Starting phenix.real_space_refine on Tue Feb 20 15:01:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rdq_24424/02_2024/7rdq_24424.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rdq_24424/02_2024/7rdq_24424.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rdq_24424/02_2024/7rdq_24424.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rdq_24424/02_2024/7rdq_24424.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rdq_24424/02_2024/7rdq_24424.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rdq_24424/02_2024/7rdq_24424.pdb" } resolution = 3.0 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 72 5.49 5 Mg 5 5.21 5 S 69 5.16 5 C 17612 2.51 5 N 5032 2.21 5 O 5421 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C TYR 1067": "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: 28213 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1782 Classifications: {'peptide': 226} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 211} Chain: "B" Number of atoms: 1750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1750 Classifications: {'peptide': 222} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 207} Chain: "C" Number of atoms: 8770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1111, 8770 Classifications: {'peptide': 1111} Link IDs: {'PCIS': 1, 'PTRANS': 71, 'TRANS': 1038} Chain breaks: 1 Chain: "D" Number of atoms: 10787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1366, 10787 Classifications: {'peptide': 1366} Link IDs: {'PCIS': 2, 'PTRANS': 66, 'TRANS': 1297} Chain breaks: 2 Chain: "E" Number of atoms: 758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 758 Classifications: {'peptide': 94} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 6, 'TRANS': 87} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 2828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2828 Classifications: {'peptide': 349} Link IDs: {'PTRANS': 14, 'TRANS': 334} Chain: "H" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 646 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain: "G" Number of atoms: 632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 632 Classifications: {'DNA': 31} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 30} Chain: "I" Number of atoms: 253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 253 Classifications: {'RNA': 11} Modifications used: {'rna2p_pur': 3, 'rna3p_pur': 8} Link IDs: {'rna2p': 3, 'rna3p': 7} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' MG': 3, ' ZN': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 20166 SG CYS D1112 42.117 87.623 88.307 1.00 21.92 S ATOM 20810 SG CYS D1194 44.900 85.211 89.263 1.00 21.29 S ATOM 20866 SG CYS D1201 43.543 87.645 91.783 1.00 19.31 S ATOM 20890 SG CYS D1204 41.642 84.539 91.041 1.00 19.52 S ATOM 12771 SG CYS D 58 108.187 97.015 86.116 1.00 80.01 S ATOM 12782 SG CYS D 60 111.172 95.779 84.107 1.00 85.14 S ATOM 12893 SG CYS D 73 109.064 97.331 81.642 1.00 81.10 S ATOM 12919 SG CYS D 76 107.690 94.174 82.415 1.00 76.54 S Time building chain proxies: 14.44, per 1000 atoms: 0.51 Number of scatterers: 28213 At special positions: 0 Unit cell: (142.206, 138.054, 183.726, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 69 16.00 P 72 15.00 Mg 5 11.99 O 5421 8.00 N 5032 7.00 C 17612 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: 12.32 Conformation dependent library (CDL) restraints added in 4.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D2001 " pdb="ZN ZN D2001 " - pdb=" SG CYS D1204 " pdb="ZN ZN D2001 " - pdb=" SG CYS D1194 " pdb="ZN ZN D2001 " - pdb=" SG CYS D1201 " pdb="ZN ZN D2001 " - pdb=" SG CYS D1112 " pdb=" ZN D2002 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 76 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 60 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 58 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 73 " Number of angles added : 12 6700 Ramachandran restraints generated. 3350 Oldfield, 0 Emsley, 3350 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6236 Finding SS restraints... Secondary structure from input PDB file: 129 helices and 50 sheets defined 43.5% alpha, 17.8% beta 17 base pairs and 37 stacking pairs defined. Time for finding SS restraints: 10.56 Creating SS restraints... Processing helix chain 'A' and resid 31 through 47 removed outlier: 3.568A pdb=" N THR A 35 " --> pdb=" O GLY A 31 " (cutoff:3.500A) Proline residue: A 39 - end of helix Processing helix chain 'A' and resid 74 through 83 Processing helix chain 'A' and resid 112 through 114 No H-bonds generated for 'chain 'A' and resid 112 through 114' Processing helix chain 'A' and resid 152 through 157 removed outlier: 3.500A pdb=" N HIS A 156 " --> pdb=" O PRO A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 223 Processing helix chain 'A' and resid 224 through 226 No H-bonds generated for 'chain 'A' and resid 224 through 226' Processing helix chain 'B' and resid 31 through 47 Proline residue: B 39 - end of helix Processing helix chain 'B' and resid 74 through 84 removed outlier: 3.506A pdb=" N GLU B 84 " --> pdb=" O LEU B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 114 removed outlier: 3.508A pdb=" N ASP B 113 " --> pdb=" O LYS B 110 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE B 114 " --> pdb=" O ALA B 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 110 through 114' Processing helix chain 'B' and resid 152 through 157 removed outlier: 3.516A pdb=" N HIS B 156 " --> pdb=" O PRO B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 223 Processing helix chain 'B' and resid 224 through 226 No H-bonds generated for 'chain 'B' and resid 224 through 226' Processing helix chain 'C' and resid 19 through 31 removed outlier: 4.506A pdb=" N SER C 25 " --> pdb=" O ILE C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 39 Processing helix chain 'C' and resid 43 through 52 Processing helix chain 'C' and resid 79 through 86 Processing helix chain 'C' and resid 193 through 200 Processing helix chain 'C' and resid 203 through 211 removed outlier: 3.542A pdb=" N LEU C 207 " --> pdb=" O ASP C 203 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ARG C 209 " --> pdb=" O GLU C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 219 removed outlier: 3.718A pdb=" N GLN C 219 " --> pdb=" O GLY C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 229 removed outlier: 3.799A pdb=" N MET C 229 " --> pdb=" O SER C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 243 Processing helix chain 'C' and resid 249 through 262 Processing helix chain 'C' and resid 270 through 282 Processing helix chain 'C' and resid 302 through 