Starting phenix.real_space_refine on Sat Jun 21 14:31:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hsg_34996/06_2025/8hsg_34996.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hsg_34996/06_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_34996/06_2025/8hsg_34996.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hsg_34996/06_2025/8hsg_34996.map" model { file = "/net/cci-nas-00/data/ceres_data/8hsg_34996/06_2025/8hsg_34996.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hsg_34996/06_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): 0.75s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 15.07, per 1000 atoms: 0.61 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: 6.10 Conformation dependent library (CDL) restraints added in 3.1 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: 9.56 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: 14.73 Time building geometry restraints manager: 7.23 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: 2.500 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: 0.040 Extract box with map and model: 1.060 Check model and map are aligned: 0.180 Set scattering table: 0.220 Process input model: 72.970 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.120 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.540 ------------------------------------------------------------------------------- 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 : 2.721 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: 0.4006 time to fit residues: 142.5851 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 : 2.673 ------------------------------------------------------------------------------- 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 = 0.3719 r_free = 0.3719 target = 0.092854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.063711 restraints weight = 67204.017| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 3.59 r_work: 0.2926 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.2926 ------------------------------------------------------------------------------- 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 : 2.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 102 LYS cc_start: 0.9142 (mmpt) cc_final: 0.8760 (mmmt) REVERT: H 4 SER cc_start: 0.6906 (m) cc_final: 0.6554 (p) REVERT: H 84 GLU cc_start: 0.8364 (mp0) cc_final: 0.8084 (mp0) REVERT: I 219 GLN cc_start: 0.9014 (mp10) cc_final: 0.8494 (mp10) REVERT: I 275 TYR cc_start: 0.8715 (OUTLIER) cc_final: 0.8113 (m-80) REVERT: I 338 GLU cc_start: 0.8395 (tp30) cc_final: 0.7993 (tp30) REVERT: I 420 ARG cc_start: 0.7354 (ttp-170) cc_final: 0.6701 (ttp-170) REVERT: I 711 GLU cc_start: 0.9072 (pm20) cc_final: 0.8643 (pm20) REVERT: J 127 LEU cc_start: 0.9261 (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: 0.7788 (t0) cc_final: 0.7288 (t0) REVERT: K 72 ARG cc_start: 0.8456 (mpt-90) cc_final: 0.8244 (mtt-85) REVERT: K 89 MET cc_start: 0.5841 (tpt) cc_final: 0.5139 (mtt) outliers start: 18 outliers final: 12 residues processed: 202 average time/residue: 0.4320 time to fit residues: 133.4566 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 : 3.857 ------------------------------------------------------------------------------- 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: 1.9990 chunk 114 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 chunk 199 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 I 45 GLN J 762 GLN ** J1364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.092627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.063377 restraints weight = 67135.217| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 3.57 r_work: 0.2916 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 25231 Z= 0.177 Angle : 0.601 9.809 34456 Z= 0.305 Chirality : 0.043 0.158 3906 Planarity : 0.005 0.050 4246 Dihedral : 14.789 141.407 4101 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 1.41 % Allowed : 10.87 % Favored : 87.72 % 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: -0.31 (0.16), residues: 2905 helix: 0.89 (0.17), residues: 1011 sheet: -0.38 (0.26), residues: 385 loop : -0.89 (0.16), residues: 1509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J 511 HIS 0.006 0.001 HIS I 141 PHE 0.013 0.001 PHE J 806 TYR 0.027 0.001 TYR J1207 ARG 0.004 0.000 ARG I1031 Details of bonding type rmsd hydrogen bonds : bond 0.05285 ( 1031) hydrogen bonds : angle 4.62660 ( 2786) metal coordination : bond 0.01054 ( 4) metal coordination : angle 3.52290 ( 6) covalent geometry : bond 0.00407 (25227) covalent geometry : angle 0.59932 (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 213 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 178 time to evaluate : 2.