Starting phenix.real_space_refine on Mon Feb 19 12:04:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hsg_34996/02_2024/8hsg_34996.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hsg_34996/02_2024/8hsg_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hsg_34996/02_2024/8hsg_34996.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hsg_34996/02_2024/8hsg_34996.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hsg_34996/02_2024/8hsg_34996.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hsg_34996/02_2024/8hsg_34996.pdb" } 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 Residue "I PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 1207": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 24636 Number of models: 1 Model: "" Number of chains: 9 Chain: "G" Number of atoms: 1806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1806 Classifications: {'peptide': 229} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 214} Chain: "H" Number of atoms: 1806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1806 Classifications: {'peptide': 229} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 214} Chain: "I" Number of atoms: 8644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1096, 8644 Classifications: {'peptide': 1096} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 69, 'TRANS': 1025} Chain breaks: 1 Chain: "J" Number of atoms: 10078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1278, 10078 Classifications: {'peptide': 1278} Link IDs: {'PTRANS': 62, 'TRANS': 1215} Chain breaks: 3 Chain: "K" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 735 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 5, 'TRANS': 85} Chain: "T" Number of atoms: 764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 764 Classifications: {'DNA': 37} Link IDs: {'rna3p': 36} Chain: "R" Number of atoms: 246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 246 Classifications: {'RNA': 12} Modifications used: {'rna3p_pur': 3, 'rna3p_pyr': 9} Link IDs: {'rna3p': 11} Chain: "N" Number of atoms: 555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 555 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain breaks: 1 Chain: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 19413 SG CYS J1112 67.862 89.540 32.227 1.00100.93 S ATOM 20057 SG CYS J1194 67.627 89.462 36.108 1.00 94.30 S ATOM 20113 SG CYS J1201 65.512 87.092 33.975 1.00 92.47 S ATOM 20137 SG CYS J1204 68.990 86.439 34.225 1.00 91.33 S Time building chain proxies: 13.16, per 1000 atoms: 0.53 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.40 Conformation dependent library (CDL) restraints added in 4.2 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: 8.79 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: 12.32 Time building geometry restraints manager: 12.17 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: 99.79 - 106.64: 1225 106.64 - 113.48: 13714 113.48 - 120.33: 9299 120.33 - 127.18: 9859 127.18 - 134.02: 353 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 2.520 nonbonded pdb=" OG1 THR J 121 " pdb=" OE1 GLU J 122 " model vdw 2.136 2.440 ... (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 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: 2.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 8.190 Check model and map are aligned: 0.360 Set scattering table: 0.220 Process input model: 79.630 Find NCS groups from input model: 0.970 Set up NCS constraints: 0.090 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:3.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 95.830 ------------------------------------------------------------------------------- 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 25227 Z= 0.171 Angle : 0.589 10.235 34450 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 229 time to evaluate : 2.611 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: 0.3909 time to fit residues: 138.9670 Evaluate side-chains 181 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 181 time to evaluate : 3.137 ------------------------------------------------------------------------------- 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: 8.9990 chunk 150 optimal weight: 0.8980 chunk 119 optimal weight: 6.9990 chunk 231 optimal weight: 0.8980 chunk 89 optimal weight: 4.9990 chunk 140 optimal weight: 5.9990 chunk 172 optimal weight: 9.9990 chunk 267 optimal weight: 2.