316 Processing helix chain 'C' and resid 335 through 359 removed outlier: 3.595A pdb=" N GLY C 354 " --> pdb=" O ARG C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 375 through 388 Processing helix chain 'C' and resid 399 through 408 Processing helix chain 'C' and resid 431 through 435 removed outlier: 3.794A pdb=" N TYR C 435 " --> pdb=" O ARG C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 492 Processing helix chain 'C' and resid 525 through 529 Processing helix chain 'C' and resid 535 through 540 Processing helix chain 'C' and resid 541 through 546 Processing helix chain 'C' and resid 549 through 553 Processing helix chain 'C' and resid 554 through 566 removed outlier: 3.927A pdb=" N MET C 560 " --> pdb=" O ASN C 556 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N THR C 566 " --> pdb=" O SER C 562 " (cutoff:3.500A) Processing helix chain 'C' and resid 583 through 591 Processing helix chain 'C' and resid 692 through 697 Processing helix chain 'C' and resid 768 through 779 Processing helix chain 'C' and resid 854 through 858 Processing helix chain 'C' and resid 874 through 880 removed outlier: 4.582A pdb=" N SER C 878 " --> pdb=" O LEU C 874 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ARG C 879 " --> pdb=" O GLY C 875 " (cutoff:3.500A) Processing helix chain 'C' and resid 882 through 898 removed outlier: 3.591A pdb=" N LEU C 886 " --> pdb=" O LEU C 882 " (cutoff:3.500A) Processing helix chain 'C' and resid 910 through 932 removed outlier: 3.505A pdb=" N VAL C 924 " --> pdb=" O GLN C 920 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS C 928 " --> pdb=" O VAL C 924 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ARG C 929 " --> pdb=" O TYR C 925 " (cutoff:3.500A) Processing helix chain 'C' and resid 937 through 950 Processing helix chain 'C' and resid 958 through 969 removed outlier: 3.554A pdb=" N GLN C 969 " --> pdb=" O GLU C 965 " (cutoff:3.500A) Processing helix chain 'C' and resid 1001 through 1005 Processing helix chain 'C' and resid 1033 through 1044 Processing helix chain 'C' and resid 1045 through 1054 Processing helix chain 'C' and resid 1059 through 1072 Processing helix chain 'C' and resid 1082 through 1095 removed outlier: 3.659A pdb=" N ARG C1086 " --> pdb=" O PRO C1082 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 21 Processing helix chain 'D' and resid 46 through 51 Processing helix chain 'D' and resid 82 through 88 removed outlier: 3.758A pdb=" N VAL D 85 " --> pdb=" O LYS D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 105 Processing helix chain 'D' and resid 110 through 117 Processing helix chain 'D' and resid 119 through 128 Processing helix chain 'D' and resid 154 through 163 Processing helix chain 'D' and resid 423 through 426 Processing helix chain 'D' and resid 457 through 467 Processing helix chain 'D' and resid 469 through 482 removed outlier: 3.871A pdb=" N LYS D 482 " --> pdb=" O LEU D 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 485 through 506 Processing helix chain 'D' and resid 508 through 511 Processing helix chain 'D' and resid 521 through 525 Processing helix chain 'D' and resid 538 through 560 removed outlier: 3.914A pdb=" N ASP D 542 " --> pdb=" O SER D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 563 through 583 Processing helix chain 'D' and resid 603 through 608 removed outlier: 3.782A pdb=" N LEU D 607 " --> pdb=" O LEU D 603 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER D 608 " --> pdb=" O THR D 604 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 603 through 608' Processing helix chain 'D' and resid 612 through 618 Processing helix chain 'D' and resid 646 through 653 Processing helix chain 'D' and resid 653 through 664 Processing helix chain 'D' and resid 669 through 679 removed outlier: 4.058A pdb=" N ARG D 679 " --> pdb=" O ARG D 675 " (cutoff:3.500A) Processing helix chain 'D' and resid 680 through 683 Processing helix chain 'D' and resid 685 through 695 removed outlier: 4.000A pdb=" N ASP D 689 " --> pdb=" O ASP D 685 " (cutoff:3.500A) Processing helix chain 'D' and resid 709 through 711 No H-bonds generated for 'chain 'D' and resid 709 through 711' Processing helix chain 'D' and resid 732 through 737 Processing helix chain 'D' and resid 752 through 763 Processing helix chain 'D' and resid 764 through 768 Processing helix chain 'D' and resid 783 through 794 Processing helix chain 'D' and resid 808 through 818 Processing helix chain 'D' and resid 836 through 841 Processing helix chain 'D' and resid 845 through 855 Processing helix chain 'D' and resid 876 through 891 Processing helix chain 'D' and resid 892 through 900 removed outlier: 3.602A pdb=" N TRP D 897 " --> pdb=" O GLU D 893 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU D 898 " --> pdb=" O LYS D 894 " (cutoff:3.500A) Processing helix chain 'D' and resid 907 through 923 Processing helix chain 'D' and resid 924 through 944 removed outlier: 3.510A pdb=" N THR D 944 " --> pdb=" O THR D 940 " (cutoff:3.500A) Processing helix chain 'D' and resid 950 through 954 removed outlier: 3.704A pdb=" N ALA D 954 " --> pdb=" O ILE D 951 " (cutoff:3.500A) Processing helix chain 'D' and resid 957 through 980 removed outlier: 4.521A pdb=" N LYS D 961 " --> pdb=" O PRO D 957 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLN D 962 " --> pdb=" O GLU D 958 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N MET D 980 " --> pdb=" O GLN D 976 " (cutoff:3.500A) Processing helix chain 'D' and resid 984 through 1015 Processing helix chain 'D' and resid 1018 through 1026 Processing helix chain 'D' and resid 1031 through 1040 Processing helix chain 'D' and resid 1066 through 1102 removed outlier: 3.723A pdb=" N HIS D1075 " --> pdb=" O PHE D1071 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLY D1076 " --> pdb=" O ILE D1072 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N THR D1088 " --> pdb=" O THR D1084 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N ALA D1089 " --> pdb=" O ALA D1085 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ASP D1090 " --> pdb=" O LEU D1086 " (cutoff:3.500A) Processing helix chain 'D' and resid 1136 through 1145 Processing helix chain 'D' and resid 1167 through 1180 Processing helix chain 'D' and resid 1190 through 1194 Processing helix chain 'D' and resid 1202 through 1206 Processing helix chain 'D' and resid 1220 through 1231 removed outlier: 3.547A pdb=" N VAL D1224 " --> pdb=" O ALA D1220 " (cutoff:3.500A) Processing helix chain 'D' and resid 1232 through 1236 Processing helix chain 'D' and resid 1255 through 1264 Processing helix chain 'D' and resid 1331 through 1340 