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 102 LYS cc_start: 0.9135 (mmpt) cc_final: 0.8712 (mmmt) REVERT: H 4 SER cc_start: 0.6673 (m) cc_final: 0.6397 (p) REVERT: H 84 GLU cc_start: 0.8453 (mp0) cc_final: 0.8094 (mp0) REVERT: I 184 MET cc_start: 0.7481 (tmm) cc_final: 0.7281 (tmm) REVERT: I 209 ARG cc_start: 0.9161 (ptm-80) cc_final: 0.8744 (tmm-80) REVERT: I 219 GLN cc_start: 0.9004 (mp10) cc_final: 0.8470 (mp10) REVERT: I 275 TYR cc_start: 0.8734 (t80) cc_final: 0.8154 (m-10) REVERT: I 420 ARG cc_start: 0.7453 (ttp-170) cc_final: 0.6711 (ttp-170) REVERT: I 711 GLU cc_start: 0.9055 (pm20) cc_final: 0.8600 (pm20) REVERT: J 49 ILE cc_start: 0.8741 (OUTLIER) cc_final: 0.8474 (tt) REVERT: J 54 LYS cc_start: 0.7725 (tmmt) cc_final: 0.7464 (tmtt) REVERT: J 481 MET cc_start: 0.8827 (tmm) cc_final: 0.8533 (ttt) REVERT: J 1482 ARG cc_start: 0.8446 (ttp80) cc_final: 0.8212 (ttm-80) REVERT: J 1483 PHE cc_start: 0.8685 (OUTLIER) cc_final: 0.7750 (p90) REVERT: K 8 LYS cc_start: 0.8700 (ptpt) cc_final: 0.8457 (pttt) REVERT: K 59 ASN cc_start: 0.7602 (t0) cc_final: 0.7145 (t0) REVERT: K 89 MET cc_start: 0.5552 (tpt) cc_final: 0.5188 (mtt) outliers start: 35 outliers final: 25 residues processed: 202 average time/residue: 0.4362 time to fit residues: 136.8911 Evaluate side-chains 198 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 171 time to evaluate : 3.070 ------------------------------------------------------------------------------- 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 J residue 1483 PHE 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: 3.9990 chunk 77 optimal weight: 3.9990 chunk 72 optimal weight: 0.3980 chunk 188 optimal weight: 0.7980 chunk 193 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 169 optimal weight: 20.0000 chunk 107 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 226 optimal weight: 2.9990 chunk 217 optimal weight: 5.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 229 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 = 0.3714 r_free = 0.3714 target = 0.092549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.063360 restraints weight = 67104.440| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 3.57 r_work: 0.2918 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 25231 Z= 0.152 Angle : 0.580 9.517 34456 Z= 0.293 Chirality : 0.042 0.157 3906 Planarity : 0.004 0.042 4246 Dihedral : 14.760 140.456 4101 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 1.69 % Allowed : 12.52 % Favored : 85.79 % 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: -0.24 (0.16), residues: 2905 helix: 0.99 (0.17), residues: 1010 sheet: -0.36 (0.26), residues: 385 loop : -0.88 (0.16), residues: 1510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J 511 HIS 0.005 0.001 HIS J1075 PHE 0.014 0.001 PHE I 114 TYR 0.026 0.001 TYR J1207 ARG 0.006 0.000 ARG J 679 Details of bonding type rmsd hydrogen bonds : bond 0.05104 ( 1031) hydrogen bonds : angle 4.53357 ( 2786) metal coordination : bond 0.00813 ( 4) metal coordination : angle 3.55969 ( 6) covalent geometry : bond 0.00353 (25227) covalent geometry : angle 0.57806 (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 224 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 182 time to evaluate : 2.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 84 GLU cc_start: 0.9155 (mt-10) cc_final: 0.8929 (mp0) REVERT: G 102 LYS cc_start: 0.9092 (mmpt) cc_final: 0.8687 (mmmt) REVERT: G 163 ASN cc_start: 0.8849 (m-40) cc_final: 0.8623 (t0) REVERT: H 4 SER cc_start: 0.6505 (m) cc_final: 0.6300 (p) REVERT: H 84 GLU cc_start: 0.8447 (mp0) cc_final: 0.8070 (mp0) REVERT: I 82 GLU cc_start: 0.9218 (OUTLIER) cc_final: 0.8848 (pm20) REVERT: I 184 MET cc_start: 0.7574 (tmm) cc_final: 0.7179 (tmm) REVERT: I 209 ARG cc_start: 0.9111 (ptm-80) cc_final: 0.8695 (tmm-80) REVERT: I 219 GLN cc_start: 0.9031 (mp10) cc_final: 0.8705 (mp10) REVERT: I 275 TYR cc_start: 0.8735 (t80) cc_final: 0.8264 (m-10) REVERT: I 420 ARG cc_start: 0.7332 (ttp-170) cc_final: 0.6643 (ttp-170) REVERT: I 711 GLU cc_start: 0.9055 (pm20) cc_final: 0.8604 (pm20) REVERT: J 49 ILE