Starting phenix.real_space_refine on Sat May 24 02:20:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hsg_34996/05_2025/8hsg_34996.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hsg_34996/05_2025/8hsg_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8hsg_34996/05_2025/8hsg_34996.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hsg_34996/05_2025/8hsg_34996.map" model { file = "/net/cci-nas-00/data/ceres_data/8hsg_34996/05_2025/8hsg_34996.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hsg_34996/05_2025/8hsg_34996.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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): 0.51s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'RNA': 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: 13.83, per 1000 atoms: 0.56 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: 6.31 Conformation dependent library (CDL) restraints added in 2.9 seconds 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: 9.68 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: 14.39 Time building geometry restraints manager: 7.37 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=" CA LEU K 54 " pdb=" C LEU K 54 " ideal model delta sigma weight residual 1.523 1.498 0.025 1.34e-02 5.57e+03 3.50e+00 bond pdb=" C ASP J 136 " pdb=" N PRO J 137 " ideal model delta sigma weight residual 1.335 1.358 -0.022 1.30e-02 5.92e+03 2.99e+00 bond pdb=" C GLY I 43 " pdb=" O GLY I 43 " ideal model delta sigma weight residual 1.236 1.244 -0.009 5.30e-03 3.56e+04 2.59e+00 bond pdb=" CB LYS G 7 " pdb=" CG LYS G 7 " ideal model delta sigma weight residual 1.520 1.562 -0.042 3.00e-02 1.11e+03 1.98e+00 bond pdb=" C GLU K 41 " pdb=" N PRO K 42 " ideal model delta sigma weight residual 1.334 1.365 -0.031 2.34e-02 1.83e+03 1.72e+00 ... (remaining 25222 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 33884 2.05 - 4.09: 498 4.09 - 6.14: 54 6.14 - 8.19: 9 8.19 - 10.23: 5 Bond angle restraints: 34450 Sorted by residual: angle pdb=" CB ARG K 32 " pdb=" CG ARG K 32 " pdb=" CD ARG K 32 " ideal model delta sigma weight residual 111.30 119.54 -8.24 2.30e+00 1.89e-01 1.28e+01 angle pdb=" N GLY I 7 " pdb=" CA GLY I 7 " pdb=" C GLY I 7 " ideal model delta sigma weight residual 111.36 115.22 -3.86 1.17e+00 7.31e-01 1.09e+01 angle pdb=" N ILE I 163 " pdb=" CA ILE I 163 " pdb=" C ILE I 163 " ideal model delta sigma weight residual 108.15 111.39 -3.24 9.90e-01 1.02e+00 1.07e+01 angle pdb=" CB LYS J1307 " pdb=" CG LYS J1307 " pdb=" CD LYS J1307 " ideal model delta sigma weight residual 111.30 118.65 -7.35 2.30e+00 1.89e-01 1.02e+01 angle pdb=" N GLU I 421 " pdb=" CA GLU I 421 " pdb=" C GLU I 421 " ideal model delta sigma weight residual 111.07 114.32 -3.25 1.07e+00 8.73e-01 9.24e+00 ... (remaining 34445 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.39: 14617 30.39 - 60.77: 668 60.77 - 91.16: 38 91.16 - 121.54: 0 121.54 - 151.93: 1 Dihedral angle restraints: 15324 sinusoidal: 6932 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=" 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 dihedral pdb=" CA GLU I 421 " pdb=" C GLU I 421 " pdb=" N ARG I 422 " pdb=" CA ARG I 422 " ideal model delta harmonic sigma weight residual -180.00 -154.77 -25.23 0 5.00e+00 4.00e-02 2.55e+01 ... (remaining 15321 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 2684 0.036 - 0.072: 826 0.072 - 0.108: 306 0.108 - 0.144: 85 0.144 - 0.180: 5 Chirality restraints: 3906 Sorted by residual: chirality pdb=" CA VAL J1128 " pdb=" N VAL J1128 " pdb=" C VAL J1128 " pdb=" CB VAL J1128 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 8.09e-01 chirality pdb=" CB VAL J 591 " pdb=" CA VAL J 591 " pdb=" CG1 VAL J 591 " pdb=" CG2 VAL J 591 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.48e-01 chirality pdb=" CA ILE J 713 " pdb=" N ILE J 713 " pdb=" C ILE J 713 " pdb=" CB ILE J 713 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.47e-01 ... (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: 1.730 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: 0.930 Check model and map are aligned: 0.180 Set scattering table: 0.210 Process input model: 69.300 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 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 0.042 25231 Z= 0.121 Angle : 0.592 10.235 34456 Z= 0.305 Chirality : 0.042 0.180 3906 Planarity : 0.005 0.064 4246 Dihedral : 15.673 151.927 9928 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 12.05 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (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 TRP 0.028 0.001 TRP K 63 HIS 0.005 0.001 HIS K 33 PHE 0.014 0.001 PHE I 148 TYR 0.022 0.001 TYR J1207 ARG 0.014 0.000 ARG K 32 Details of bonding type rmsd hydrogen bonds : bond 0.14710 ( 1031) hydrogen bonds : angle 5.86651 ( 2786) metal coordination : bond 0.00734 ( 4) metal coordination : angle 4.40994 ( 6) covalent geometry : bond 0.00261 (25227) covalent geometry : angle 0.58924 (34450) *********************** 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 : 2.883 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: 0.3769 time to fit residues: 134.1093 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 : 2.