Processing helix chain 'D' and resid 1340 through 1359 removed outlier: 4.103A pdb=" N VAL D1355 " --> pdb=" O GLU D1351 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N TYR D1356 " --> pdb=" O ILE D1352 " (cutoff:3.500A) Processing helix chain 'D' and resid 1364 through 1376 removed outlier: 4.096A pdb=" N ILE D1368 " --> pdb=" O HIS D1364 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL D1371 " --> pdb=" O HIS D1367 " (cutoff:3.500A) Processing helix chain 'D' and resid 1397 through 1408 Processing helix chain 'D' and resid 1423 through 1430 Processing helix chain 'D' and resid 1433 through 1441 removed outlier: 3.753A pdb=" N ALA D1437 " --> pdb=" O SER D1433 " (cutoff:3.500A) Processing helix chain 'D' and resid 1442 through 1454 Processing helix chain 'D' and resid 1461 through 1468 removed outlier: 4.282A pdb=" N ASN D1465 " --> pdb=" O GLY D1461 " (cutoff:3.500A) Processing helix chain 'D' and resid 1474 through 1478 Processing helix chain 'D' and resid 1489 through 1502 removed outlier: 3.514A pdb=" N ALA D1502 " --> pdb=" O ALA D1498 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 12 Processing helix chain 'E' and resid 15 through 33 Processing helix chain 'E' and resid 41 through 45 removed outlier: 3.523A pdb=" N ARG E 45 " --> pdb=" O PRO E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 71 removed outlier: 3.631A pdb=" N TRP E 63 " --> pdb=" O ASN E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 93 Processing helix chain 'F' and resid 79 through 89 Processing helix chain 'F' and resid 95 through 121 Processing helix chain 'F' and resid 123 through 137 Processing helix chain 'F' and resid 152 through 164 Processing helix chain 'F' and resid 167 through 191 removed outlier: 3.634A pdb=" N LYS F 171 " --> pdb=" O PRO F 167 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ARG F 172 " --> pdb=" O LYS F 168 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N TYR F 173 " --> pdb=" O GLU F 169 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA F 182 " --> pdb=" O ARG F 178 " (cutoff:3.500A) Processing helix chain 'F' and resid 191 through 200 removed outlier: 4.100A pdb=" N VAL F 195 " --> pdb=" O ASN F 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 208 through 227 Processing helix chain 'F' and resid 228 through 232 removed outlier: 3.894A pdb=" N ARG F 231 " --> pdb=" O GLU F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 255 removed outlier: 3.898A pdb=" N TYR F 238 " --> pdb=" O LYS F 234 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N TRP F 241 " --> pdb=" O THR F 237 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N TRP F 242 " --> pdb=" O TYR F 238 " (cutoff:3.500A) Processing helix chain 'F' and resid 261 through 283 Processing helix chain 'F' and resid 287 through 296 Processing helix chain 'F' and resid 300 through 311 Processing helix chain 'F' and resid 328 through 333 removed outlier: 3.575A pdb=" N ASP F 331 " --> pdb=" O PHE F 328 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE F 332 " --> pdb=" O TYR F 329 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE F 333 " --> pdb=" O GLY F 330 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 328 through 333' Processing helix chain 'F' and resid 340 through 359 Processing helix chain 'F' and resid 362 through 374 removed outlier: 3.516A pdb=" N LEU F 369 " --> pdb=" O GLU F 365 " (cutoff:3.500A) Processing helix chain 'F' and resid 382 through 391 Processing helix chain 'F' and resid 393 through 416 Processing helix chain 'F' and resid 419 through 423 removed outlier: 3.835A pdb=" N ASP F 423 " --> pdb=" O ASP F 420 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 16 removed outlier: 6.716A pdb=" N ASP A 193 " --> pdb=" O PRO A 27 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 96 through 104 removed outlier: 7.407A pdb=" N ASN A 139 " --> pdb=" O ILE A 58 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N ILE A 58 " --> pdb=" O ASN A 139 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N GLU A 141 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N VAL A 56 " --> pdb=" O GLU A 141 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ARG A 143 " --> pdb=" O THR A 54 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 87 through 89 Processing sheet with id=AA4, first strand: chain 'A' and resid 108 through 110 removed outlier: 6.904A pdb=" N VAL A 109 " --> pdb=" O ILE A 129 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 150 through 151 Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 16 removed outlier: 6.425A pdb=" N ASP B 193 " --> pdb=" O PRO B 27 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N THR B 190 " --> pdb=" O LEU B 186 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N LEU B 186 " --> pdb=" O THR B 190 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 96 through 104 removed outlier: 7.310A pdb=" N ASN B 139 " --> pdb=" O ILE B 58 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N ILE B 58 " --> pdb=" O ASN B 139 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N GLU B 141 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N VAL B 56 " --> pdb=" O GLU B 141 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ARG B 143 " --> pdb=" O THR B 54 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 87 through 89 Processing sheet with id=AA9, first strand: chain 'B' and resid 107 through 109 removed outlier: 3.724A pdb=" N ALA B 130 " --> pdb=" O VAL B 109 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 150 through 151 Processing sheet with id=AB2, first strand: chain 'C' and resid 3 through 5 Processing sheet with id=AB3, first strand: chain 'C' and resid 65 through 73 removed outlier: 6.815A pdb=" N ARG C 97 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N TYR C 71 " --> pdb=" O TYR C 95 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N TYR C 95 " --> pdb=" O TYR C 71 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LEU C 73 " --> pdb=" O PRO C 93 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N ALA C 92 " --> pdb=" O HIS C 117 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N HIS C 117 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N LEU C 94 " --> pdb=" O LEU C 115 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 127 through 129 Processing sheet with id=AB5, first strand: chain 'C' and resid 331 through 334 removed outlier: 6.298A pdb=" N SER C 138 " --> pdb=" O SER C 411 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 145 through 150 removed outlier: 6.856A pdb=" N TYR C 158 " --> pdb=" O VAL C 176 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N