cc_start: 0.8742 (OUTLIER) cc_final: 0.8487 (tt) REVERT: J 54 LYS cc_start: 0.7723 (tmmt) cc_final: 0.7462 (tmtt) REVERT: J 123 LEU cc_start: 0.9074 (mp) cc_final: 0.8758 (mt) REVERT: J 481 MET cc_start: 0.8850 (tmm) cc_final: 0.8581 (ttt) REVERT: K 59 ASN cc_start: 0.7526 (t0) cc_final: 0.7140 (t0) outliers start: 42 outliers final: 28 residues processed: 211 average time/residue: 0.4101 time to fit residues: 133.3953 Evaluate side-chains 202 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 172 time to evaluate : 2.991 ------------------------------------------------------------------------------- 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 229 GLN Chi-restraints excluded: chain H residue 172 SER Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 82 GLU Chi-restraints excluded: chain I residue 83 CYS Chi-restraints excluded: chain I residue 102 HIS Chi-restraints excluded: chain I residue 107 LEU 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 560 MET Chi-restraints excluded: chain I residue 564 MET Chi-restraints excluded: chain I residue 865 THR Chi-restraints excluded: chain I residue 988 VAL Chi-restraints excluded: chain I residue 995 MET Chi-restraints excluded: chain I residue 1005 MET Chi-restraints excluded: chain I residue 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 J residue 1483 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 249 optimal weight: 5.9990 chunk 81 optimal weight: 0.6980 chunk 263 optimal weight: 0.0060 chunk 251 optimal weight: 3.9990 chunk 274 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 91 optimal weight: 0.5980 chunk 262 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 chunk 152 optimal weight: 0.0980 chunk 209 optimal weight: 0.0870 overall best weight: 0.2974 ------------------------------------------------------------------------------- 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** ** J1364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.094592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.065484 restraints weight = 67328.606| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 3.60 r_work: 0.2968 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 25231 Z= 0.104 Angle : 0.559 9.531 34456 Z= 0.280 Chirality : 0.042 0.154 3906 Planarity : 0.004 0.047 4246 Dihedral : 14.673 143.411 4101 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 1.41 % Allowed : 13.93 % Favored : 84.66 % 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: -0.07 (0.16), residues: 2905 helix: 1.12 (0.17), residues: 1003 sheet: -0.25 (0.27), residues: 379 loop : -0.77 (0.16), residues: 1523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 63 HIS 0.010 0.001 HIS K 33 PHE 0.010 0.001 PHE I 114 TYR 0.022 0.001 TYR J1207 ARG 0.008 0.000 ARG I1031 Details of bonding type rmsd hydrogen bonds : bond 0.04848 ( 1031) hydrogen bonds : angle 4.40743 ( 2786) metal coordination : bond 0.00311 ( 4) metal coordination : angle 3.69786 ( 6) covalent geometry : bond 0.00235 (25227) covalent geometry : angle 0.55741 (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: 35 poor density : 192 time to evaluate : 2.730 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: 0.9153 (mt-10) cc_final: 0.8861 (mp0) REVERT: G 102 LYS cc_start: 0.9074 (mmpt) cc_final: 0.8825 (mmtt) REVERT: G 163 ASN cc_start: 0.8870 (m-40) cc_final: 0.8629 (t0) REVERT: G 175 ARG cc_start: 0.8562 (ttp-110) cc_final: 0.8204 (mtt90) REVERT: I 82 GLU cc_start: 0.9212 (OUTLIER) cc_final: 0.8852 (pm20) REVERT: I 184 MET cc_start: 0.7498 (tmm) cc_final: 0.7053 (tmm) REVERT: I 209 ARG cc_start: 0.9123 (ptm-80) cc_final: 0.8704 (tmm-80) REVERT: I 219 GLN cc_start: 0.9012 (mp10) cc_final: 0.8792 (mp10) REVERT: I 275 TYR cc_start: 0.8651 (t80) cc_final: 0.8346 (m-10) REVERT: I 420 ARG cc_start: 0.7232 (ttp-170) cc_final: 0.6624 (ttp-170) REVERT: I 711 GLU cc_start: 0.9089 (pm20) cc_final: 0.8642 (pm20) REVERT: I 1003 ASP cc_start: 0.5067 (OUTLIER) cc_final: 0.0990 (t70) REVERT: J 49 ILE cc_start: 0.8681 (OUTLIER) cc_final: 0.8423 (tt) REVERT: J 54 LYS cc_start: 0.7693 (tmmt) cc_final: 0.7437 (tmtt) REVERT: J 123 LEU cc_start: 0.9054 (mp) cc_final: 0.8837 (mp) REVERT: J 456 MET cc_start: 0.4851 (ttp) cc_final: 0.3994 (ttt) REVERT: J 481 MET cc_start: 0.8866 (tmm) cc_final: 0.8401 (ttt) REVERT: K 8 LYS cc_start: 0.8381 (pttt) cc_final: 0.8135 (pttm) REVERT: K 59 ASN cc_start: 0.7320 (t0) cc_final: 0.7003 (t0) REVERT: K 89 MET cc_start: 0.6014 (tpt) cc_final: 0.5632 (mtt) outliers start: 35 outliers final: 17 residues processed: 220 average time/residue: 0.4145 time to fit residues: 140.5482 Evaluate side-chains 191 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 171 time to evaluate : 2.720 ------------------------------------------------------------------------------- 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 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 307 LEU Chi-restraints excluded: chain I residue 464 LEU Chi-restraints excluded: chain I residue 564 MET Chi-restraints excluded: chain I residue 865 THR 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 127 LEU Chi-restraints excluded: chain J residue 762 GLN 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: 2.9990 chunk 39 optimal weight: 3.9990 chunk 224 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 211 optimal weight: 0.5980 chunk 75 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 202 optimal weight: 4.9990 chunk 120 optimal weight: 10.0000 chunk 249 optimal weight: 6.9990 chunk 66 optimal weight: 5.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- 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** J 762 GLN J 845 ASN ** J1364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 33 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.091214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.061944 restraints weight = 66799.141| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 3.54 r_work: 0.2883 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 25231 Z= 0.223 Angle : 0.631 11.757 34456 Z= 0.318 Chirality : 0.044 0.181 3906 Planarity : 0.005 0.060 4246 Dihedral : 14.733 132.783 4101 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 1.85 % Allowed : 14.49 % Favored : 83.66 % 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: -0.23 (0.16), residues: 2905 helix: 0.97 (0.17), residues: 1009 sheet: -0.34 (0.25), residues: 423 loop : -0.87 (0.16), residues: 1473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP J 511 HIS 0.005 0.001 HIS I 141 PHE 0.016 0.001 PHE J 806 TYR 0.031 0.001 TYR J1207 ARG 0.009 0.000 ARG I1031 Details of bonding type rmsd hydrogen bonds : bond 0.05213 ( 1031) hydrogen bonds : angle 4.50801 ( 2786) metal coordination : bond 0.01308 ( 4) metal coordination : angle 3.53205 ( 6) covalent geometry : bond 0.00520 (25227) covalent geometry : angle 0.62928 (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 216 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 170 time to evaluate : 2.981 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: 0.9196 (mt-10) cc_final: 0.8954 (mp0) REVERT: I 82 GLU cc_start: 0.9181 (OUTLIER) cc_final: 0.8857 (pm20) REVERT: I 209 ARG cc_start: 0.9117 (ptm-80) cc_final: 0.8682 (tmm-80) REVERT: I 219 GLN cc_start: 0.8992 (mp10) cc_final: 0.8657 (mp10) REVERT: I 420 ARG cc_start: 0.7382 (ttp-170) cc_final: 0.6520 (ttp-170) REVERT: I 1003 ASP cc_start: 0.5080 (OUTLIER) cc_final: 0.0884 (t70) REVERT: J 49 ILE cc_start: 0.8811 (OUTLIER) cc_final: 0.8555 (tt) REVERT: J 54 LYS cc_start: 0.7671 (tmmt) cc_final: 0.7406 (tmtt) REVERT: J 123 LEU cc_start: 0.9066 (mp) cc_final: 0.8742 (mp) REVERT: J 481 MET cc_start: 0.8878 (tmm) cc_final: 0.8599 (ttt) REVERT: J 1090 ASP cc_start: 0.8624 (m-30) cc_final: 0.8393 (m-30) REVERT: K 59 ASN cc_start: 0.7556 (t0) cc_final: 0.7179 (t0) REVERT: K 89 MET cc_start: 0.5994 (tpt) cc_final: 0.5792 (mtt) outliers start: 46 outliers final: 34 residues processed: 203 average time/residue: 0.4158 time to fit residues: 130.3823 Evaluate side-chains 204 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 167 time to evaluate : 2.727 ------------------------------------------------------------------------------- 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 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 102 HIS 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 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 127 LEU 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 1466 VAL Chi-restraints excluded: chain J residue 1483 PHE Chi-restraints excluded: chain K residue 31 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 205 optimal weight: 1.9990 chunk 123 optimal weight: 7.9990 chunk 160 optimal weight: 3.9990 chunk 130 optimal weight: 0.7980 chunk 90 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 211 optimal weight: 0.7980 chunk 187 optimal weight: 2.9990 chunk 50 optimal weight: 10.0000 chunk 135 optimal weight: 0.7980 chunk 268 optimal weight: 6.