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 163 ASN ** G 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 229 GLN ** H 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 99 GLN J 762 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.1191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 25227 Z= 0.328 Angle : 0.635 10.758 34450 Z= 0.321 Chirality : 0.044 0.174 3906 Planarity : 0.005 0.049 4246 Dihedral : 14.780 142.137 4101 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 0.97 % Allowed : 8.78 % Favored : 90.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.16), residues: 2905 helix: 0.96 (0.17), residues: 990 sheet: -0.38 (0.26), residues: 390 loop : -0.95 (0.16), residues: 1525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP J 511 HIS 0.008 0.001 HIS I 141 PHE 0.020 0.002 PHE I 191 TYR 0.030 0.002 TYR J1207 ARG 0.011 0.000 ARG J1482 *********************** 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 211 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 187 time to evaluate : 2.758 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 102 LYS cc_start: 0.9011 (mmpt) cc_final: 0.8678 (mmmt) REVERT: H 4 SER cc_start: 0.6304 (m) cc_final: 0.6052 (p) REVERT: H 84 GLU cc_start: 0.7826 (mp0) cc_final: 0.7564 (mp0) REVERT: I 219 GLN cc_start: 0.8870 (mp10) cc_final: 0.8363 (mp10) REVERT: I 275 TYR cc_start: 0.8350 (t80) cc_final: 0.7799 (m-80) REVERT: I 338 GLU cc_start: 0.7853 (tp30) cc_final: 0.7482 (tp30) REVERT: I 420 ARG cc_start: 0.6905 (ttp-170) cc_final: 0.6395 (ttp-170) REVERT: I 711 GLU cc_start: 0.8723 (pm20) cc_final: 0.8287 (pm20) REVERT: J 32 ILE cc_start: 0.9018 (OUTLIER) cc_final: 0.8804 (pt) REVERT: J 481 MET cc_start: 0.8779 (tmm) cc_final: 0.8384 (ttt) REVERT: K 59 ASN cc_start: 0.7904 (t0) cc_final: 0.7485 (t0) REVERT: K 89 MET cc_start: 0.5913 (tpt) cc_final: 0.5520 (mtt) outliers start: 24 outliers final: 19 residues processed: 201 average time/residue: 0.4232 time to fit residues: 130.2675 Evaluate side-chains 193 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 173 time to evaluate : 2.772 ------------------------------------------------------------------------------- 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 163 ASN 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 87 ASP Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain I residue 307 LEU Chi-restraints excluded: chain I residue 464 LEU Chi-restraints excluded: chain I residue 560 MET Chi-restraints excluded: chain I residue 564 MET Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain J residue 32 ILE Chi-restraints excluded: chain J residue 125 GLN Chi-restraints excluded: chain J residue 592 THR Chi-restraints excluded: chain J residue 859 ASP Chi-restraints excluded: chain J residue 1420 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 148 optimal weight: 3.9990 chunk 83 optimal weight: 0.6980 chunk 222 optimal weight: 0.9980 chunk 182 optimal weight: 3.9990 chunk 73 optimal weight: 8.9990 chunk 268 optimal weight: 0.9980 chunk 289 optimal weight: 10.0000 chunk 239 optimal weight: 3.9990 chunk 266 optimal weight: 6.9990 chunk 91 optimal weight: 5.9990 chunk 215 optimal weight: 6.9990 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 139 ASN I 45 GLN ** J1364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.1431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 25227 Z= 0.301 Angle : 0.600 9.735 34450 Z= 0.305 Chirality : 0.043 0.156 3906 Planarity : 0.004 0.049 4246 Dihedral : 14.757 137.677 4101 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 1.45 % Allowed : 11.39 % Favored : 87.16 % 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: 0.92 (0.17), residues: 1006 sheet: -0.35 (0.27), residues: 379 loop : -0.97 (0.16), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 511 HIS 0.006 0.001 HIS I 141 PHE 0.014 0.001 PHE J 806 TYR 0.029 0.001 TYR J1207 ARG 0.005 0.000 ARG I1031 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5810 Ramachandran restraints generated. 2905 Oldfield, 0 Emsley, 2905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5810 Ramachandran restraints generated. 2905 Oldfield, 0 Emsley, 2905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 174 time to evaluate : 2.