VAL C 176 " --> pdb=" O TYR C 158 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP C 173 " --> pdb=" O LYS C 185 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 291 through 294 Processing sheet with id=AB8, first strand: chain 'C' and resid 460 through 461 removed outlier: 6.598A pdb=" N ILE C 467 " --> pdb=" O MET C 486 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N MET C 486 " --> pdb=" O ILE C 467 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N THR C 469 " --> pdb=" O VAL C 484 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N VAL C 484 " --> pdb=" O THR C 469 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N TYR C 471 " --> pdb=" O GLU C 482 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N GLU C 482 " --> pdb=" O TYR C 471 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N ARG C 473 " --> pdb=" O THR C 480 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 460 through 461 Processing sheet with id=AC1, first strand: chain 'C' and resid 503 through 504 Processing sheet with id=AC2, first strand: chain 'C' and resid 595 through 596 removed outlier: 6.638A pdb=" N LEU C 595 " --> pdb=" O LEU C 655 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 620 through 624 removed outlier: 6.844A pdb=" N ARG C 610 " --> pdb=" O VAL C 606 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N VAL C 606 " --> pdb=" O ARG C 610 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N VAL C 612 " --> pdb=" O ALA C 604 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 629 through 630 Processing sheet with id=AC5, first strand: chain 'C' and resid 661 through 662 Processing sheet with id=AC6, first strand: chain 'C' and resid 971 through 972 removed outlier: 5.378A pdb=" N LYS C 838 " --> pdb=" O LEU C 997 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N ASP C 837 " --> pdb=" O VAL C 849 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N ILE C 688 " --> pdb=" O ALA C 850 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ILE C 852 " --> pdb=" O ILE C 688 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ILE C 690 " --> pdb=" O ILE C 852 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL C 689 " --> pdb=" O ILE C 870 " (cutoff:3.500A) removed outlier: 8.932A pdb=" N VAL C 869 " --> pdb=" O ASN C 671 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N LEU C 673 " --> pdb=" O VAL C 869 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N LEU C 871 " --> pdb=" O LEU C 673 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ALA C 675 " --> pdb=" O LEU C 871 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N VAL C 988 " --> pdb=" O ILE C 676 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 718 through 719 removed outlier: 3.655A pdb=" N GLU C 821 " --> pdb=" O ALA C 712 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ASP C 714 " --> pdb=" O VAL C 819 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N VAL C 819 " --> pdb=" O ASP C 714 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG C 802 " --> pdb=" O TYR C 826 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ALA C 828 " --> pdb=" O VAL C 800 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N VAL C 800 " --> pdb=" O ALA C 828 " (cutoff:3.500A) removed outlier: 8.677A pdb=" N LYS C 830 " --> pdb=" O GLY C 798 " (cutoff:3.500A) removed outlier: 9.039A pdb=" N GLY C 798 " --> pdb=" O LYS C 830 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 754 through 756 removed outlier: 6.738A pdb=" N LEU C 790 " --> pdb=" O LEU C 755 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 759 through 761 Processing sheet with id=AD1, first strand: chain 'C' and resid 1006 through 1008 Processing sheet with id=AD2, first strand: chain 'C' and resid 1031 through 1032 Processing sheet with id=AD3, first strand: chain 'C' and resid 1097 through 1102 Processing sheet with id=AD4, first strand: chain 'D' and resid 22 through 25 removed outlier: 7.716A pdb=" N HIS D 92 " --> pdb=" O TYR D 23 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N GLU D 25 " --> pdb=" O HIS D 92 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N GLU D 94 " --> pdb=" O GLU D 25 " (cutoff:3.500A) removed outlier: 10.400A pdb=" N LEU D 95 " --> pdb=" O PRO D 518 " (cutoff:3.500A) removed outlier: 10.974A pdb=" N THR D 97 " --> pdb=" O ALA D 516 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N ALA D 516 " --> pdb=" O THR D 97 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 152 through 153 removed outlier: 5.274A pdb=" N VAL D 134 " --> pdb=" O ARG D 455 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ARG D 455 " --> pdb=" O VAL D 134 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 141 through 142 Processing sheet with id=AD7, first strand: chain 'D' and resid 166 through 170 Processing sheet with id=AD8, first strand: chain 'D' and resid 190 through 192 removed outlier: 3.739A pdb=" N ALA D 192 " --> pdb=" O VAL D 195 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 339 through 346 removed outlier: 7.010A pdb=" N GLU D 389 " --> pdb=" O ARG D 209 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N VAL D 211 " --> pdb=" O LEU D 387 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N LEU D 387 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N VAL D 213 " --> pdb=" O VAL D 385 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N VAL D 385 " --> pdb=" O VAL D 213 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N TYR D 215 " --> pdb=" O GLY D 383 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N GLY D 383 " --> pdb=" O TYR D 215 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA D 359 " --> pdb=" O VAL D 385 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 352 through 353 removed outlier: 3.664A pdb=" N ASN D 352 " --> pdb=" O ALA D 369 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N VAL D 377 " --> pdb=" O ILE D 367 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 398 through 402 Processing sheet with id=AE3, first strand: chain 'D' and resid 420 through 422 removed outlier: 7.444A pdb=" N VAL D 427 " --> pdb=" O LEU D 421 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 528 through 529 Processing sheet with id=AE5, first strand: chain 'D' and resid 805 through 806 Processing sheet with id=AE6, first strand: chain 'D' and resid 842 through 843 Processing sheet with id=AE7, first strand: chain 'D' and resid 1106 through 1109 Processing sheet with id=AE8, first strand: chain 'D' and resid 1118 through 1121 Processing sheet with id=AE9, first strand: chain 'D' and resid 1123 through 1126 Processing sheet with id=AF1, first strand: chain 'D' and resid 1153 through 1155 Processing sheet with id=AF2, first strand: chain 'D' and resid 1300 through 1303 removed outlier: 3.782A pdb=" N GLY D1279 " --> pdb=" O VAL D1319 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 1394 through 1396 removed outlier: 6.859A pdb=" N ALA D1416 " --> pdb=" O THR D1382 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 1484 through 1488 Processing sheet with id=AF5, first strand: chain 'E' and resid 47 through 49 1251 hydrogen bonds defined for protein. 