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 249 optimal weight: 5.9990 chunk 223 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 76 optimal weight: 7.9990 chunk 150 optimal weight: 0.8980 chunk 119 optimal weight: 5.9990 chunk 231 optimal weight: 0.5980 chunk 89 optimal weight: 4.9990 chunk 140 optimal weight: 5.9990 chunk 172 optimal weight: 9.9990 chunk 267 optimal weight: 1.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 229 GLN ** H 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 229 GLN I 99 GLN ** J1364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.093017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.063804 restraints weight = 67304.806| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 3.58 r_work: 0.2927 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.1083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 25231 Z= 0.204 Angle : 0.633 11.129 34456 Z= 0.321 Chirality : 0.044 0.172 3906 Planarity : 0.005 0.048 4246 Dihedral : 14.780 145.795 4101 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 0.72 % Allowed : 8.29 % Favored : 90.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.16), residues: 2905 helix: 0.89 (0.17), residues: 1001 sheet: -0.40 (0.25), residues: 402 loop : -0.92 (0.16), residues: 1502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP J 511 HIS 0.007 0.001 HIS I 141 PHE 0.018 0.002 PHE I 191 TYR 0.028 0.002 TYR J1207 ARG 0.006 0.000 ARG J 162 Details of bonding type rmsd hydrogen bonds : bond 0.05695 ( 1031) hydrogen bonds : angle 4.78782 ( 2786) metal coordination : bond 0.01229 ( 4) metal coordination : angle 3.56774 ( 6) covalent geometry : bond 0.00472 (25227) covalent geometry : angle 0.63172 (34450) *********************** 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 212 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 194 time to evaluate : 2.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 102 LYS cc_start: 0.9141 (mmpt) cc_final: 0.8758 (mmmt) REVERT: H 4 SER cc_start: 0.6906 (m) cc_final: 0.6553 (p) REVERT: H 84 GLU cc_start: 0.8362 (mp0) cc_final: 0.8081 (mp0) REVERT: I 219 GLN cc_start: 0.9011 (mp10) cc_final: 0.8490 (mp10) REVERT: I 275 TYR cc_start: 0.8709 (OUTLIER) cc_final: 0.8108 (m-80) REVERT: I 338 GLU cc_start: 0.8394 (tp30) cc_final: 0.7992 (tp30) REVERT: I 420 ARG cc_start: 0.7355 (ttp-170) cc_final: 0.6702 (ttp-170) REVERT: I 711 GLU cc_start: 0.9076 (pm20) cc_final: 0.8648 (pm20) REVERT: J 127 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.8924 (tp) REVERT: J 481 MET cc_start: 0.8832 (tmm) cc_final: 0.8390 (ttt) REVERT: K 59 ASN cc_start: 0.7796 (t0) cc_final: 0.7298 (t0) REVERT: K 72 ARG cc_start: 0.8460 (mpt-90) cc_final: 0.8250 (mtt-85) REVERT: K 89 MET cc_start: 0.5838 (tpt) cc_final: 0.5139 (mtt) outliers start: 18 outliers final: 12 residues processed: 202 average time/residue: 0.4229 time to fit residues: 130.4635 Evaluate side-chains 189 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 175 time to evaluate : 2.528 ------------------------------------------------------------------------------- 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 155 LYS Chi-restraints excluded: chain G residue 229 GLN Chi-restraints excluded: chain H residue 172 SER Chi-restraints excluded: chain I residue 51 THR 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 564 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 K residue 31 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 138 optimal weight: 4.9990 chunk 219 optimal weight: 4.9990 chunk 195 optimal weight: 0.9980 chunk 223 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 270 optimal weight: 10.0000 chunk 50 optimal weight: 10.0000 chunk 176 optimal weight: 8.9990 chunk 114 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 chunk 199 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 139 ASN I 45 GLN J 762 GLN ** J1364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.092207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.063018 restraints weight = 67021.120| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 3.57 r_work: 0.2905 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 25231 Z= 0.190 Angle : 0.610 9.745 34456 Z= 0.310 Chirality : 0.043 0.160 3906 Planarity : 0.005 0.053 4246 Dihedral : 14.802 140.256 4101 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 1.37 % Allowed : 10.83 % Favored : 87.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.16), residues: 2905 helix: 0.88 (0.17), residues: 1009 sheet: -0.39 (0.26), residues: 385 loop : -0.90 (0.16), residues: 1511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 511 HIS 0.007 0.001 HIS I 141 PHE 0.014 0.001 PHE I1112 TYR 0.028 0.001 TYR J1207 ARG 0.007 0.000 ARG J 679 Details of bonding type rmsd hydrogen bonds : bond 0.05327 ( 1031) hydrogen bonds : angle 4.64376 ( 2786) metal coordination : bond 0.01155 ( 4) metal coordination : angle 3.54551 ( 6) covalent geometry : bond 0.00439 (25227) covalent geometry : angle 0.60842 (34450) *********************** 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 211 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 177 time to evaluate : 2.