-restraints excluded: chain J residue 1099 VAL Chi-restraints excluded: chain J residue 1415 VAL Chi-restraints excluded: chain J residue 1424 VAL Chi-restraints excluded: chain J residue 1466 VAL Chi-restraints excluded: chain J residue 1483 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 246 optimal weight: 2.9990 chunk 241 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 chunk 221 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 6 optimal weight: 5.9990 chunk 263 optimal weight: 4.9990 chunk 30 optimal weight: 0.8980 chunk 207 optimal weight: 2.9990 chunk 278 optimal weight: 7.9990 chunk 57 optimal weight: 1.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 575 GLN ** J1364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.092011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.062658 restraints weight = 66909.205| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 3.56 r_work: 0.2901 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 25231 Z= 0.159 Angle : 0.615 10.782 34456 Z= 0.307 Chirality : 0.045 0.356 3906 Planarity : 0.004 0.049 4246 Dihedral : 14.362 137.474 4065 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 1.49 % Allowed : 15.82 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.16), residues: 2905 helix: 1.02 (0.17), residues: 1006 sheet: -0.35 (0.26), residues: 409 loop : -0.87 (0.16), residues: 1490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I1031 TYR 0.028 0.001 TYR J1207 PHE 0.014 0.001 PHE J 806 TRP 0.010 0.001 TRP J 511 HIS 0.004 0.001 HIS J1075 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 (25227) covalent geometry : angle 0.61292 / 0.31 (34450) hydrogen bonds : bond 0.05101 / 3.62 ( 1031) hydrogen bonds : angle 4.47087 / 3.12 ( 2786) metal coordination : bond 0.00807 / 0.41 ( 4) metal coordination : angle 3.53140 / 1.80 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5810 Ramachandran restraints generated. 2905 Oldfield, 0 Emsley, 2905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5810 Ramachandran restraints generated. 2905 Oldfield, 0 Emsley, 2905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 166 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 84 GLU cc_start: 0.9203 (mt-10) cc_final: 0.8916 (mp0) REVERT: I 82 GLU cc_start: 0.9188 (OUTLIER) cc_final: 0.8903 (pm20) REVERT: I 219 GLN cc_start: 0.9013 (mp10) cc_final: 0.8677 (mp10) REVERT: I 275 TYR cc_start: 0.8708 (t80) cc_final: 0.8378 (m-10) REVERT: I 711 GLU cc_start: 0.9051 (pm20) cc_final: 0.8674 (pm20) REVERT: I 1003 ASP cc_start: 0.4953 (OUTLIER) cc_final: 0.0828 (t70) REVERT: J 49 ILE cc_start: 0.8762 (OUTLIER) cc_final: 0.8513 (tt) REVERT: J 54 LYS cc_start: 0.7624 (tmmt) cc_final: 0.7374 (tmtt) REVERT: J 123 LEU cc_start: 0.9171 (mp) cc_final: 0.8819 (mp) REVERT: J 481 MET cc_start: 0.8857 (tmm) cc_final: 0.8544 (ttt) REVERT: J 1219 GLU cc_start: 0.9152 (tt0) cc_final: 0.8668 (tt0) REVERT: K 59 ASN cc_start: 0.7458 (t0) cc_final: 0.7064 (t0) REVERT: K 89 MET cc_start: 0.5715 (tpt) cc_final: 0.5184 (tpp) outliers start: 37 outliers final: 33 residues processed: 193 average time/residue: 0.1651 time to fit residues: 50.0370 Evaluate side-chains 198 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 162 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 74 ASP Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 82 GLU Chi-restraints excluded: chain I residue 83 CYS Chi-restraints excluded: chain I residue 102 HIS Chi-restraints excluded: chain I residue 158 TYR Chi-restraints excluded: chain I residue 290 LEU Chi-restraints excluded: chain I residue 307 LEU Chi-restraints excluded: chain I residue 464 LEU Chi-restraints excluded: chain I residue 513 VAL Chi-restraints excluded: chain I residue 514 VAL Chi-restraints excluded: chain I residue 560 MET Chi-restraints excluded: chain I residue 865 THR Chi-restraints excluded: chain I residue 995 MET