3477 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 43 hydrogen bonds 82 hydrogen bond angles 0 basepair planarities 17 basepair parallelities 37 stacking parallelities Total time for adding SS restraints: 15.07 Time building geometry restraints manager: 12.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 8158 1.33 - 1.45: 4285 1.45 - 1.57: 16162 1.57 - 1.69: 140 1.69 - 1.81: 125 Bond restraints: 28870 Sorted by residual: bond pdb=" O3' G I 6 " pdb=" P G I 7 " ideal model delta sigma weight residual 1.607 1.555 0.052 1.50e-02 4.44e+03 1.21e+01 bond pdb=" O3' G I 9 " pdb=" P G I 10 " ideal model delta sigma weight residual 1.607 1.555 0.052 1.50e-02 4.44e+03 1.20e+01 bond pdb=" O5' G I 2 " pdb=" C5' G I 2 " ideal model delta sigma weight residual 1.420 1.444 -0.024 1.50e-02 4.44e+03 2.62e+00 bond pdb=" CA THR F 319 " pdb=" CB THR F 319 " ideal model delta sigma weight residual 1.529 1.550 -0.020 1.37e-02 5.33e+03 2.24e+00 bond pdb=" C GLU D 776 " pdb=" N PRO D 777 " ideal model delta sigma weight residual 1.332 1.350 -0.018 1.30e-02 5.92e+03 2.00e+00 ... (remaining 28865 not shown) Histogram of bond angle deviations from ideal: 98.95 - 105.96: 1131 105.96 - 112.97: 15555 112.97 - 119.98: 10050 119.98 - 126.99: 12163 126.99 - 134.00: 471 Bond angle restraints: 39370 Sorted by residual: angle pdb=" O ASP C 429 " pdb=" C ASP C 429 " pdb=" N VAL C 430 " ideal model delta sigma weight residual 123.10 117.09 6.01 1.15e+00 7.56e-01 2.73e+01 angle pdb=" C3' G I 6 " pdb=" C2' G I 6 " pdb=" O2' G I 6 " ideal model delta sigma weight residual 110.70 103.01 7.69 1.50e+00 4.44e-01 2.63e+01 angle pdb=" N ARG C 420 " pdb=" CA ARG C 420 " pdb=" C ARG C 420 " ideal model delta sigma weight residual 111.07 115.61 -4.54 1.07e+00 8.73e-01 1.80e+01 angle pdb=" N HIS C 431 " pdb=" CA HIS C 431 " pdb=" C HIS C 431 " ideal model delta sigma weight residual 110.50 116.32 -5.82 1.41e+00 5.03e-01 1.71e+01 angle pdb=" N LYS F 325 " pdb=" CA LYS F 325 " pdb=" C LYS F 325 " ideal model delta sigma weight residual 112.99 106.78 6.21 1.61e+00 3.86e-01 1.49e+01 ... (remaining 39365 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.88: 17064 34.88 - 69.76: 515 69.76 - 104.63: 34 104.63 - 139.51: 0 139.51 - 174.39: 2 Dihedral angle restraints: 17615 sinusoidal: 7925 harmonic: 9690 Sorted by residual: dihedral pdb=" O4' G I 3 " pdb=" C1' G I 3 " pdb=" N9 G I 3 " pdb=" C4 G I 3 " ideal model delta sinusoidal sigma weight residual 68.00 158.91 -90.91 1 1.70e+01 3.46e-03 3.37e+01 dihedral pdb=" CA TYR D1207 " pdb=" C TYR D1207 " pdb=" N ASP D1208 " pdb=" CA ASP D1208 " ideal model delta harmonic sigma weight residual 180.00 154.16 25.84 0 5.00e+00 4.00e-02 2.67e+01 dihedral pdb=" C4' DA G 23 " pdb=" C3' DA G 23 " pdb=" O3' DA G 23 " pdb=" P DA G 24 " ideal model delta sinusoidal sigma weight residual -140.00 34.39 -174.39 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 17612 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 3526 0.050 - 0.100: 720 0.100 - 0.149: 180 0.149 - 0.199: 9 0.199 - 0.249: 2 Chirality restraints: 4437 Sorted by residual: chirality pdb=" C3' G I 6 " pdb=" C4' G I 6 " pdb=" O3' G I 6 " pdb=" C2' G I 6 " both_signs ideal model delta sigma weight residual False -2.48 -2.73 0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CA VAL C 430 " pdb=" N VAL C 430 " pdb=" C VAL C 430 " pdb=" CB VAL C 430 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" C3' G I 2 " pdb=" C4' G I 2 " pdb=" O3' G I 2 " pdb=" C2' G I 2 " both_signs ideal model delta sigma weight residual False -2.48 -2.67 0.19 2.00e-01 2.50e+01 8.82e-01 ... (remaining 4434 not shown) Planarity restraints: 4892 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP C 429 " 0.022 2.00e-02 2.50e+03 4.19e-02 1.76e+01 pdb=" C ASP C 429 " -0.073 2.00e-02 2.50e+03 pdb=" O ASP C 429 " 0.027 2.00e-02 2.50e+03 pdb=" N VAL C 430 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU D 389 " 0.067 5.00e-02 4.00e+02 1.02e-01 1.65e+01 pdb=" N PRO D 390 " -0.176 5.00e-02 4.00e+02 pdb=" CA PRO D 390 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO D 390 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 227 " -0.061 5.00e-02 4.00e+02 9.38e-02 1.41e+01 pdb=" N PRO A 228 " 0.162 5.00e-02 4.00e+02 pdb=" CA PRO A 228 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO A 228 " -0.050 5.00e-02 4.00e+02 ... (remaining 4889 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 271 2.64 - 3.20: 24268 3.20 - 3.77: 42608 3.77 - 4.33: 60081 4.33 - 4.90: 99078 Nonbonded interactions: 226306 Sorted by model distance: nonbonded pdb=" O LYS D 840 " pdb="MG MG D2004 " model vdw 2.071 2.170 nonbonded pdb=" O SER C 143 " pdb=" OH TYR C 147 " model vdw 2.208 2.440 nonbonded pdb=" O3' G I 11 " pdb="MG MG D2003 " model vdw 2.209 2.170 nonbonded pdb=" OG1 THR E 50 " pdb=" O GLY E 53 " model vdw 2.210 2.440 nonbonded pdb=" OD1 ASP D 739 " pdb="MG MG D2003 " model vdw 2.217 2.170 ... (remaining 226301 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 'A' and resid 7 through 228) selection = (chain 'B' and resid 7 through 228) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.30 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.000 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: 5.330 Check model and map are aligned: 0.460 Set scattering table: 0.260 Process input model: 91.070 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 112.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 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 0.052 28870 Z= 0.174 Angle : 0.608 8.101 39370 Z= 0.357 Chirality : 0.043 0.249 4437 Planarity : 0.005 0.102 4892 Dihedral : 15.538 174.390 11379 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.21 % Allowed : 0.24 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.50 (0.14), residues: 3350 helix: 1.32 (0.15), residues: 1281 sheet: -0.12 (0.23), residues: 448 loop : -0.26 (0.14), residues: 1621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 996 HIS 0.004 0.001 HIS C 327 PHE 0.022 0.001 PHE D 754 TYR 0.020 0.001 TYR D 205 ARG 0.008 0.000 ARG D1062 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6700 Ramachandran restraints generated. 