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 102 LYS cc_start: 0.9009 (mmpt) cc_final: 0.8668 (mmmt) REVERT: H 84 GLU cc_start: 0.7921 (mp0) cc_final: 0.7661 (mp0) REVERT: I 209 ARG cc_start: 0.9021 (ptm-80) cc_final: 0.8736 (ptm-80) REVERT: I 219 GLN cc_start: 0.8878 (mp10) cc_final: 0.8366 (mp10) REVERT: I 275 TYR cc_start: 0.8364 (OUTLIER) cc_final: 0.7929 (m-10) REVERT: I 420 ARG cc_start: 0.7118 (ttp-170) cc_final: 0.6483 (ttp-170) REVERT: I 711 GLU cc_start: 0.8766 (pm20) cc_final: 0.8305 (pm20) REVERT: J 49 ILE cc_start: 0.8835 (OUTLIER) cc_final: 0.8570 (tt) REVERT: J 481 MET cc_start: 0.8772 (tmm) cc_final: 0.8479 (ttt) REVERT: K 59 ASN cc_start: 0.7816 (t0) cc_final: 0.7329 (t0) outliers start: 36 outliers final: 24 residues processed: 198 average time/residue: 0.3961 time to fit residues: 121.9770 Evaluate side-chains 191 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 165 time to evaluate : 2.750 ------------------------------------------------------------------------------- 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 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 87 ASP Chi-restraints excluded: chain I residue 102 HIS Chi-restraints excluded: chain I residue 275 TYR Chi-restraints excluded: chain I residue 290 LEU Chi-restraints excluded: chain I residue 307 LEU Chi-restraints excluded: chain I residue 367 LEU Chi-restraints excluded: chain I residue 464 LEU Chi-restraints excluded: chain I residue 560 MET Chi-restraints excluded: chain I residue 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 49 ILE Chi-restraints excluded: chain J residue 125 GLN Chi-restraints excluded: chain J residue 676 MET Chi-restraints excluded: chain J residue 859 ASP 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 265 optimal weight: 0.7980 chunk 201 optimal weight: 5.9990 chunk 139 optimal weight: 0.8980 chunk 29 optimal weight: 6.9990 chunk 128 optimal weight: 3.9990 chunk 180 optimal weight: 8.9990 chunk 269 optimal weight: 0.0040 chunk 285 optimal weight: 0.9990 chunk 140 optimal weight: 0.9980 chunk 255 optimal weight: 0.2980 chunk 76 optimal weight: 4.9990 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 180 GLN G 229 GLN ** H 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 25227 Z= 0.163 Angle : 0.555 10.090 34450 Z= 0.278 Chirality : 0.041 0.154 3906 Planarity : 0.004 0.045 4246 Dihedral : 14.675 141.280 4101 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 1.57 % Allowed : 13.12 % Favored : 85.31 % 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: 1.10 (0.17), residues: 1001 sheet: -0.27 (0.27), residues: 389 loop : -0.86 (0.16), residues: 1515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 200 HIS 0.005 0.001 HIS J1075 PHE 0.014 0.001 PHE I 114 TYR 0.023 0.001 TYR J1207 ARG 0.009 0.000 ARG I1031 *********************** 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 221 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 182 time to evaluate : 2.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 102 LYS cc_start: 0.8926 (mmpt) cc_final: 0.8628 (mmmt) REVERT: I 209 ARG cc_start: 0.9016 (ptm-80) cc_final: 0.8562 (tmm-80) REVERT: I 219 GLN cc_start: 0.8883 (mp10) cc_final: 0.8352 (mp10) REVERT: I 275 TYR cc_start: 0.8266 (t80) cc_final: 0.7905 (m-10) REVERT: I 420 ARG cc_start: 0.6849 (ttp-170) cc_final: 0.6394 (ttp-170) REVERT: I 711 GLU cc_start: 0.8727 (pm20) cc_final: 0.8277 (pm20) REVERT: J 49 ILE cc_start: 0.8791 (OUTLIER) cc_final: 0.8548 (tt) REVERT: J 127 LEU cc_start: 0.9092 (tt) cc_final: 0.8808 (tt) REVERT: J 456 MET cc_start: 0.4556 (ttp) cc_final: 0.4093 (ttt) REVERT: J 481 MET cc_start: 0.8758 (tmm) cc_final: 0.8352 (ttt) REVERT: K 8 LYS cc_start: 0.8643 (ptpt) cc_final: 0.8052 (ptmt) REVERT: K 59 ASN cc_start: 0.7730 (t0) cc_final: 0.7320 (t0) outliers start: 39 outliers final: 24 residues processed: 214 average time/residue: 0.3953 time to fit residues: 131.5792 Evaluate side-chains 191 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 166 time to evaluate : 2.