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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** I 567 GLN I 575 GLN ** 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 = 0.3705 r_free = 0.3705 target = 0.092161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.062813 restraints weight = 67394.402| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 3.56 r_work: 0.2899 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 25231 Z= 0.154 Angle : 0.592 10.462 34456 Z= 0.298 Chirality : 0.042 0.183 3906 Planarity : 0.004 0.045 4246 Dihedral : 14.715 133.406 4101 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 1.65 % Allowed : 15.10 % Favored : 83.25 % 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: -0.16 (0.16), residues: 2905 helix: 1.09 (0.17), residues: 996 sheet: -0.29 (0.26), residues: 409 loop : -0.86 (0.16), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J 511 HIS 0.005 0.001 HIS J1075 PHE 0.013 0.001 PHE J 806 TYR 0.027 0.001 TYR J1207 ARG 0.005 0.000 ARG I1031 Details of bonding type rmsd hydrogen bonds : bond 0.05004 ( 1031) hydrogen bonds : angle 4.45318 ( 2786) metal coordination : bond 0.00850 ( 4) metal coordination : angle 3.51416 ( 6) covalent geometry : bond 0.00359 (25227) covalent geometry : angle 0.59022 (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 216 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 175 time to evaluate : 3.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 84 GLU cc_start: 0.9169 (mt-10) cc_final: 0.8940 (mp0) REVERT: I 82 GLU cc_start: 0.9204 (OUTLIER) cc_final: 0.8881 (pm20) REVERT: I 209 ARG cc_start: 0.9158 (ptm-80) cc_final: 0.8727 (tmm-80) REVERT: I 219 GLN cc_start: 0.8996 (mp10) cc_final: 0.8661 (mp10) REVERT: I 275 TYR cc_start: 0.8682 (t80) cc_final: 0.8297 (m-10) REVERT: I 420 ARG cc_start: 0.7320 (ttp-170) cc_final: 0.6524 (ttp-170) REVERT: I 711 GLU cc_start: 0.9055 (pm20) cc_final: 0.8715 (pm20) REVERT: I 1003 ASP cc_start: 0.4930 (OUTLIER) cc_final: 0.0715 (t70) REVERT: J 49 ILE cc_start: 0.8756 (OUTLIER) cc_final: 0.8501 (tt) REVERT: J 54 LYS cc_start: 0.7627 (tmmt) cc_final: 0.7367 (tmtt) REVERT: J 123 LEU cc_start: 0.9058 (mp) cc_final: 0.8728 (mp) REVERT: J 481 MET cc_start: 0.8858 (tmm) cc_final: 0.8553 (ttt) REVERT: J 661 MET cc_start: 0.9171 (ptp) cc_final: 0.8932 (ptp) REVERT: J 1090 ASP cc_start: 0.8622 (m-30) cc_final: 0.8388 (m-30) REVERT: K 59 ASN cc_start: 0.7501 (t0) cc_final: 0.7124 (t0) REVERT: K 89 MET cc_start: 0.5756 (tpt) cc_final: 0.5222 (mtt) outliers start: 41 outliers final: 33 residues processed: 208 average time/residue: 0.4227 time to fit residues: 137.0599 Evaluate side-chains 204 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 168 time to evaluate : 2.711 ------------------------------------------------------------------------------- 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 54 THR Chi-restraints excluded: chain H residue 120 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 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 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 127 LEU Chi-restraints excluded: chain J residue 540 LEU 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 1468 LEU Chi-restraints excluded: chain J residue 1483 PHE Chi-restraints excluded: chain K residue 31 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 143 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 285 optimal weight: 0.0870 chunk 264 optimal weight: 0.0770 chunk 163 optimal weight: 6.9990 chunk 29 optimal weight: 8.9990 chunk 25 optimal weight: 3.9990 chunk 139 optimal weight: 4.9990 chunk 278 optimal weight: 7.9990 chunk 56 optimal weight: 2.9990 overall best weight: 1.0320 ------------------------------------------------------------------------------- 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** ** 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 = 0.3715 r_free = 0.3715 target = 0.092777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.063653 restraints weight = 66448.780| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 3.54 r_work: 0.2920 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.2134 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= 0.128 Angle : 0.582 11.026 34456 Z= 0.291 Chirality : 0.042 0.182 