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 102 LYS cc_start: 0.9130 (mmpt) cc_final: 0.8707 (mmmt) REVERT: G 229 GLN cc_start: 0.8641 (OUTLIER) cc_final: 0.7958 (pp30) REVERT: H 4 SER cc_start: 0.6492 (m) cc_final: 0.6205 (p) REVERT: H 84 GLU cc_start: 0.8453 (mp0) cc_final: 0.8088 (mp0) REVERT: I 184 MET cc_start: 0.7504 (tmm) cc_final: 0.7303 (tmm) REVERT: I 209 ARG cc_start: 0.9163 (ptm-80) cc_final: 0.8741 (tmm-80) REVERT: I 219 GLN cc_start: 0.9008 (mp10) cc_final: 0.8474 (mp10) REVERT: I 275 TYR cc_start: 0.8731 (t80) cc_final: 0.8148 (m-10) REVERT: I 420 ARG cc_start: 0.7467 (ttp-170) cc_final: 0.6705 (ttp-170) REVERT: I 711 GLU cc_start: 0.9060 (pm20) cc_final: 0.8607 (pm20) REVERT: J 49 ILE cc_start: 0.8747 (OUTLIER) cc_final: 0.8476 (tt) REVERT: J 54 LYS cc_start: 0.7731 (tmmt) cc_final: 0.7467 (tmtt) REVERT: J 481 MET cc_start: 0.8832 (tmm) cc_final: 0.8543 (ttt) REVERT: J 1482 ARG cc_start: 0.8463 (ttp80) cc_final: 0.8223 (ttm-80) REVERT: K 8 LYS cc_start: 0.8705 (ptpt) cc_final: 0.8445 (pttt) REVERT: K 59 ASN cc_start: 0.7603 (t0) cc_final: 0.7146 (t0) outliers start: 34 outliers final: 24 residues processed: 201 average time/residue: 0.4061 time to fit residues: 125.3392 Evaluate side-chains 195 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 169 time to evaluate : 2.492 ------------------------------------------------------------------------------- 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 I residue 21 ILE Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 83 CYS 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 560 MET Chi-restraints excluded: chain I residue 564 MET Chi-restraints excluded: chain I residue 865 THR Chi-restraints excluded: chain I residue 995 MET 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 32 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 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 160 optimal weight: 0.5980 chunk 77 optimal weight: 0.7980 chunk 72 optimal weight: 4.9990 chunk 188 optimal weight: 1.9990 chunk 193 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 169 optimal weight: 40.0000 chunk 107 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 226 optimal weight: 2.9990 chunk 217 optimal weight: 0.0050 overall best weight: 0.8196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 139 ASN ** 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 = 0.3730 r_free = 0.3730 target = 0.093445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.064283 restraints weight = 66966.445| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 3.58 r_work: 0.2940 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25231 Z= 0.121 Angle : 0.569 9.555 34456 Z= 0.286 Chirality : 0.042 0.156 3906 Planarity : 0.004 0.042 4246 Dihedral : 14.741 142.383 4101 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 1.37 % Allowed : 12.76 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.16), residues: 2905 helix: 1.02 (0.17), residues: 1009 sheet: -0.35 (0.26), residues: 385 loop : -0.86 (0.16), residues: 1511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 200 HIS 0.005 0.001 HIS J1075 PHE 0.013 0.001 PHE I 114 TYR 0.024 0.001 TYR J1207 ARG 0.008 0.000 ARG I1031 Details of bonding type rmsd hydrogen bonds : bond 0.05015 ( 1031) hydrogen bonds : angle 4.50126 ( 2786) metal coordination : bond 0.00518 ( 4) metal coordination : angle 3.65643 ( 6) covalent geometry : bond 0.00277 (25227) covalent geometry : angle 0.56660 (34450) *********************** 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 218 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 184 time to evaluate : 2.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 84 GLU cc_start: 0.9169 (mt-10) cc_final: 0.8933 (mp0) REVERT: G 102 LYS cc_start: 0.9088 (mmpt) cc_final: 0.8680 (mmmt) REVERT: G 163 ASN cc_start: 0.8834 (m-40) cc_final: 0.8612 (t0) REVERT: H 84 GLU cc_start: 0.8433 (mp0) cc_final: 0.8049 (mp0) REVERT: I 82 GLU cc_start: 0.9203 (OUTLIER) cc_final: 0.8832 (pm20) REVERT: I 184 MET cc_start: 0.7548 (tmm) cc_final: 0.7156 (tmm) REVERT: I 209 ARG cc_start: 0.9124 (ptm-80) cc_final: 0.8688 (tmm-80) REVERT: I 219 GLN cc_start: 0.9028 (mp10) cc_final: 0.8692 (mp10) REVERT: I 275 TYR cc_start: 0.8702 (t80) cc_final: 0.8251 (m-10) REVERT: I 420 ARG cc_start: 0.7356 (ttp-170) cc_final: 0.6666 (ttp-170) REVERT: I 698 ASP cc_start: 0.8639 (m-30) cc_final: 0.8388 (m-30) REVERT: I 711 GLU cc_start: 0.9065 (pm20) cc_final: 0.8619 (pm20) REVERT: J 49 ILE cc_start: 0.8711 (OUTLIER) cc_final: 0.8466 (tt) REVERT: J 54 LYS cc_start: 0.7719 (tmmt) cc_final: 0.7464 (tmtt) REVERT: J 123 LEU cc_start: 0.9059 (mp) cc_final: 0.8739 (mt) REVERT: J 456 MET cc_start: 0.4975 (ttp) cc_final: 0.4115 (ttt) REVERT: J 481 MET cc_start: 0.8847 (tmm) cc_final: 0.8519 (ttt) REVERT: K 59 ASN cc_start: 0.7474 (t0) cc_final: 0.7097 (t0) REVERT: K 89 MET cc_start: 0.6419 (mtt) cc_final: 0.5404 (tpp) outliers start: 34 outliers final: 20 residues processed: 211 average time/residue: 0.4027 time to fit residues: 129.0615 Evaluate side-chains 192 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 170 time to evaluate : 2.