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 74 ASP Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain H residue 4 SER Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 87 ASP Chi-restraints excluded: chain I residue 102 HIS Chi-restraints excluded: chain I residue 115 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 564 MET Chi-restraints excluded: chain I residue 865 THR Chi-restraints excluded: chain I residue 988 VAL 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 778 LEU Chi-restraints excluded: chain J residue 859 ASP Chi-restraints excluded: chain K residue 31 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 237 optimal weight: 0.6980 chunk 161 optimal weight: 0.0670 chunk 4 optimal weight: 3.9990 chunk 212 optimal weight: 9.9990 chunk 117 optimal weight: 7.9990 chunk 243 optimal weight: 7.9990 chunk 197 optimal weight: 0.9990 chunk 0 optimal weight: 9.9990 chunk 145 optimal weight: 3.9990 chunk 255 optimal weight: 3.9990 chunk 71 optimal weight: 0.3980 overall best weight: 1.2322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 180 GLN G 229 GLN H 139 ASN J 845 ASN ** J1364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 25227 Z= 0.212 Angle : 0.560 8.922 34450 Z= 0.281 Chirality : 0.042 0.152 3906 Planarity : 0.004 0.047 4246 Dihedral : 14.627 137.737 4101 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 1.97 % Allowed : 13.81 % Favored : 84.22 % 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: 1007 sheet: -0.27 (0.26), residues: 391 loop : -0.87 (0.16), residues: 1507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J 511 HIS 0.004 0.001 HIS J1075 PHE 0.012 0.001 PHE J 806 TYR 0.026 0.001 TYR J1207 ARG 0.010 0.000 ARG I1031 *********************** 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 225 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 176 time to evaluate : 2.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 1 MET cc_start: 0.6281 (tpt) cc_final: 0.5980 (tpt) REVERT: G 102 LYS cc_start: 0.8881 (mmpt) cc_final: 0.8589 (mmmt) REVERT: I 82 GLU cc_start: 0.8967 (OUTLIER) cc_final: 0.8742 (pm20) REVERT: I 209 ARG cc_start: 0.9032 (ptm-80) cc_final: 0.8582 (tmm-80) REVERT: I 219 GLN cc_start: 0.8915 (mp10) cc_final: 0.8595 (mp10) REVERT: I 275 TYR cc_start: 0.8275 (t80) cc_final: 0.7973 (m-10) REVERT: I 420 ARG cc_start: 0.6884 (ttp-170) cc_final: 0.6377 (ttp-170) REVERT: I 711 GLU cc_start: 0.8762 (pm20) cc_final: 0.8307 (pm20) REVERT: I 1003 ASP cc_start: 0.4194 (OUTLIER) cc_final: 0.0561 (t70) REVERT: J 49 ILE cc_start: 0.8853 (OUTLIER) cc_final: 0.8617 (tt) REVERT: J 54 LYS cc_start: 0.7746 (tmmt) cc_final: 0.7510 (tmtt) REVERT: J 127 LEU cc_start: 0.9151 (tt) cc_final: 0.8851 (tt) REVERT: J 481 MET cc_start: 0.8772 (tmm) cc_final: 0.8406 (ttt) REVERT: K 59 ASN cc_start: 0.7723 (t0) cc_final: 0.7332 (t0) outliers start: 49 outliers final: 30 residues processed: 214 average time/residue: 0.3887 time to fit residues: 129.3111 Evaluate side-chains 200 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 167 time to evaluate : 2.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 74 ASP Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 82 GLU Chi-restraints excluded: chain I residue 87 ASP 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 367 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 564 MET Chi-restraints excluded: chain I residue 865 THR Chi-restraints excluded: chain I residue 940 GLU Chi-restraints excluded: chain I residue 988 VAL 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 778 LEU Chi-restraints excluded: chain J residue 859 ASP Chi-restraints excluded: chain J residue 1415 VAL Chi-restraints excluded: chain J residue 1483 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 95 optimal weight: 0.7980 chunk 256 optimal weight: 3.9990 chunk 56 optimal weight: 0.0070 chunk 167 optimal weight: 20.0000 chunk 70 optimal weight: 6.9990 chunk 285 optimal weight: 7.9990 chunk 236 optimal weight: 4.9990 chunk 132 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 chunk 94 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.9604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 180 GLN G 229 GLN ** J1364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 25227 Z= 0.283 Angle : 0.597 15.261 34450 Z= 0.300 Chirality : 0.043 0.183 3906 Planarity : 0.004 0.047 4246 Dihedral : 14.661 131.413 4101 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 2.21 % Allowed : 14.65 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.16), residues: 2905 helix: 1.06 (0.17), residues: 1007 sheet: -0.25 (0.26), residues: 403 loop : -0.87 (0.16), residues: 1495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP J 511 HIS 0.006 0.001 HIS I 141 PHE 0.015 0.001 PHE J 806 TYR 0.029 0.001 TYR J1207 ARG 0.007 0.000 ARG I1031 *********************** 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 223 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 168 time to evaluate : 2.