Chi-restraints excluded: chain I residue 1003 ASP Chi-restraints excluded: chain I residue 1005 MET Chi-restraints excluded: chain I residue 1006 HIS Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain J residue 49 ILE Chi-restraints excluded: chain J residue 125 GLN Chi-restraints excluded: chain J residue 126 VAL Chi-restraints excluded: chain J residue 127 LEU Chi-restraints excluded: chain J residue 747 VAL Chi-restraints excluded: chain J residue 778 LEU Chi-restraints excluded: chain J residue 1415 VAL Chi-restraints excluded: chain J residue 1424 VAL Chi-restraints excluded: chain J residue 1466 VAL Chi-restraints excluded: chain J residue 1468 LEU Chi-restraints excluded: chain J residue 1483 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 219 optimal weight: 7.9990 chunk 3 optimal weight: 0.6980 chunk 93 optimal weight: 4.9990 chunk 132 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 248 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 224 optimal weight: 0.9980 chunk 125 optimal weight: 0.8980 chunk 142 optimal weight: 3.9990 chunk 165 optimal weight: 2.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 38 ASN ** J1364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.092164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.062980 restraints weight = 66623.233| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 3.53 r_work: 0.2909 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 25231 Z= 0.143 Angle : 0.605 12.726 34456 Z= 0.301 Chirality : 0.044 0.338 3906 Planarity : 0.004 0.045 4246 Dihedral : 14.315 137.042 4065 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 1.53 % Allowed : 16.06 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.18 (0.16), residues: 2905 helix: 1.07 (0.17), residues: 1004 sheet: -0.39 (0.25), residues: 415 loop : -0.84 (0.17), residues: 1486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 420 TYR 0.027 0.001 TYR J1207 PHE 0.013 0.001 PHE J 806 TRP 0.008 0.001 TRP J 511 HIS 0.004 0.001 HIS J1075 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (25227) covalent geometry : angle 0.60310 / 0.30 (34450) hydrogen bonds : bond 0.05003 / 3.53 ( 1031) hydrogen bonds : angle 4.44117 / 3.10 ( 2786) metal coordination : bond 0.00660 / 0.33 ( 4) metal coordination : angle 3.54003 / 1.78 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5810 Ramachandran restraints generated. 2905 Oldfield, 0 Emsley, 2905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5810 Ramachandran restraints generated. 2905 Oldfield, 0 Emsley, 2905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 166 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 84 GLU cc_start: 0.9189 (mt-10) cc_final: 0.8904 (mp0) REVERT: H 84 GLU cc_start: 0.8656 (mp0) cc_final: 0.7856 (mp0) REVERT: I 82 GLU cc_start: 0.9211 (OUTLIER) cc_final: 0.8922 (pm20) REVERT: I 219 GLN cc_start: 0.9004 (mp10) cc_final: 0.8664 (mp10) REVERT: I 275 TYR cc_start: 0.8693 (t80) cc_final: 0.8373 (m-10) REVERT: I 321 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7061 (pt0) REVERT: I 711 GLU cc_start: 0.9056 (pm20) cc_final: 0.8698 (pm20) REVERT: I 1003 ASP cc_start: 0.4940 (OUTLIER) cc_final: 0.0782 (t70) REVERT: J 49 ILE cc_start: 0.8763 (OUTLIER) cc_final: 0.8519 (tt) REVERT: J 54 LYS cc_start: 0.7614 (tmmt) cc_final: 0.7368 (tmtt) REVERT: J 123 LEU cc_start: 0.9173 (mp) cc_final: 0.8829 (mp) REVERT: J 481 MET cc_start: 0.8854 (tmm) cc_final: 0.8522 (ttt) REVERT: J 1219 GLU cc_start: 0.9139 (tt0) cc_final: 0.8658 (tt0) outliers start: 38 outliers final: 33 residues processed: 194 average time/residue: 0.1629 time to fit residues: 49.3616 Evaluate side-chains 198 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 161 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 74 ASP Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain H residue 172 SER Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 