3350 Oldfield, 0 Emsley, 3350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6700 Ramachandran restraints generated. 3350 Oldfield, 0 Emsley, 3350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 370 time to evaluate : 3.718 Fit side-chains REVERT: A 191 ASP cc_start: 0.5954 (m-30) cc_final: 0.5641 (t0) REVERT: B 12 THR cc_start: 0.8070 (m) cc_final: 0.7542 (p) REVERT: C 196 LEU cc_start: 0.7539 (tp) cc_final: 0.7333 (tm) REVERT: C 229 MET cc_start: 0.4756 (ptp) cc_final: 0.4484 (ptm) REVERT: C 560 MET cc_start: 0.7365 (mtp) cc_final: 0.7164 (ttm) REVERT: D 30 GLU cc_start: 0.6199 (mt-10) cc_final: 0.5831 (mt-10) REVERT: D 54 LYS cc_start: 0.7692 (mmtt) cc_final: 0.7315 (mmmm) REVERT: D 393 ILE cc_start: 0.5906 (mm) cc_final: 0.5289 (mt) REVERT: D 497 GLU cc_start: 0.6530 (mt-10) cc_final: 0.6327 (mt-10) REVERT: D 1325 LEU cc_start: 0.7521 (mp) cc_final: 0.7156 (mp) REVERT: E 8 LYS cc_start: 0.8509 (ttmm) cc_final: 0.8178 (tttp) REVERT: F 152 ASP cc_start: 0.5743 (p0) cc_final: 0.5368 (m-30) outliers start: 6 outliers final: 0 residues processed: 374 average time/residue: 1.8821 time to fit residues: 794.5271 Evaluate side-chains 244 residues out of total 2872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 244 time to evaluate : 3.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 287 optimal weight: 8.9990 chunk 258 optimal weight: 5.9990 chunk 143 optimal weight: 7.9990 chunk 88 optimal weight: 8.9990 chunk 174 optimal weight: 0.5980 chunk 138 optimal weight: 6.9990 chunk 267 optimal weight: 0.5980 chunk 103 optimal weight: 9.9990 chunk 162 optimal weight: 7.9990 chunk 198 optimal weight: 4.9990 chunk 309 optimal weight: 9.9990 overall best weight: 3.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 GLN C 187 ASN C 204 GLN C 556 ASN ** D 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 962 GLN ** D1124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1359 GLN F 312 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.1289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 28870 Z= 0.336 Angle : 0.636 9.254 39370 Z= 0.334 Chirality : 0.046 0.185 4437 Planarity : 0.006 0.062 4892 Dihedral : 14.954 173.783 4604 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.85 % Allowed : 9.37 % Favored : 88.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.39 (0.14), residues: 3350 helix: 1.22 (0.14), residues: 1299 sheet: -0.14 (0.24), residues: 462 loop : -0.35 (0.15), residues: 1589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 200 HIS 0.009 0.002 HIS C 327 PHE 0.024 0.002 PHE D 982 TYR 0.018 0.002 TYR A 20 ARG 0.008 0.001 ARG D 486 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6700 Ramachandran restraints generated. 3350 Oldfield, 0 Emsley, 3350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6700 Ramachandran restraints generated. 3350 Oldfield, 0 Emsley, 3350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 258 time to evaluate : 3.291 Fit side-chains REVERT: A 96 THR cc_start: 0.8587 (OUTLIER) cc_final: 0.8297 (m) REVERT: A 191 ASP cc_start: 0.5931 (m-30) cc_final: 0.5638 (t0) REVERT: B 12 THR cc_start: 0.8024 (m) cc_final: 0.7529 (p) REVERT: B 102 LYS cc_start: 0.7044 (ptpt) cc_final: 0.6762 (mmtt) REVERT: C 222 MET cc_start: 0.2262 (OUTLIER) cc_final: 0.2021 (mpp) REVERT: C 580 MET cc_start: 0.8113 (mtt) cc_final: 0.7893 (mtt) REVERT: C 984 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7432 (mt-10) REVERT: C 1034 GLU cc_start: 0.7150 (OUTLIER) cc_final: 0.6407 (mp0) REVERT: D 30 GLU cc_start: 0.6423 (mt-10) cc_final: 0.5895 (mt-10) REVERT: D 54 LYS cc_start: 0.7734 (mmtt) cc_final: 0.7301 (mmmm) REVERT: D 393 ILE cc_start: 0.5962 (mm) cc_final: 0.5408 (mt) REVERT: D 455 ARG cc_start: 0.7887 (OUTLIER) cc_final: 0.7301 (mtp180) REVERT: D 483 HIS cc_start: 0.7699 (t-90) cc_final: 0.7483 (t-90) REVERT: D 979 GLU cc_start: 0.6860 (mm-30) cc_final: 0.6071 (tp30) REVERT: D 1325 LEU cc_start: 0.7557 (mp) cc_final: 0.7205 (mp) REVERT: E 8 LYS cc_start: 0.8500 (ttmm) cc_final: 0.8127 (tttp) REVERT: F 152 ASP cc_start: 0.5761 (p0) cc_final: 0.5428 (m-30) outliers start: 53 outliers final: 22 residues processed: 290 average time/residue: 1.6524 time to fit residues: 550.9861 Evaluate side-chains 256 residues out of total 2872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 229 time to evaluate : 3.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 140 MET Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 121 MET Chi-restraints excluded: chain C residue 184 MET Chi-restraints excluded: chain C residue 222 MET Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain C residue 984 GLU Chi-restraints excluded: chain C residue 995 MET Chi-restraints excluded: chain C residue 1034 GLU Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 428 LYS Chi-restraints excluded: chain D residue 455 ARG Chi-restraints excluded: chain D residue 682 ASP Chi-restraints excluded: chain D residue 821 VAL Chi-restraints excluded: chain D residue 892 ASP Chi-restraints excluded: chain D residue 975 GLU Chi-restraints excluded: chain D residue 995 LEU Chi-restraints excluded: chain D residue 1139 ASP Chi-restraints excluded: chain D residue 1154 GLU Chi-restraints excluded: chain D residue 1176 LYS Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain F residue 305 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 172 optimal weight: 0.9990 chunk 96 optimal weight: 0.7980 chunk 257 optimal weight: 0.9980 chunk 210 optimal weight: 8.9990 chunk 85 optimal weight: 9.9990 chunk 310 optimal weight: 20.0000 chunk 335 optimal weight: 10.0000 chunk 276 optimal weight: 5.9990 chunk 307 optimal weight: 1.9990 chunk 105 optimal weight: 4.9990 chunk 248 optimal weight: 6.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 38 ASN C 204 GLN ** D 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 59 ASN F 312 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 28870 Z= 0.211 Angle : 0.546 9.085 39370 Z= 0.288 Chirality : 0.043 0.179 4437 Planarity : 0.005 0.053 4892 Dihedral : 14.846 173.870 4604 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.67 % Allowed : 11.46 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.58 (0.14), residues: 3350 helix: 1.44 (0.14), residues: 1307 sheet: -0.18 (0.23), residues: 479 loop : -0.25 (0.15), residues: 1564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 200 HIS 0.006 0.001 HIS A 156 PHE 0.025 0.002 PHE C 191 TYR 0.013 0.001 TYR D1207 ARG 0.008 0.000 ARG D 489 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6700 Ramachandran restraints generated. 