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 84 GLU cc_start: 0.8159 (mp0) cc_final: 0.7890 (mp0) REVERT: H 84 GLU cc_start: 0.8129 (mp0) cc_final: 0.7825 (mp0) REVERT: I 219 GLN cc_start: 0.8929 (mp10) cc_final: 0.8610 (mp10) REVERT: I 275 TYR cc_start: 0.8282 (t80) cc_final: 0.7948 (m-10) REVERT: I 420 ARG cc_start: 0.6776 (ttp-170) cc_final: 0.6112 (ttp-170) REVERT: I 1003 ASP cc_start: 0.4135 (OUTLIER) cc_final: 0.0424 (t70) REVERT: J 49 ILE cc_start: 0.8861 (OUTLIER) cc_final: 0.8614 (tt) REVERT: J 54 LYS cc_start: 0.7808 (tmmt) cc_final: 0.7544 (tmtt) REVERT: J 481 MET cc_start: 0.8829 (tmm) cc_final: 0.8440 (ttt) REVERT: J 661 MET cc_start: 0.9219 (ptp) cc_final: 0.8963 (ptp) REVERT: J 1100 ASP cc_start: 0.8147 (OUTLIER) cc_final: 0.7943 (p0) REVERT: K 8 LYS cc_start: 0.8539 (pttt) cc_final: 0.8278 (pttm) REVERT: K 59 ASN cc_start: 0.7867 (t0) cc_final: 0.7378 (t0) REVERT: K 89 MET cc_start: 0.6264 (mtt) cc_final: 0.5614 (tpt) outliers start: 55 outliers final: 42 residues processed: 205 average time/residue: 0.3838 time to fit residues: 124.0254 Evaluate side-chains 207 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 162 time to evaluate : 3.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 74 ASP Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain H residue 4 SER Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain H residue 87 VAL 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 83 CYS Chi-restraints excluded: chain I residue 87 ASP 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 367 LEU Chi-restraints excluded: chain I residue 452 ILE 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 564 MET Chi-restraints excluded: chain I residue 865 THR Chi-restraints excluded: chain I residue 940 GLU 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 778 LEU Chi-restraints excluded: chain J residue 859 ASP Chi-restraints excluded: chain J residue 1100 ASP 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 38 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 275 optimal weight: 4.9990 chunk 32 optimal weight: 0.6980 chunk 162 optimal weight: 0.9990 chunk 208 optimal weight: 1.9990 chunk 161 optimal weight: 0.4980 chunk 240 optimal weight: 3.9990 chunk 159 optimal weight: 3.9990 chunk 284 optimal weight: 9.9990 chunk 177 optimal weight: 3.9990 chunk 173 optimal weight: 0.9980 chunk 131 optimal weight: 3.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 180 GLN G 229 GLN ** J1364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 25227 Z= 0.189 Angle : 0.560 10.230 34450 Z= 0.281 Chirality : 0.042 0.179 3906 Planarity : 0.004 0.061 4246 Dihedral : 14.600 132.693 4101 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 1.85 % Allowed : 15.54 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.16), residues: 2905 helix: 1.15 (0.17), residues: 1000 sheet: -0.24 (0.26), residues: 406 loop : -0.80 (0.16), residues: 1499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 200 HIS 0.004 0.001 HIS J1075 PHE 0.012 0.001 PHE J 806 TYR 0.026 0.001 TYR J1207 ARG 0.011 0.000 ARG J1388 *********************** 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 220 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 174 time to evaluate : 2.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 84 GLU cc_start: 0.8130 (mp0) cc_final: 0.7837 (mp0) REVERT: H 84 GLU cc_start: 0.8066 (mp0) cc_final: 0.7304 (mp0) REVERT: I 209 ARG cc_start: 0.9029 (ptm-80) cc_final: 0.8605 (tmm-80) REVERT: I 219 GLN cc_start: 0.8933 (mp10) cc_final: 0.8601 (mp10) REVERT: I 275 TYR cc_start: 0.8234 (t80) cc_final: 0.8026 (m-10) REVERT: I 420 ARG cc_start: 0.6917 (ttp-170) cc_final: 0.6341 (ttp-170) REVERT: I 1003 ASP cc_start: 0.3994 (OUTLIER) cc_final: 0.0346 (t70) REVERT: J 49 ILE cc_start: 0.8802 (OUTLIER) cc_final: 0.8555 (tt) REVERT: J 54 LYS cc_start: 0.7799 (tmmt) cc_final: 0.7544 (tmtt) REVERT: J 481 MET cc_start: 0.8797 (tmm) cc_final: 0.8379 (ttt) REVERT: J 661 MET cc_start: 0.9201 (ptp) cc_final: 0.8942 (ptp) REVERT: J 1488 ASP cc_start: 0.8364 (OUTLIER) cc_final: 0.7568 (p0) REVERT: K 59 ASN cc_start: 0.7708 (t0) cc_final: 0.7318 (t0) REVERT: K 89 MET cc_start: 0.6215 (mtt) cc_final: 0.5437 (tpt) outliers start: 46 outliers final: 38 residues processed: 208 average time/residue: 0.3825 time to fit residues: 124.1767 Evaluate side-chains 205 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 164 time to evaluate : 2.