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 74 ASP Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain I residue 21 ILE 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 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 564 MET Chi-restraints excluded: chain I residue 865 THR Chi-restraints excluded: chain I residue 995 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 676 MET Chi-restraints excluded: chain J residue 778 LEU 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 249 optimal weight: 6.9990 chunk 81 optimal weight: 9.9990 chunk 263 optimal weight: 5.9990 chunk 251 optimal weight: 3.9990 chunk 274 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 262 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 152 optimal weight: 5.9990 chunk 209 optimal weight: 4.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 229 GLN H 38 ASN ** H 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 762 GLN ** J1364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.090035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.060709 restraints weight = 67527.326| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 3.54 r_work: 0.2851 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.098 25231 Z= 0.265 Angle : 0.664 9.391 34456 Z= 0.336 Chirality : 0.045 0.182 3906 Planarity : 0.005 0.050 4246 Dihedral : 14.826 129.804 4101 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 2.25 % Allowed : 13.73 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.16), residues: 2905 helix: 0.87 (0.17), residues: 1007 sheet: -0.44 (0.25), residues: 409 loop : -0.96 (0.16), residues: 1489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP J 511 HIS 0.007 0.001 HIS I 141 PHE 0.019 0.002 PHE J 806 TYR 0.033 0.002 TYR J1207 ARG 0.010 0.001 ARG I1031 Details of bonding type rmsd hydrogen bonds : bond 0.05517 ( 1031) hydrogen bonds : angle 4.65920 ( 2786) metal coordination : bond 0.01607 ( 4) metal coordination : angle 3.59623 ( 6) covalent geometry : bond 0.00609 (25227) covalent geometry : angle 0.66266 (34450) *********************** 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 227 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 171 time to evaluate : 2.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 84 GLU cc_start: 0.9187 (mt-10) cc_final: 0.8956 (mp0) REVERT: I 82 GLU cc_start: 0.9176 (OUTLIER) cc_final: 0.8769 (pm20) REVERT: I 184 MET cc_start: 0.7660 (tmm) cc_final: 0.7419 (tmm) REVERT: I 209 ARG cc_start: 0.9112 (ptm-80) cc_final: 0.8677 (tmm-80) REVERT: I 219 GLN cc_start: 0.9010 (mp10) cc_final: 0.8692 (mp10) REVERT: I 1003 ASP cc_start: 0.5051 (OUTLIER) cc_final: 0.1264 (t70) REVERT: J 49 ILE cc_start: 0.8816 (OUTLIER) cc_final: 0.8547 (tt) REVERT: J 54 LYS cc_start: 0.7692 (tmmt) cc_final: 0.7427 (tmtt) REVERT: J 123 LEU cc_start: 0.9071 (mp) cc_final: 0.8737 (mp) REVERT: J 481 MET cc_start: 0.8888 (tmm) cc_final: 0.8671 (ttt) REVERT: J 1090 ASP cc_start: 0.8674 (m-30) cc_final: 0.8439 (m-30) REVERT: J 1219 GLU cc_start: 0.9164 (tt0) cc_final: 0.8693 (tt0) REVERT: K 59 ASN cc_start: 0.7686 (t0) cc_final: 0.7277 (t0) REVERT: K 89 MET cc_start: 0.6489 (mtt) cc_final: 0.5540 (tpp) outliers start: 56 outliers final: 34 residues processed: 214 average time/residue: 0.3955 time to fit residues: 131.1718 Evaluate side-chains 201 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 164 time to evaluate : 2.523 ------------------------------------------------------------------------------- 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 4 SER Chi-restraints excluded: chain H residue 139 ASN Chi-restraints excluded: chain H residue 172 SER Chi-restraints excluded: chain H residue 181 VAL 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 115 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 317 VAL 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 676 MET Chi-restraints excluded: chain J residue 747 VAL Chi-restraints excluded: chain J residue 762 GLN Chi-restraints excluded: chain J residue 778 LEU Chi-restraints excluded: chain J residue 1415 VAL Chi-restraints excluded: chain J residue 1483 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 98 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 224 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 211 optimal weight: 0.9990 chunk 75 optimal weight: 7.9990 chunk 17 optimal weight: 0.8980 chunk 202 optimal weight: 2.9990 chunk 120 optimal weight: 10.0000 chunk 249 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 575 GLN J 845 ASN ** 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 = 0.3693 r_free = 0.3693 target = 0.091526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.062147 restraints weight = 66775.496| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 3.55 r_work: 0.2886 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2075 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= 0.161 Angle : 0.597 9.637 34456 Z= 0.302 Chirality : 0.043 0.179 3906 Planarity : 0.004 0.045 4246 Dihedral : 14.781 131.711 4101 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 1.85 % Allowed : 15.02 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.16), residues: 2905 helix: 0.95 (0.17), residues: 1006 sheet: -0.40 (0.25), residues: 417 loop : -0.89 (0.16), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J 511 HIS 0.005 0.001 HIS J1075 PHE 0.014 0.001 PHE J 806 TYR 0.028 0.001 TYR J1207 ARG 0.006 0.000 ARG I1031 Details of bonding type rmsd hydrogen bonds : bond 0.05126 ( 1031) hydrogen bonds : angle 4.55546 ( 2786) metal coordination : bond 0.00875 ( 4) metal coordination : angle 3.61539 ( 6) covalent geometry : bond 0.00373 (25227) covalent geometry : angle 0.59485 (34450) *********************** 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 219 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 173 time to evaluate : 2.