3906 Planarity : 0.004 0.065 4246 Dihedral : 14.649 134.172 4101 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 1.61 % Allowed : 15.46 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (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: -0.09 (0.16), residues: 2905 helix: 1.16 (0.17), residues: 995 sheet: -0.32 (0.26), residues: 415 loop : -0.80 (0.17), residues: 1495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 200 HIS 0.005 0.001 HIS J1075 PHE 0.011 0.001 PHE J 806 TYR 0.025 0.001 TYR J1207 ARG 0.017 0.000 ARG I 284 Details of bonding type rmsd hydrogen bonds : bond 0.04831 ( 1031) hydrogen bonds : angle 4.37764 ( 2786) metal coordination : bond 0.00563 ( 4) metal coordination : angle 3.52790 ( 6) covalent geometry : bond 0.00299 (25227) covalent geometry : angle 0.57997 (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 212 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 172 time to evaluate : 3.462 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: 0.9170 (mt-10) cc_final: 0.8927 (mp0) REVERT: G 102 LYS cc_start: 0.9001 (mmpt) cc_final: 0.8679 (mmtt) REVERT: G 163 ASN cc_start: 0.8822 (m-40) cc_final: 0.8569 (t0) REVERT: G 229 GLN cc_start: 0.8452 (OUTLIER) cc_final: 0.8173 (pm20) REVERT: H 57 TYR cc_start: 0.9183 (t80) cc_final: 0.8977 (t80) REVERT: H 84 GLU cc_start: 0.8623 (mp0) cc_final: 0.7911 (mp0) REVERT: I 82 GLU cc_start: 0.9188 (OUTLIER) cc_final: 0.8884 (pm20) REVERT: I 219 GLN cc_start: 0.9002 (mp10) cc_final: 0.8661 (mp10) REVERT: I 275 TYR cc_start: 0.8639 (t80) cc_final: 0.8338 (m-80) REVERT: I 420 ARG cc_start: 0.7307 (ttp-170) cc_final: 0.6627 (ttp-170) REVERT: I 711 GLU cc_start: 0.9066 (pm20) cc_final: 0.8753 (pm20) REVERT: I 1003 ASP cc_start: 0.4876 (OUTLIER) cc_final: 0.0696 (t70) REVERT: J 49 ILE cc_start: 0.8728 (OUTLIER) cc_final: 0.8481 (tt) REVERT: J 54 LYS cc_start: 0.7617 (tmmt) cc_final: 0.7368 (tmtt) REVERT: J 123 LEU cc_start: 0.9099 (mp) cc_final: 0.8776 (mp) REVERT: J 456 MET cc_start: 0.4605 (ttp) cc_final: 0.3622 (ttt) REVERT: J 481 MET cc_start: 0.8868 (tmm) cc_final: 0.8508 (ttt) REVERT: J 661 MET cc_start: 0.9158 (ptp) cc_final: 0.8914 (ptp) REVERT: K 8 LYS cc_start: 0.8536 (pttt) cc_final: 0.8297 (pttm) REVERT: K 59 ASN cc_start: 0.7421 (t0) cc_final: 0.7077 (t0) REVERT: K 89 MET cc_start: 0.5882 (tpt) cc_final: 0.5525 (mtt) outliers start: 40 outliers final: 33 residues processed: 203 average time/residue: 0.4082 time to fit residues: 128.1609 Evaluate side-chains 204 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 167 time to evaluate : 2.856 ------------------------------------------------------------------------------- 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 54 THR Chi-restraints excluded: chain H residue 120 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 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 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 1052 MET Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain J residue 49 ILE Chi-restraints excluded: chain J residue 125 GLN Chi-restraints excluded: chain J residue 127 LEU Chi-restraints excluded: chain J residue 747 VAL Chi-restraints excluded: chain J residue 778 LEU Chi-restraints excluded: chain J residue 1415 VAL 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: 2.9990 chunk 6 optimal weight: 6.9990 chunk 260 optimal weight: 5.9990 chunk 129 optimal weight: 0.6980 chunk 32 optimal weight: 9.9990 chunk 30 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 22 optimal weight: 0.3980 chunk 13 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 157 optimal weight: 3.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- 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** ** H 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 762 GLN ** J1364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.092006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.062679 restraints weight = 67139.310| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 3.56 r_work: 0.2896 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 25231 Z= 0.162 Angle : 0.597 12.301 34456 Z= 0.299 Chirality : 0.042 0.181 3906 Planarity : 0.004 0.048 4246 Dihedral : 14.639 129.884 4101 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 1.77 % Allowed : 15.42 % Favored : 82.81 % 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: -0.15 (0.16), residues: 2905 helix: 1.08 (0.17), residues: 1007 sheet: -0.35 (0.25), residues: 419 loop : -0.83 (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 0.014 0.001 PHE J 806 TYR 0.028 0.001 TYR J1207 ARG 0.007 0.000 ARG J1388 Details of bonding type rmsd hydrogen bonds : bond 0.04904 ( 1031) hydrogen bonds : angle 4.40220 ( 2786) metal coordination : bond 0.00857 ( 4) metal coordination : angle 3.40803 ( 6) covalent geometry : bond 0.00378 (25227) covalent geometry : angle 0.59581 (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 210 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 166 time to evaluate : 3.050 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: 0.9168 (mt-10) cc_final: 0.8938 (mp0) REVERT: G 163 ASN cc_start: 0.8861 (m-40) cc_final: 0.8602 (t0) REVERT: H 57 TYR cc_start: 0.9195 (t80) cc_final: 0.8957 (t80) REVERT: H 84 GLU cc_start: 0.8624 (mp0) cc_final: 0.8250 (mp0) REVERT: I 82 GLU cc_start: 0.9176 (OUTLIER) cc_final: 0.8887 (pm20) REVERT: I 209 ARG cc_start: 0.9166 (ptm-80) cc_final: 0.8724 (tmm-80) REVERT: I 219 GLN cc_start: 0.8999 (mp10) cc_final: 0.8658 (mp10) REVERT: I 321 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7090 (pt0) REVERT: I 420 ARG cc_start: 0.7437 (ttp-170) cc_final: 0.6674 (ttp-170) REVERT: I 711 GLU cc_start: 0.9059 (pm20) cc_final: 0.8701 (pm20) REVERT: I 1003 ASP cc_start: 0.4891 (OUTLIER) cc_final: 0.0649 (t70) REVERT: J 49 ILE cc_start: 0.8753 (OUTLIER) cc_final: 0.8495 (tt) REVERT: J 54 LYS cc_start: 0.7620 (tmmt) cc_final: 0.7371 (tmtt) REVERT: J 481 MET cc_start: 0.8891 (tmm) cc_final: 0.8465 (ttt) REVERT: J 523 ASP cc_start: 0.8546 (m-30) cc_final: 0.8342 (m-30) REVERT: J 661 MET cc_start: 0.9177 (ptp) cc_final: 0.8927 (ptp) REVERT: J 1090 ASP cc_start: 0.8609 (m-30) cc_final: 0.8370 (m-30) REVERT: J 1219 GLU cc_start: 0.9153 (tt0) cc_final: 0.8733 (tt0) REVERT: K 8 LYS cc_start: 0.8570 (pttt) cc_final: 0.8320 (pttm) REVERT: K 89 MET cc_start: 0.5695 (tpt) cc_final: 0.5279 (mtt) outliers start: 44 outliers final: 35 residues processed: 200 average time/residue: 0.4196 time to fit residues: 129.3272 Evaluate side-chains 203 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 164 time to evaluate : 3.008 ------------------------------------------------------------------------------- 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 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 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 1005 MET Chi-restraints excluded: chain I residue 1006 HIS Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain J residue 49 ILE Chi-restraints excluded: chain J residue 125 GLN Chi-restraints excluded: chain J residue 127 LEU Chi-restraints excluded: chain J residue 747 VAL Chi-restraints excluded: chain J residue 762 GLN Chi-restraints excluded: chain J residue 778 LEU Chi-restraints excluded: chain J residue 1415 VAL Chi-restraints excluded: chain J residue 1466 VAL Chi-restraints excluded: chain J residue 1468 LEU Chi-restraints excluded: chain J residue 1483 PHE Chi-restraints excluded: chain K residue 15 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 199 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 113 optimal weight: 0.7980 chunk 127 optimal weight: 0.7980 chunk 117 optimal weight: 0.2980 chunk 157 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 168 optimal weight: 0.2980 overall best weight: 0.6382 ------------------------------------------------------------------------------- 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 = 0.3732 r_free = 0.3732 target = 0.093672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.064510 restraints weight = 66914.523| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 3.58 r_work: 0.2939 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 25231 Z= 0.111 Angle : 0.584 13.723 34456 Z= 0.289 Chirality : 0.042 0.181 3906 Planarity : 0.004 0.060 4246 Dihedral : 14.591 132.853 4101 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 1.45 % Allowed : 15.74 % Favored : 82.81 % 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: -0.03 (0.16), residues: 2905 helix: 1.16 (0.17), residues: 1009 sheet: -0.28 (0.26), residues: 404 loop : -0.75 (0.17), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 200 HIS 0.004 0.001 HIS J1075 PHE 0.012 0.001 PHE H 65 TYR 0.024 0.001 TYR J1207 ARG 0.018 0.000 ARG I1031 Details of bonding type rmsd hydrogen bonds : bond 0.04712 ( 1031) hydrogen bonds : angle 