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 61 VAL Chi-restraints excluded: chain G residue 74 ASP Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain H residue 4 SER 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 83 CYS Chi-restraints excluded: chain I residue 87 ASP Chi-restraints excluded: chain I residue 102 HIS Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain I residue 158 TYR Chi-restraints excluded: chain I residue 290 LEU Chi-restraints excluded: chain I residue 307 LEU Chi-restraints excluded: chain I residue 367 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 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 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 747 VAL Chi-restraints excluded: chain J residue 778 LEU Chi-restraints excluded: chain J residue 859 ASP 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 J residue 1488 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 175 optimal weight: 6.9990 chunk 113 optimal weight: 0.0270 chunk 169 optimal weight: 30.0000 chunk 85 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 180 optimal weight: 7.9990 chunk 193 optimal weight: 0.6980 chunk 140 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 223 optimal weight: 0.7980 chunk 258 optimal weight: 10.0000 overall best weight: 1.3042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 575 GLN ** J1364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 25227 Z= 0.218 Angle : 0.575 11.671 34450 Z= 0.287 Chirality : 0.042 0.182 3906 Planarity : 0.004 0.052 4246 Dihedral : 14.557 129.962 4101 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 2.01 % Allowed : 15.90 % Favored : 82.09 % 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: -0.08 (0.16), residues: 2905 helix: 1.14 (0.17), residues: 1006 sheet: -0.22 (0.26), residues: 406 loop : -0.81 (0.16), residues: 1493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J 511 HIS 0.004 0.001 HIS J1075 PHE 0.014 0.001 PHE J 806 TYR 0.027 0.001 TYR J1207 ARG 0.005 0.000 ARG J1388 *********************** 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 220 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 170 time to evaluate : 2.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 84 GLU cc_start: 0.8141 (mp0) cc_final: 0.7842 (mp0) REVERT: G 102 LYS cc_start: 0.8836 (mmpt) cc_final: 0.8542 (mmmt) REVERT: I 209 ARG cc_start: 0.9048 (ptm-80) cc_final: 0.8646 (mtm110) REVERT: I 219 GLN cc_start: 0.8942 (mp10) cc_final: 0.8611 (mp10) REVERT: I 275 TYR cc_start: 0.8259 (t80) cc_final: 0.8033 (m-80) REVERT: I 420 ARG cc_start: 0.6895 (ttp-170) cc_final: 0.6322 (ttp-170) REVERT: I 1003 ASP cc_start: 0.4062 (OUTLIER) cc_final: 0.0376 (t70) REVERT: J 49 ILE cc_start: 0.8826 (OUTLIER) cc_final: 0.8583 (tt) REVERT: J 54 LYS cc_start: 0.7794 (tmmt) cc_final: 0.7540 (tmtt) REVERT: J 123 LEU cc_start: 0.8964 (mp) cc_final: 0.8621 (mp) REVERT: J 481 MET cc_start: 0.8809 (tmm) cc_final: 0.8412 (ttt) REVERT: J 661 MET cc_start: 0.9216 (ptp) cc_final: 0.8959 (ptp) REVERT: J 1488 ASP cc_start: 0.8365 (OUTLIER) cc_final: 0.7568 (p0) REVERT: K 8 LYS cc_start: 0.8578 (pttt) cc_final: 0.8335 (pttm) REVERT: K 59 ASN cc_start: 0.7803 (t0) cc_final: 0.7395 (t0) REVERT: K 89 MET cc_start: 0.6223 (mtt) cc_final: 0.5410 (tpt) outliers start: 50 outliers final: 41 residues processed: 209 average time/residue: 0.4175 time to fit residues: 135.5795 Evaluate side-chains 210 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 166 time to evaluate : 2.