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 84 GLU cc_start: 0.9179 (mt-10) cc_final: 0.8939 (mp0) REVERT: I 82 GLU cc_start: 0.9186 (OUTLIER) cc_final: 0.8857 (pm20) REVERT: I 184 MET cc_start: 0.7571 (tmm) cc_final: 0.7307 (tmm) REVERT: I 209 ARG cc_start: 0.9152 (ptm-80) cc_final: 0.8723 (tmm-80) REVERT: I 219 GLN cc_start: 0.9005 (mp10) cc_final: 0.8679 (mp10) REVERT: I 275 TYR cc_start: 0.8681 (t80) cc_final: 0.8283 (m-80) REVERT: I 711 GLU cc_start: 0.9045 (pm20) cc_final: 0.8709 (pm20) REVERT: I 1003 ASP cc_start: 0.4924 (OUTLIER) cc_final: 0.0623 (t70) REVERT: J 49 ILE cc_start: 0.8740 (OUTLIER) cc_final: 0.8468 (tt) REVERT: J 54 LYS cc_start: 0.7684 (tmmt) cc_final: 0.7436 (tmtt) REVERT: J 123 LEU cc_start: 0.9048 (mp) cc_final: 0.8714 (mp) REVERT: J 481 MET cc_start: 0.8900 (tmm) cc_final: 0.8565 (ttt) REVERT: J 661 MET cc_start: 0.9190 (ptp) cc_final: 0.8898 (ptp) REVERT: J 1090 ASP cc_start: 0.8666 (m-30) cc_final: 0.8445 (m-30) REVERT: K 59 ASN cc_start: 0.7494 (t0) cc_final: 0.7098 (t0) REVERT: K 89 MET cc_start: 0.6482 (mtt) cc_final: 0.5802 (tpt) outliers start: 46 outliers final: 32 residues processed: 207 average time/residue: 0.4166 time to fit residues: 131.3570 Evaluate side-chains 198 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 163 time to evaluate : 2.642 ------------------------------------------------------------------------------- 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 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 988 VAL Chi-restraints excluded: chain I residue 995 MET Chi-restraints excluded: chain I residue 1003 ASP 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 676 MET Chi-restraints excluded: chain J residue 762 GLN Chi-restraints excluded: chain J residue 778 LEU Chi-restraints excluded: chain J residue 1422 MET Chi-restraints excluded: chain J residue 1466 VAL Chi-restraints excluded: chain J residue 1483 PHE Chi-restraints excluded: chain K residue 15 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 205 optimal weight: 0.9980 chunk 123 optimal weight: 5.9990 chunk 160 optimal weight: 3.9990 chunk 130 optimal weight: 0.0040 chunk 90 optimal weight: 0.2980 chunk 56 optimal weight: 0.6980 chunk 211 optimal weight: 0.9990 chunk 187 optimal weight: 4.9990 chunk 50 optimal weight: 9.9990 chunk 135 optimal weight: 0.9990 chunk 268 optimal weight: 6.9990 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 229 GLN ** H 139 ASN ** 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 = 0.3725 r_free = 0.3725 target = 0.093303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.064052 restraints weight = 67165.454| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 3.57 r_work: 0.2930 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.2090 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= 0.113 Angle : 0.576 12.566 34456 Z= 0.288 Chirality : 0.042 0.181 3906 Planarity : 0.004 0.053 4246 Dihedral : 14.679 136.491 4101 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 1.45 % Allowed : 15.86 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.16), residues: 2905 helix: 1.14 (0.17), residues: 994 sheet: -0.37 (0.26), residues: 408 loop : -0.82 (0.17), residues: 1503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 200 HIS 0.005 0.001 HIS J1075 PHE 0.011 0.001 PHE J 806 TYR 0.024 0.001 TYR J1207 ARG 0.006 0.000 ARG I1031 Details of bonding type rmsd hydrogen bonds : bond 0.04847 ( 1031) hydrogen bonds : angle 4.41741 ( 2786) metal coordination : bond 0.00353 ( 4) metal coordination : angle 3.85091 ( 6) covalent geometry : bond 0.00259 (25227) covalent geometry : angle 0.57383 (34450) *********************** 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 207 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 171 time to evaluate : 2.675 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: G 84 GLU cc_start: 0.9179 (mt-10) cc_final: 0.8930 (mp0) REVERT: G 163 ASN cc_start: 0.8853 (m-40) cc_final: 0.8614 (t0) REVERT: H 84 GLU cc_start: 0.8638 (mp0) cc_final: 0.8352 (mp0) REVERT: I 82 GLU cc_start: 0.9193 (OUTLIER) cc_final: 0.8897 (pm20) REVERT: I 184 MET cc_start: 0.7518 (tmm) cc_final: 0.7248 (tmm) REVERT: I 209 ARG cc_start: 0.9165 (ptm-80) cc_final: 0.8735 (tmm-80) REVERT: I 219 GLN cc_start: 0.8991 (mp10) cc_final: 0.8651 (mp10) REVERT: I 275 TYR cc_start: 0.8653 (t80) cc_final: 0.8366 (m-10) REVERT: I 321 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.6743 (mt-10) REVERT: I 711 GLU cc_start: 0.9063 (pm20) cc_final: 0.8692 (pm20) REVERT: I 1003 ASP cc_start: 0.4853 (OUTLIER) cc_final: 0.0646 (t70) REVERT: J 49 ILE cc_start: 0.8717 (OUTLIER) cc_final: 0.8467 (tt) REVERT: J 54 LYS cc_start: 0.7614 (tmmt) cc_final: 0.7373 (tmtt) REVERT: J 481 MET cc_start: 0.8883 (tmm) cc_final: 0.8524 (ttt) REVERT: J 661 MET cc_start: 0.9137 (ptp) cc_final: 0.8834 (ptp) REVERT: K 8 LYS cc_start: 0.8525 (pttt) cc_final: 0.8281 (pttm) REVERT: K 59 ASN cc_start: 0.7401 (t0) cc_final: 0.7047 (t0) REVERT: K 89 MET cc_start: 0.6607 (mtt) cc_final: 0.5916 (tpt) outliers start: 36 outliers final: 29 residues processed: 199 average time/residue: 0.4042 time to fit residues: 124.1854 Evaluate side-chains 195 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 162 time to evaluate : 2.