82 GLU Chi-restraints excluded: chain I residue 83 CYS Chi-restraints excluded: chain I residue 102 HIS Chi-restraints excluded: chain I residue 158 TYR Chi-restraints excluded: chain I residue 290 LEU Chi-restraints excluded: chain I residue 307 LEU Chi-restraints excluded: chain I residue 321 GLU Chi-restraints excluded: chain I residue 464 LEU Chi-restraints excluded: chain I residue 513 VAL Chi-restraints excluded: chain I residue 514 VAL Chi-restraints excluded: chain I residue 560 MET Chi-restraints excluded: chain I residue 865 THR Chi-restraints excluded: chain I residue 995 MET Chi-restraints excluded: chain I residue 1003 ASP Chi-restraints excluded: chain I residue 1005 MET Chi-restraints excluded: chain I residue 1006 HIS Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain J residue 49 ILE Chi-restraints excluded: chain J residue 125 GLN Chi-restraints excluded: chain J residue 126 VAL Chi-restraints excluded: chain J residue 127 LEU Chi-restraints excluded: chain J residue 747 VAL Chi-restraints excluded: chain J residue 778 LEU Chi-restraints excluded: chain J residue 1415 VAL Chi-restraints excluded: chain J residue 1424 VAL Chi-restraints excluded: chain J residue 1466 VAL Chi-restraints excluded: chain J residue 1468 LEU Chi-restraints excluded: chain J residue 1483 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 238 optimal weight: 5.9990 chunk 276 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 285 optimal weight: 9.9990 chunk 59 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 137 optimal weight: 1.9990 chunk 216 optimal weight: 3.9990 chunk 223 optimal weight: 1.9990 chunk 247 optimal weight: 9.9990 chunk 261 optimal weight: 6.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 229 GLN ** J1334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.090572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.061117 restraints weight = 67008.007| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 3.54 r_work: 0.2862 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 25231 Z= 0.229 Angle : 0.663 15.176 34456 Z= 0.330 Chirality : 0.046 0.393 3906 Planarity : 0.005 0.050 4246 Dihedral : 14.339 129.584 4065 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 1.65 % Allowed : 16.06 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.16), residues: 2905 helix: 0.99 (0.17), residues: 1005 sheet: -0.40 (0.25), residues: 409 loop : -0.91 (0.16), residues: 1491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG K 32 TYR 0.032 0.002 TYR J1207 PHE 0.019 0.002 PHE J 806 TRP 0.015 0.002 TRP J 511 HIS 0.004 0.001 HIS I 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00529 / 0.23 (25227) covalent geometry : angle 0.66188 / 0.33 (34450) hydrogen bonds : bond 0.05249 / 3.68 ( 1031) hydrogen bonds : angle 4.54613 / 3.17 ( 2786) metal coordination : bond 0.01425 / 0.72 ( 4) metal coordination : angle 3.44146 / 1.76 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5810 Ramachandran restraints generated. 2905 Oldfield, 0 Emsley, 2905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5810 Ramachandran restraints generated. 2905 Oldfield, 0 Emsley, 2905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 161 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 84 GLU cc_start: 0.9202 (mt-10) cc_final: 0.8928 (mp0) REVERT: G 102 LYS cc_start: 0.9003 (mmpt) cc_final: 0.8694 (mmtt) REVERT: H 84 GLU cc_start: 0.8678 (mp0) cc_final: 0.7824 (mp0) REVERT: I 82 GLU cc_start: 0.9149 (OUTLIER) cc_final: 0.8863 (pm20) REVERT: I 209 ARG cc_start: 0.9246 (ptm160) cc_final: 0.8828 (tmm-80) REVERT: I 219 GLN cc_start: 0.9023 (mp10) cc_final: 0.8687 (mp10) REVERT: I 321 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.7242 (pt0) REVERT: I 711 GLU cc_start: 0.9047 (pm20) cc_final: 0.8767 (pm20) REVERT: I 1003 ASP cc_start: 0.5046 (OUTLIER) cc_final: 0.0775 (t70) REVERT: J 49 ILE cc_start: 