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 61 VAL Chi-restraints excluded: chain G residue 74 ASP Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain H residue 4 SER Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain H residue 87 VAL 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 83 CYS Chi-restraints excluded: chain I residue 87 ASP 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 367 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 564 MET Chi-restraints excluded: chain I residue 865 THR Chi-restraints excluded: chain I residue 940 GLU 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 747 VAL Chi-restraints excluded: chain J residue 778 LEU Chi-restraints excluded: chain J residue 859 ASP 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 J residue 1488 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 272 optimal weight: 0.8980 chunk 248 optimal weight: 0.8980 chunk 264 optimal weight: 0.6980 chunk 159 optimal weight: 0.9990 chunk 115 optimal weight: 6.9990 chunk 208 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 239 optimal weight: 0.6980 chunk 250 optimal weight: 0.9990 chunk 173 optimal weight: 0.9980 chunk 280 optimal weight: 0.0270 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J1364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 25227 Z= 0.165 Angle : 0.561 12.424 34450 Z= 0.279 Chirality : 0.041 0.180 3906 Planarity : 0.004 0.055 4246 Dihedral : 14.513 131.582 4101 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 1.73 % Allowed : 16.30 % Favored : 81.96 % 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: 1.17 (0.17), residues: 1007 sheet: -0.14 (0.26), residues: 409 loop : -0.77 (0.17), residues: 1489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 200 HIS 0.004 0.001 HIS J1075 PHE 0.012 0.001 PHE J 806 TYR 0.027 0.001 TYR J 450 ARG 0.009 0.000 ARG I 265 *********************** 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 216 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 173 time to evaluate : 2.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 209 ARG cc_start: 0.9059 (ptm-80) cc_final: 0.8652 (tmm-80) REVERT: I 219 GLN cc_start: 0.8943 (mp10) cc_final: 0.8400 (mp10) REVERT: I 284 ARG cc_start: 0.7416 (ttp80) cc_final: 0.7189 (tmm-80) REVERT: I 420 ARG cc_start: 0.6821 (ttp-170) cc_final: 0.6308 (ttp-170) REVERT: I 1003 ASP cc_start: 0.4077 (OUTLIER) cc_final: 0.0507 (t70) REVERT: I 1031 ARG cc_start: 0.7719 (tpp80) cc_final: 0.7494 (tpp80) REVERT: J 49 ILE cc_start: 0.8795 (OUTLIER) cc_final: 0.8548 (tt) REVERT: J 54 LYS cc_start: 0.7815 (tmmt) cc_final: 0.7575 (tmtt) REVERT: J 481 MET cc_start: 0.8824 (tmm) cc_final: 0.8374 (ttt) REVERT: J 661 MET cc_start: 0.9185 (ptp) cc_final: 0.8922 (ptp) REVERT: J 1488 ASP cc_start: 0.8341 (OUTLIER) cc_final: 0.7546 (p0) REVERT: K 8 LYS cc_start: 0.8583 (pttt) cc_final: 0.8342 (pttm) REVERT: K 59 ASN cc_start: 0.7727 (t0) cc_final: 0.7354 (t0) outliers start: 43 outliers final: 37 residues processed: 207 average time/residue: 0.4129 time to fit residues: 133.7826 Evaluate side-chains 206 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 166 time to evaluate : 3.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 61 VAL Chi-restraints excluded: chain G residue 74 ASP Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain H residue 4 SER Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain H residue 87 VAL 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 83 CYS Chi-restraints excluded: chain I residue 87 ASP Chi-restraints excluded: chain I residue 102 HIS Chi-restraints excluded: chain I residue 158 TYR Chi-restraints excluded: chain I residue 290 LEU Chi-restraints excluded: chain I residue 307 LEU Chi-restraints excluded: chain I residue 367 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 564 MET Chi-restraints excluded: chain I residue 865 THR Chi-restraints excluded: chain I residue 940 GLU 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 540 LEU Chi-restraints excluded: chain J residue 747 VAL Chi-restraints excluded: chain J residue 778 LEU Chi-restraints excluded: chain J residue 859 ASP 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 J residue 1488 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 171 optimal weight: 5.9990 chunk 132 optimal weight: 0.4980 chunk 194 optimal weight: 3.9990 chunk 293 optimal weight: 9.9990 chunk 270 optimal weight: 8.9990 chunk 234 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 180 optimal weight: 10.0000 chunk 143 optimal weight: 0.0770 chunk 185 optimal weight: 0.9990 chunk 249 optimal weight: 5.9990 overall best weight: 1.3144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 38 ASN ** J1364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 25227 Z= 0.217 Angle : 0.573 13.510 34450 Z= 0.285 Chirality : 0.042 0.181 3906 Planarity : 0.004 0.056 4246 Dihedral : 14.493 128.866 4101 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 1.85 % Allowed : 16.10 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.16), residues: 2905 helix: 1.19 (0.17), residues: 1008 sheet: -0.18 (0.26), residues: 414 loop : -0.79 (0.17), residues: 1483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J1398 HIS 0.004 0.001 HIS J1075 PHE 0.013 0.001 PHE J 806 TYR 0.029 0.001 TYR J 450 ARG 0.006 0.000 ARG J1388 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5810 Ramachandran restraints generated. 