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 120 VAL 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 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 321 GLU Chi-restraints excluded: chain I residue 464 LEU Chi-restraints excluded: chain I residue 514 VAL Chi-restraints excluded: chain I residue 560 MET Chi-restraints excluded: chain I residue 699 PHE 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 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 762 GLN Chi-restraints excluded: chain J residue 778 LEU Chi-restraints excluded: chain J residue 1422 MET Chi-restraints excluded: chain J residue 1466 VAL Chi-restraints excluded: chain J residue 1468 LEU Chi-restraints excluded: chain J residue 1483 PHE Chi-restraints excluded: chain K residue 15 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 143 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 285 optimal weight: 0.6980 chunk 264 optimal weight: 0.8980 chunk 163 optimal weight: 6.9990 chunk 29 optimal weight: 8.9990 chunk 25 optimal weight: 3.9990 chunk 139 optimal weight: 0.8980 chunk 278 optimal weight: 8.9990 chunk 56 optimal weight: 5.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 762 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 = 0.3693 r_free = 0.3693 target = 0.091501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.062268 restraints weight = 66517.890| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 3.53 r_work: 0.2889 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 25231 Z= 0.182 Angle : 0.605 11.916 34456 Z= 0.302 Chirality : 0.043 0.185 3906 Planarity : 0.004 0.051 4246 Dihedral : 14.667 131.315 4101 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 1.61 % Allowed : 15.70 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.16), residues: 2905 helix: 1.06 (0.17), residues: 1007 sheet: -0.39 (0.25), residues: 419 loop : -0.85 (0.17), residues: 1479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 511 HIS 0.005 0.001 HIS J1075 PHE 0.015 0.001 PHE J 806 TYR 0.028 0.001 TYR J1207 ARG 0.010 0.000 ARG I 284 Details of bonding type rmsd hydrogen bonds : bond 0.04958 ( 1031) hydrogen bonds : angle 4.44631 ( 2786) metal coordination : bond 0.00977 ( 4) metal coordination : angle 3.61514 ( 6) covalent geometry : bond 0.00424 (25227) covalent geometry : angle 0.60298 (34450) *********************** 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: 40 poor density : 163 time to evaluate : 2.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 84 GLU cc_start: 0.9172 (mt-10) cc_final: 0.8939 (mp0) REVERT: G 102 LYS cc_start: 0.8957 (mmpt) cc_final: 0.8630 (mmtt) REVERT: G 163 ASN cc_start: 0.8882 (m-40) cc_final: 0.8644 (t0) REVERT: H 84 GLU cc_start: 0.8658 (mp0) cc_final: 0.7780 (mp0) REVERT: I 82 GLU cc_start: 0.9173 (OUTLIER) cc_final: 0.8885 (pm20) REVERT: I 184 MET cc_start: 0.7439 (tmm) cc_final: 0.7163 (tmm) REVERT: I 209 ARG cc_start: 0.9164 (ptm-80) cc_final: 0.8721 (tmm-80) REVERT: I 219 GLN cc_start: 0.8981 (mp10) cc_final: 0.8639 (mp10) REVERT: I 321 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.6899 (mt-10) REVERT: I 711 GLU cc_start: 0.9065 (pm20) cc_final: 0.8751 (pm20) REVERT: I 1003 ASP cc_start: 0.4900 (OUTLIER) cc_final: 0.0684 (t70) REVERT: J 49 ILE cc_start: 0.8760 (OUTLIER) cc_final: 0.8508 (tt) REVERT: J 54 LYS cc_start: 0.7623 (tmmt) cc_final: 0.7383 (tmtt) REVERT: J 481 MET cc_start: 0.8880 (tmm) cc_final: 0.8564 (ttt) REVERT: J 661 MET cc_start: 0.9208 (ptp) cc_final: 0.8910 (ptp) REVERT: J 1090 ASP cc_start: 0.8621 (m-30) cc_final: 0.8386 (m-30) REVERT: J 1219 GLU cc_start: 0.9161 (tt0) cc_final: 0.8698 (tt0) REVERT: K 89 MET cc_start: 0.6564 (mtt) cc_final: 0.5798 (tpp) outliers start: 40 outliers final: 33 residues processed: 196 average time/residue: 0.4054 time to fit residues: 124.3284 Evaluate side-chains 195 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 158 time to evaluate : 2.