4.34398 ( 2786) metal coordination : bond 0.00346 ( 4) metal coordination : angle 3.56123 ( 6) covalent geometry : bond 0.00259 (25227) covalent geometry : angle 0.58252 (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 209 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 173 time to evaluate : 3.083 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: 0.9151 (mt-10) cc_final: 0.8863 (mp0) REVERT: G 102 LYS cc_start: 0.8992 (mmpt) cc_final: 0.8617 (mmmt) REVERT: G 163 ASN cc_start: 0.8835 (m-40) cc_final: 0.8562 (t0) REVERT: H 57 TYR cc_start: 0.9188 (t80) cc_final: 0.8983 (t80) REVERT: H 84 GLU cc_start: 0.8530 (mp0) cc_final: 0.7720 (mp0) REVERT: I 82 GLU cc_start: 0.9199 (OUTLIER) cc_final: 0.8906 (pm20) REVERT: I 209 ARG cc_start: 0.9168 (ptm-80) cc_final: 0.8728 (tmm-80) REVERT: I 219 GLN cc_start: 0.8991 (mp10) cc_final: 0.8650 (mp10) REVERT: I 275 TYR cc_start: 0.8616 (t80) cc_final: 0.8330 (m-80) REVERT: I 321 GLU cc_start: 0.7375 (OUTLIER) cc_final: 0.6492 (mt-10) REVERT: I 420 ARG cc_start: 0.7327 (ttp-170) cc_final: 0.6732 (ttp-170) REVERT: I 711 GLU cc_start: 0.9065 (pm20) cc_final: 0.8705 (pm20) REVERT: I 1003 ASP cc_start: 0.4846 (OUTLIER) cc_final: 0.0738 (t70) REVERT: J 49 ILE cc_start: 0.8739 (OUTLIER) cc_final: 0.8486 (tt) REVERT: J 54 LYS cc_start: 0.7673 (tmmt) cc_final: 0.7416 (tmtt) REVERT: J 456 MET cc_start: 0.4434 (ttp) cc_final: 0.3950 (ttt) REVERT: J 481 MET cc_start: 0.8900 (tmm) cc_final: 0.8419 (ttt) REVERT: J 1219 GLU cc_start: 0.9121 (tt0) cc_final: 0.8664 (tt0) REVERT: K 8 LYS cc_start: 0.8568 (pttt) cc_final: 0.8329 (pttm) REVERT: K 59 ASN cc_start: 0.7454 (t0) cc_final: 0.7120 (t0) REVERT: K 89 MET cc_start: 0.5862 (tpt) cc_final: 0.5385 (mtt) outliers start: 36 outliers final: 31 residues processed: 202 average time/residue: 0.4300 time to fit residues: 133.5824 Evaluate side-chains 200 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 165 time to evaluate : 2.859 ------------------------------------------------------------------------------- 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 102 HIS 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 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 127 LEU Chi-restraints excluded: chain J residue 747 VAL Chi-restraints excluded: chain J residue 778 LEU Chi-restraints excluded: chain J residue 1415 VAL Chi-restraints excluded: chain J residue 1466 VAL Chi-restraints excluded: chain J residue 1468 LEU Chi-restraints excluded: chain J residue 1483 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 19 optimal weight: 4.9990 chunk 207 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 125 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 chunk 18 optimal weight: 6.9990 chunk 272 optimal weight: 0.9980 chunk 86 optimal weight: 4.9990 chunk 209 optimal weight: 0.0050 chunk 155 optimal weight: 6.9990 chunk 132 optimal weight: 0.5980 overall best weight: 0.6794 ------------------------------------------------------------------------------- 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** 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 = 0.3733 r_free = 0.3733 target = 0.093735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.064622 restraints weight = 66752.107| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 3.57 r_work: 0.2944 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.2364 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= 0.112 Angle : 0.581 13.374 34456 Z= 0.288 Chirality : 0.041 0.180 3906 Planarity : 0.004 0.058 4246 Dihedral : 14.529 132.977 4101 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 1.45 % Allowed : 15.98 % Favored : 82.57 % 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: -0.01 (0.16), residues: 2905 helix: 1.19 (0.17), residues: 1009 sheet: -0.26 (0.26), residues: 394 loop : -0.75 (0.17), residues: 1502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 200 HIS 0.005 0.001 HIS J1075 PHE 0.023 0.001 PHE I 191 TYR 0.023 0.001 TYR J1207 ARG 0.009 0.000 ARG I 284 Details of bonding type rmsd hydrogen bonds : bond 0.04651 ( 1031) hydrogen bonds : angle 4.29137 ( 2786) metal coordination : bond 0.00383 ( 4) metal coordination : angle 3.53498 ( 6) covalent geometry : bond 0.00264 (25227) covalent geometry : angle 0.57887 (34450) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13125.15 seconds wall clock time: 224 minutes 56.56 seconds (13496.56 seconds total)