2905 Oldfield, 0 Emsley, 2905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5810 Ramachandran restraints generated. 2905 Oldfield, 0 Emsley, 2905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 165 time to evaluate : 2.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 209 ARG cc_start: 0.9058 (ptm-80) cc_final: 0.8657 (tmm-80) REVERT: I 219 GLN cc_start: 0.8931 (mp10) cc_final: 0.8406 (mp10) REVERT: I 275 TYR cc_start: 0.7945 (OUTLIER) cc_final: 0.7462 (m-80) REVERT: I 420 ARG cc_start: 0.6756 (ttp-170) cc_final: 0.6247 (ttp-170) REVERT: I 1003 ASP cc_start: 0.4068 (OUTLIER) cc_final: 0.0381 (t70) REVERT: J 49 ILE cc_start: 0.8819 (OUTLIER) cc_final: 0.8580 (tt) REVERT: J 54 LYS cc_start: 0.7797 (tmmt) cc_final: 0.7572 (tmtt) REVERT: J 481 MET cc_start: 0.8833 (tmm) cc_final: 0.8405 (ttt) REVERT: J 661 MET cc_start: 0.9234 (ptp) cc_final: 0.8968 (ptp) REVERT: J 1488 ASP cc_start: 0.8350 (OUTLIER) cc_final: 0.7560 (p0) REVERT: K 8 LYS cc_start: 0.8553 (pttt) cc_final: 0.8294 (pttm) REVERT: K 59 ASN cc_start: 0.7916 (t0) cc_final: 0.7519 (t0) outliers start: 46 outliers final: 39 residues processed: 201 average time/residue: 0.3911 time to fit residues: 123.5642 Evaluate side-chains 204 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 161 time to evaluate : 2.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 61 VAL Chi-restraints excluded: chain G residue 74 ASP Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain H residue 4 SER Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain H residue 87 VAL 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 83 CYS Chi-restraints excluded: chain I residue 87 ASP 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 275 TYR Chi-restraints excluded: chain I residue 290 LEU Chi-restraints excluded: chain I residue 307 LEU Chi-restraints excluded: chain I residue 367 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 699 PHE Chi-restraints excluded: chain I residue 865 THR Chi-restraints excluded: chain I residue 940 GLU 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 747 VAL Chi-restraints excluded: chain J residue 778 LEU Chi-restraints excluded: chain J residue 859 ASP 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 J residue 1488 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 71 optimal weight: 2.9990 chunk 215 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 65 optimal weight: 9.9990 chunk 234 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 chunk 240 optimal weight: 8.9990 chunk 29 optimal weight: 7.9990 chunk 43 optimal weight: 0.9990 chunk 205 optimal weight: 0.5980 chunk 13 optimal weight: 5.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J1364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J1367 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.093241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.064120 restraints weight = 66968.503| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 3.57 r_work: 0.2931 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25227 Z= 0.195 Angle : 0.567 13.478 34450 Z= 0.282 Chirality : 0.041 0.180 3906 Planarity : 0.004 0.054 4246 Dihedral : 14.473 128.383 4101 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 1.77 % Allowed : 16.10 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.16), residues: 2905 helix: 1.18 (0.17), residues: 1015 sheet: -0.16 (0.26), residues: 414 loop : -0.77 (0.17), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J1398 HIS 0.004 0.001 HIS J1075 PHE 0.030 0.001 PHE I 227 TYR 0.027 0.001 TYR J 450 ARG 0.006 0.000 ARG I1031 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4797.32 seconds wall clock time: 87 minutes 53.27 seconds (5273.27 seconds total)