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 120 VAL 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 82 GLU Chi-restraints excluded: chain I residue 83 CYS 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 699 PHE 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 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 747 VAL Chi-restraints excluded: chain J residue 762 GLN Chi-restraints excluded: chain J residue 778 LEU Chi-restraints excluded: chain J residue 1415 VAL Chi-restraints excluded: chain J residue 1422 MET Chi-restraints excluded: chain J residue 1466 VAL Chi-restraints excluded: chain J residue 1468 LEU Chi-restraints excluded: chain J residue 1483 PHE Chi-restraints excluded: chain K residue 15 SER Chi-restraints excluded: chain K residue 40 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 221 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 chunk 260 optimal weight: 4.9990 chunk 129 optimal weight: 0.9990 chunk 32 optimal weight: 10.0000 chunk 30 optimal weight: 0.2980 chunk 91 optimal weight: 0.9990 chunk 22 optimal weight: 0.1980 chunk 13 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 157 optimal weight: 2.9990 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 188 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 = 0.3719 r_free = 0.3719 target = 0.092981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.063826 restraints weight = 66737.765| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 3.55 r_work: 0.2927 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25231 Z= 0.114 Angle : 0.573 12.565 34456 Z= 0.286 Chirality : 0.042 0.183 3906 Planarity : 0.004 0.051 4246 Dihedral : 14.630 133.835 4101 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 1.85 % Allowed : 15.46 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.16), residues: 2905 helix: 1.13 (0.17), residues: 1004 sheet: -0.31 (0.26), residues: 394 loop : -0.80 (0.16), residues: 1507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 200 HIS 0.005 0.001 HIS K 33 PHE 0.014 0.001 PHE I 227 TYR 0.027 0.001 TYR J 450 ARG 0.006 0.000 ARG I 8 Details of bonding type rmsd hydrogen bonds : bond 0.04767 ( 1031) hydrogen bonds : angle 4.38186 ( 2786) metal coordination : bond 0.00378 ( 4) metal coordination : angle 3.67463 ( 6) covalent geometry : bond 0.00265 (25227) covalent geometry : angle 0.57066 (34450) *********************** 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 212 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 166 time to evaluate : 2.782 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: G 84 GLU cc_start: 0.9172 (mt-10) cc_final: 0.8931 (mp0) REVERT: G 163 ASN cc_start: 0.8857 (m-40) cc_final: 0.8597 (t0) REVERT: H 84 GLU cc_start: 0.8591 (mp0) cc_final: 0.7855 (mp0) REVERT: I 82 GLU cc_start: 0.9184 (OUTLIER) cc_final: 0.8883 (pm20) REVERT: I 184 MET cc_start: 0.7421 (tmm) cc_final: 0.7147 (tmm) REVERT: I 209 ARG cc_start: 0.9167 (ptm-80) cc_final: 0.8722 (tmm-80) REVERT: I 219 GLN cc_start: 0.8979 (mp10) cc_final: 0.8637 (mp10) REVERT: I 275 TYR cc_start: 0.8648 (t80) cc_final: 0.8350 (m-80) REVERT: I 321 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.6646 (mt-10) REVERT: I 1003 ASP cc_start: 0.4859 (OUTLIER) cc_final: 0.0647 (t70) REVERT: J 49 ILE cc_start: 0.8735 (OUTLIER) cc_final: 0.8489 (tt) REVERT: J 54 LYS cc_start: 0.7620 (tmmt) cc_final: 0.7385 (tmtt) REVERT: J 456 MET cc_start: 0.5221 (ttp) cc_final: 0.4257 (ttt) REVERT: J 481 MET cc_start: 0.8907 (tmm) cc_final: 0.8445 (ttt) REVERT: J 661 MET cc_start: 0.9158 (ptp) cc_final: 0.8858 (ptp) REVERT: J 1219 GLU cc_start: 0.9126 (tt0) cc_final: 0.8606 (tt0) REVERT: K 8 LYS cc_start: 0.8559 (pttt) cc_final: 0.8322 (pttm) REVERT: K 89 MET cc_start: 0.6847 (mtt) cc_final: 0.5960 (tpp) outliers start: 46 outliers final: 38 residues processed: 202 average time/residue: 0.3944 time to fit residues: 123.1167 Evaluate side-chains 204 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 162 time to evaluate : 2.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 120 VAL Chi-restraints excluded: chain H residue 140 MET 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 107 LEU Chi-restraints excluded: chain I residue 115 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 699 PHE 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 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 623 VAL Chi-restraints excluded: chain J residue 747 VAL Chi-restraints excluded: chain J residue 762 GLN Chi-restraints excluded: chain J residue 778 LEU Chi-restraints excluded: chain J residue 1415 VAL Chi-restraints excluded: chain J residue 1422 MET Chi-restraints excluded: chain J residue 1466 VAL Chi-restraints excluded: chain J residue 1468 LEU Chi-restraints excluded: chain J residue 1483 PHE Chi-restraints excluded: chain K residue 15 SER Chi-restraints excluded: chain K residue 40 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 199 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 6 optimal weight: 6.9990 chunk 113 optimal weight: 0.7980 chunk 127 optimal weight: 2.9990 chunk 117 optimal weight: 0.0060 chunk 157 optimal weight: 1.9990 chunk 31 optimal weight: 0.0970 chunk 67 optimal weight: 9.9990 chunk 79 optimal weight: 6.9990 chunk 168 optimal weight: 2.