0.8785 (OUTLIER) cc_final: 0.8522 (tt) REVERT: J 54 LYS cc_start: 0.7620 (tmmt) cc_final: 0.7375 (tmtt) REVERT: J 123 LEU cc_start: 0.9175 (mp) cc_final: 0.8821 (mp) REVERT: J 481 MET cc_start: 0.8875 (tmm) cc_final: 0.8575 (ttt) REVERT: J 1219 GLU cc_start: 0.9164 (tt0) cc_final: 0.8649 (tt0) REVERT: K 89 MET cc_start: 0.5957 (tpt) cc_final: 0.5548 (mtt) outliers start: 41 outliers final: 35 residues processed: 191 average time/residue: 0.1613 time to fit residues: 48.2074 Evaluate side-chains 198 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 159 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 74 ASP Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain G residue 229 GLN Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain H residue 172 SER Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 82 GLU Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain I residue 158 TYR Chi-restraints excluded: chain I residue 290 LEU Chi-restraints excluded: chain I residue 307 LEU Chi-restraints excluded: chain I residue 321 GLU Chi-restraints excluded: chain I residue 464 LEU Chi-restraints excluded: chain I residue 513 VAL Chi-restraints excluded: chain I residue 514 VAL Chi-restraints excluded: chain I residue 560 MET Chi-restraints excluded: chain I residue 865 THR Chi-restraints excluded: chain I residue 988 VAL Chi-restraints excluded: chain I residue 995 MET Chi-restraints excluded: chain I residue 1003 ASP Chi-restraints excluded: chain I residue 1005 MET Chi-restraints excluded: chain I residue 1006 HIS Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain J residue 49 ILE Chi-restraints excluded: chain J residue 125 GLN Chi-restraints excluded: chain J residue 126 VAL Chi-restraints excluded: chain J residue 127 LEU Chi-restraints excluded: chain J residue 747 VAL Chi-restraints excluded: chain J residue 778 LEU Chi-restraints excluded: chain J residue 1415 VAL Chi-restraints excluded: chain J residue 1424 VAL Chi-restraints excluded: chain J residue 1466 VAL Chi-restraints excluded: chain J residue 1468 LEU Chi-restraints excluded: chain J residue 1483 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 69 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 245 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 13 optimal weight: 6.9990 chunk 255 optimal weight: 0.0010 chunk 202 optimal weight: 2.9990 chunk 66 optimal weight: 0.0170 chunk 252 optimal weight: 4.9990 chunk 246 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 overall best weight: 0.4824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** J1334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.090682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.061228 restraints weight = 67038.558| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 3.54 r_work: 0.2863 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.186 25231 Z= 0.228 Angle : 0.801 59.196 34456 Z= 0.422 Chirality : 0.046 0.561 3906 Planarity : 0.005 0.049 4246 Dihedral : 14.339 129.673 4065 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 1.65 % Allowed : 16.10 % Favored : 82.25 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.16), residues: 2905 helix: 1.01 (0.17), residues: 1005 sheet: -0.40 (0.25), residues: 409 loop : -0.91 (0.16), residues: 1491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG I1031 TYR 0.032 0.001 TYR J1207 PHE 0.018 0.001 PHE J 806 TRP 0.014 0.001 TRP J 511 HIS 0.004 0.001 HIS J1075 Details of bonding type rmsd/Z covalent geometry : bond 0.00519 / 0.23 (25227) covalent geometry : angle 0.79947 / 0.42 (34450) hydrogen bonds : bond 0.05207 / 3.65 ( 1031) hydrogen bonds : angle 4.54574 / 3.17 ( 2786) metal coordination : bond 0.01183 / 0.60 ( 4) metal coordination : angle 3.42144 / 1.75 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5511.03 seconds wall clock time: 95 minutes 2.75 seconds (5702.75 seconds total)