3350 Oldfield, 0 Emsley, 3350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6700 Ramachandran restraints generated. 3350 Oldfield, 0 Emsley, 3350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 249 time to evaluate : 3.439 Fit side-chains REVERT: A 96 THR cc_start: 0.8647 (t) cc_final: 0.8331 (m) REVERT: A 191 ASP cc_start: 0.5920 (m-30) cc_final: 0.5637 (t0) REVERT: B 12 THR cc_start: 0.7907 (m) cc_final: 0.7434 (p) REVERT: B 100 LEU cc_start: 0.6802 (OUTLIER) cc_final: 0.6239 (pp) REVERT: B 102 LYS cc_start: 0.7070 (OUTLIER) cc_final: 0.6736 (mttt) REVERT: C 524 VAL cc_start: 0.8254 (OUTLIER) cc_final: 0.8000 (p) REVERT: C 984 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7386 (mt-10) REVERT: C 1034 GLU cc_start: 0.7110 (OUTLIER) cc_final: 0.6437 (mp0) REVERT: D 30 GLU cc_start: 0.6518 (mt-10) cc_final: 0.5906 (mt-10) REVERT: D 54 LYS cc_start: 0.7710 (mmtt) cc_final: 0.7262 (mmmm) REVERT: D 393 ILE cc_start: 0.6084 (mm) cc_final: 0.5527 (mt) REVERT: D 455 ARG cc_start: 0.7896 (OUTLIER) cc_final: 0.7375 (mtp180) REVERT: D 966 GLU cc_start: 0.6313 (OUTLIER) cc_final: 0.5778 (tp30) REVERT: D 979 GLU cc_start: 0.6953 (mm-30) cc_final: 0.6353 (tp30) REVERT: D 1325 LEU cc_start: 0.7556 (mp) cc_final: 0.7232 (mp) REVERT: E 8 LYS cc_start: 0.8432 (ttmm) cc_final: 0.8081 (tttp) REVERT: E 68 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8339 (tp) REVERT: F 120 THR cc_start: 0.5941 (OUTLIER) cc_final: 0.5651 (p) REVERT: F 152 ASP cc_start: 0.5800 (p0) cc_final: 0.5479 (m-30) outliers start: 48 outliers final: 19 residues processed: 284 average time/residue: 1.5882 time to fit residues: 520.4188 Evaluate side-chains 257 residues out of total 2872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 229 time to evaluate : 3.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 102 LYS Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 984 GLU Chi-restraints excluded: chain C residue 1034 GLU Chi-restraints excluded: chain C residue 1048 THR Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 428 LYS Chi-restraints excluded: chain D residue 455 ARG Chi-restraints excluded: chain D residue 682 ASP Chi-restraints excluded: chain D residue 892 ASP Chi-restraints excluded: chain D residue 966 GLU Chi-restraints excluded: chain D residue 972 LEU Chi-restraints excluded: chain D residue 1139 ASP Chi-restraints excluded: chain D residue 1154 GLU Chi-restraints excluded: chain D residue 1176 LYS Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 253 ASP Chi-restraints excluded: chain F residue 287 THR Chi-restraints excluded: chain F residue 305 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 306 optimal weight: 30.0000 chunk 233 optimal weight: 0.0870 chunk 161 optimal weight: 7.9990 chunk 34 optimal weight: 7.9990 chunk 148 optimal weight: 5.9990 chunk 208 optimal weight: 3.9990 chunk 311 optimal weight: 9.9990 chunk 329 optimal weight: 9.9990 chunk 162 optimal weight: 0.5980 chunk 295 optimal weight: 10.0000 chunk 88 optimal weight: 2.9990 overall best weight: 2.7364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 834 GLN ** D 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 28870 Z= 0.258 Angle : 0.565 8.502 39370 Z= 0.297 Chirality : 0.044 0.179 4437 Planarity : 0.005 0.052 4892 Dihedral : 14.858 173.302 4604 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.79 % Allowed : 12.19 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.55 (0.14), residues: 3350 helix: 1.41 (0.14), residues: 1309 sheet: -0.13 (0.24), residues: 455 loop : -0.29 (0.15), residues: 1586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 200 HIS 0.007 0.001 HIS C 327 PHE 0.028 0.002 PHE C 191 TYR 0.013 0.001 TYR C 458 ARG 0.009 0.001 ARG C 420 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6700 Ramachandran restraints generated. 3350 Oldfield, 0 Emsley, 3350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6700 Ramachandran restraints generated. 3350 Oldfield, 0 Emsley, 3350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 247 time to evaluate : 3.344 Fit side-chains REVERT: A 96 THR cc_start: 0.8638 (t) cc_final: 0.8322 (m) REVERT: A 191 ASP cc_start: 0.5945 (m-30) cc_final: 0.5662 (t0) REVERT: B 12 THR cc_start: 0.7906 (m) cc_final: 0.7454 (p) REVERT: B 102 LYS cc_start: 0.7110 (OUTLIER) cc_final: 0.6799 (mmtt) REVERT: C 28 ARG cc_start: 0.7796 (OUTLIER) cc_final: 0.7423 (ttt90) REVERT: C 49 ARG cc_start: 0.7307 (mmt-90) cc_final: 0.7064 (mtp85) REVERT: C 524 VAL cc_start: 0.8278 (OUTLIER) cc_final: 0.8007 (p) REVERT: C 984 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7443 (mt-10) REVERT: C 1034 GLU cc_start: 0.7116 (OUTLIER) cc_final: 0.6381 (mp0) REVERT: D 30 GLU cc_start: 0.6599 (mt-10) cc_final: 0.6031 (mt-10) REVERT: D 54 LYS cc_start: 0.7730 (mmtt) cc_final: 0.7295 (mmmm) REVERT: D 455 ARG cc_start: 0.7921 (OUTLIER) cc_final: 0.7377 (mtp180) REVERT: D 966 GLU cc_start: 0.6253 (OUTLIER) cc_final: 0.5733 (tp30) REVERT: D 971 LEU cc_start: 0.6925 (OUTLIER) cc_final: 0.6627 (mt) REVERT: D 979 GLU cc_start: 0.6860 (mm-30) cc_final: 0.6417 (tp30) REVERT: D 980 MET cc_start: 0.6754 (ppp) cc_final: 0.6446 (pp-130) REVERT: D 982 PHE cc_start: 0.6369 (m-10) cc_final: 0.6155 (m-10) REVERT: D 1325 LEU cc_start: 0.7563 (mp) cc_final: 0.7219 (mp) REVERT: E 68 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8335 (tp) REVERT: F 93 LEU cc_start: 0.7074 (OUTLIER) cc_final: 0.6816 (mt) REVERT: F 120 THR cc_start: 0.5938 (OUTLIER) cc_final: 0.5638 (p) REVERT: F 163 LEU cc_start: 0.7169 (OUTLIER) cc_final: 0.6749 (mp) REVERT: F 264 MET cc_start: 0.7416 (mmm) cc_final: 0.6986 (mmt) outliers start: 80 outliers final: 35 residues processed: 306 average time/residue: 1.5844 time to fit residues: 560.3135 Evaluate side-chains 273 residues out of total 2872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 226 time to evaluate : 3.