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 188 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 = 0.3738 r_free = 0.3738 target = 0.093969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.064873 restraints weight = 66938.148| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 3.58 r_work: 0.2950 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 25231 Z= 0.108 Angle : 0.570 14.063 34456 Z= 0.283 Chirality : 0.041 0.181 3906 Planarity : 0.004 0.070 4246 Dihedral : 14.544 135.716 4101 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 1.45 % Allowed : 15.94 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.16), residues: 2905 helix: 1.26 (0.17), residues: 997 sheet: -0.27 (0.26), residues: 394 loop : -0.74 (0.17), residues: 1514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 63 HIS 0.005 0.001 HIS K 33 PHE 0.011 0.001 PHE H 65 TYR 0.031 0.001 TYR J 450 ARG 0.007 0.000 ARG J1388 Details of bonding type rmsd hydrogen bonds : bond 0.04629 ( 1031) hydrogen bonds : angle 4.30010 ( 2786) metal coordination : bond 0.00306 ( 4) metal coordination : angle 3.75083 ( 6) covalent geometry : bond 0.00249 (25227) covalent geometry : angle 0.56772 (34450) ********************** 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 211 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 175 time to evaluate : 2.627 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: G 84 GLU cc_start: 0.9154 (mt-10) cc_final: 0.8863 (mp0) REVERT: G 163 ASN cc_start: 0.8855 (m-40) cc_final: 0.8583 (t0) REVERT: G 175 ARG cc_start: 0.8617 (ttp-110) cc_final: 0.8179 (mtt90) REVERT: H 84 GLU cc_start: 0.8504 (mp0) cc_final: 0.7706 (mp0) REVERT: I 82 GLU cc_start: 0.9213 (OUTLIER) cc_final: 0.8915 (pm20) REVERT: I 184 MET cc_start: 0.7449 (tmm) cc_final: 0.7163 (tmm) REVERT: I 209 ARG cc_start: 0.9171 (ptm-80) cc_final: 0.8727 (tmm-80) REVERT: I 219 GLN cc_start: 0.8976 (mp10) cc_final: 0.8632 (mp10) REVERT: I 275 TYR cc_start: 0.8637 (t80) cc_final: 0.8360 (m-80) REVERT: I 321 GLU cc_start: 0.7434 (OUTLIER) cc_final: 0.6400 (mt-10) REVERT: I 422 ARG cc_start: 0.8003 (ptt180) cc_final: 0.7237 (ptt90) REVERT: I 1003 ASP cc_start: 0.4892 (OUTLIER) cc_final: 0.0878 (t70) REVERT: J 49 ILE cc_start: 0.8738 (OUTLIER) cc_final: 0.8488 (tt) REVERT: J 54 LYS cc_start: 0.7688 (tmmt) cc_final: 0.7446 (tmtt) REVERT: J 456 MET cc_start: 0.5088 (ttp) cc_final: 0.4134 (ttt) REVERT: J 481 MET cc_start: 0.8909 (tmm) cc_final: 0.8633 (ttt) REVERT: J 661 MET cc_start: 0.9145 (ptp) cc_final: 0.8844 (ptp) REVERT: J 1219 GLU cc_start: 0.9133 (tt0) cc_final: 0.8652 (tt0) REVERT: K 8 LYS cc_start: 0.8570 (pttt) cc_final: 0.8336 (pttm) REVERT: K 32 ARG cc_start: 0.8066 (tmm-80) cc_final: 0.7303 (ptm-80) REVERT: K 89 MET cc_start: 0.6646 (mtt) cc_final: 0.5724 (tpt) outliers start: 36 outliers final: 30 residues processed: 205 average time/residue: 0.4078 time to fit residues: 128.6793 Evaluate side-chains 203 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 169 time to evaluate : 2.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 120 VAL Chi-restraints excluded: chain H residue 140 MET 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 82 GLU Chi-restraints excluded: chain I residue 83 CYS Chi-restraints excluded: chain I residue 115 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 699 PHE Chi-restraints excluded: chain I residue 865 THR Chi-restraints excluded: chain I residue 988 VAL Chi-restraints excluded: chain I residue 1003 ASP 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 126 VAL 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 1422 MET Chi-restraints excluded: chain J residue 1466 VAL Chi-restraints excluded: chain J residue 1468 LEU Chi-restraints excluded: chain J residue 1483 PHE Chi-restraints excluded: chain K residue 15 SER Chi-restraints excluded: chain K residue 40 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 19 optimal weight: 2.9990 chunk 207 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 125 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 272 optimal weight: 0.9990 chunk 86 optimal weight: 7.9990 chunk 209 optimal weight: 2.9990 chunk 155 optimal weight: 0.9980 chunk 132 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 204 GLN ** J1364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J1367 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.093084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.063913 restraints weight = 66758.225| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 3.55 r_work: 0.2926 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25231 Z= 0.129 Angle : 0.579 13.542 34456 Z= 0.288 Chirality : 0.042 0.181 3906 Planarity : 0.004 0.056 4246 Dihedral : 14.518 132.825 4101 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 1.45 % Allowed : 16.14 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.16), residues: 2905 helix: 1.18 (0.17), residues: 1010 sheet: -0.24 (0.26), residues: 404 loop : -0.73 (0.17), residues: 1491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J 511 HIS 0.005 0.001 HIS J1075 PHE 0.015 0.001 PHE I 227 TYR 0.030 0.001 TYR J 450 ARG 0.006 0.000 ARG I1031 Details of bonding type rmsd hydrogen bonds : bond 0.04682 ( 1031) hydrogen bonds : angle 4.30539 ( 2786) metal coordination : bond 0.00546 ( 4) metal coordination : angle 3.60165 ( 6) covalent geometry : bond 0.00301 (25227) covalent geometry : angle 0.57700 (34450) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11848.67 seconds wall clock time: 205 minutes 28.75 seconds (12328.75 seconds total)