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 102 LYS Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 185 ARG Chi-restraints excluded: chain C residue 28 ARG Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 710 ILE Chi-restraints excluded: chain C residue 748 GLU Chi-restraints excluded: chain C residue 848 VAL Chi-restraints excluded: chain C residue 984 GLU Chi-restraints excluded: chain C residue 995 MET Chi-restraints excluded: chain C residue 1034 GLU Chi-restraints excluded: chain C residue 1048 THR Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 428 LYS Chi-restraints excluded: chain D residue 455 ARG Chi-restraints excluded: chain D residue 632 VAL Chi-restraints excluded: chain D residue 682 ASP Chi-restraints excluded: chain D residue 821 VAL Chi-restraints excluded: chain D residue 864 VAL Chi-restraints excluded: chain D residue 966 GLU Chi-restraints excluded: chain D residue 971 LEU Chi-restraints excluded: chain D residue 995 LEU Chi-restraints excluded: chain D residue 1139 ASP Chi-restraints excluded: chain D residue 1154 GLU Chi-restraints excluded: chain D residue 1176 LYS Chi-restraints excluded: chain D residue 1207 TYR Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 163 LEU Chi-restraints excluded: chain F residue 253 ASP Chi-restraints excluded: chain F residue 287 THR Chi-restraints excluded: chain F residue 305 GLU Chi-restraints excluded: chain F residue 343 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 274 optimal weight: 9.9990 chunk 187 optimal weight: 10.0000 chunk 4 optimal weight: 5.9990 chunk 245 optimal weight: 6.9990 chunk 135 optimal weight: 4.9990 chunk 281 optimal weight: 9.9990 chunk 227 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 168 optimal weight: 9.9990 chunk 295 optimal weight: 9.9990 chunk 83 optimal weight: 2.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 337 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 28870 Z= 0.424 Angle : 0.687 10.928 39370 Z= 0.359 Chirality : 0.048 0.221 4437 Planarity : 0.007 0.055 4892 Dihedral : 15.147 172.449 4604 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.03 % Allowed : 13.97 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.14), residues: 3350 helix: 0.93 (0.14), residues: 1309 sheet: -0.31 (0.24), residues: 455 loop : -0.58 (0.14), residues: 1586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 200 HIS 0.011 0.002 HIS A 156 PHE 0.029 0.003 PHE C 425 TYR 0.022 0.002 TYR C 458 ARG 0.007 0.001 ARG C 420 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6700 Ramachandran restraints generated. 3350 Oldfield, 0 Emsley, 3350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6700 Ramachandran restraints generated. 3350 Oldfield, 0 Emsley, 3350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 240 time to evaluate : 3.447 Fit side-chains REVERT: C 28 ARG cc_start: 0.7864 (OUTLIER) cc_final: 0.7574 (ttt90) REVERT: C 49 ARG cc_start: 0.7435 (mmt-90) cc_final: 0.7191 (mtp85) REVERT: C 191 PHE cc_start: 0.7704 (p90) cc_final: 0.7022 (p90) REVERT: C 560 MET cc_start: 0.7568 (OUTLIER) cc_final: 0.6982 (mtp) REVERT: C 984 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7471 (mt-10) REVERT: C 1034 GLU cc_start: 0.7178 (OUTLIER) cc_final: 0.6418 (mp0) REVERT: C 1035 MET cc_start: 0.7895 (mtt) cc_final: 0.7670 (mtt) REVERT: D 30 GLU cc_start: 0.6511 (mt-10) cc_final: 0.6205 (mt-10) REVERT: D 54 LYS cc_start: 0.7810 (mmtt) cc_final: 0.7353 (mmmm) REVERT: D 455 ARG cc_start: 0.7920 (OUTLIER) cc_final: 0.7305 (mtp180) REVERT: D 966 GLU cc_start: 0.6386 (OUTLIER) cc_final: 0.5797 (tp30) REVERT: D 979 GLU cc_start: 0.6952 (mm-30) cc_final: 0.6398 (tp30) REVERT: D 980 MET cc_start: 0.6750 (ppp) cc_final: 0.6498 (pp-130) REVERT: E 8 LYS cc_start: 0.8443 (ttmm) cc_final: 0.8051 (tttp) REVERT: F 79 ASP cc_start: 0.7164 (OUTLIER) cc_final: 0.6886 (t0) REVERT: F 120 THR cc_start: 0.5845 (OUTLIER) cc_final: 0.5622 (p) REVERT: F 163 LEU cc_start: 0.7238 (OUTLIER) cc_final: 0.6800 (mp) REVERT: F 285 GLU cc_start: 0.6646 (OUTLIER) cc_final: 0.6429 (tp30) REVERT: F 295 MET cc_start: 0.7347 (mmm) cc_final: 0.7077 (mmm) outliers start: 87 outliers final: 46 residues processed: 305 average time/residue: 1.5683 time to fit residues: 554.3397 Evaluate side-chains 282 residues out of total 2872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 226 time to evaluate : 3.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 140 MET Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain C residue 28 ARG Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 209 ARG Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 361 MET Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 560 MET Chi-restraints excluded: chain C residue 710 ILE Chi-restraints excluded: chain C residue 848 VAL Chi-restraints excluded: chain C residue 984 GLU Chi-restraints excluded: chain C residue 1034 GLU Chi-restraints excluded: chain C residue 1048 THR Chi-restraints excluded: chain D residue 8 VAL Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 428 LYS Chi-restraints excluded: chain D residue 455 ARG Chi-restraints excluded: chain D residue 632 VAL Chi-restraints excluded: chain D residue 676 MET Chi-restraints excluded: chain D residue 682 ASP Chi-restraints excluded: chain D residue 821 VAL Chi-restraints excluded: chain D residue 864 VAL Chi-restraints excluded: chain D residue 904 VAL Chi-restraints excluded: chain D residue 966 GLU Chi-restraints excluded: chain D residue 995 LEU Chi-restraints excluded: chain D residue 1051 GLU Chi-restraints excluded: chain D residue 1139 ASP Chi-restraints excluded: chain D residue 1154 GLU Chi-restraints excluded: chain D residue 1176 LYS Chi-restraints excluded: chain D residue 1207 TYR Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 79 ASP Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 150 THR Chi-restraints excluded: chain F residue 163 LEU Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 253 ASP Chi-restraints excluded: chain F residue 285 GLU Chi-restraints excluded: chain F residue 287 THR Chi-restraints excluded: chain F residue 305 GLU Chi-restraints excluded: chain F residue 343 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 110 optimal weight: 0.7980 chunk 296 optimal weight: 9.9990 chunk 65 optimal weight: 6.9990 chunk 193 optimal weight: 6.9990 chunk 81 optimal weight: 0.6980 chunk 329 optimal weight: 20.0000 chunk 273 optimal weight: 2.9990 chunk 152 optimal weight: 0.9990 chunk 27 optimal weight: 8.9990 chunk 109 optimal weight: 0.9990 chunk 173 optimal weight: 0.9980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 187 ASN ** D1124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 337 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 28870 Z= 0.161 Angle : 0.513 9.018 39370 Z= 0.272 Chirality : 0.042 0.195 4437 Planarity : 0.005 0.051 4892 Dihedral : 14.801 173.080 4604 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.95 % Allowed : 15.50 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.61 (0.14), residues: 3350 helix: 1.56 (0.14), residues: 1299 sheet: -0.13 (0.23), residues: 474 loop : -0.33 (0.15), residues: 1577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 200 HIS 0.004 0.001 HIS A 156 PHE 0.024 0.001 PHE C 191 TYR 0.012 0.001 TYR D1207 ARG 0.011 0.000 ARG D 486 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6700 Ramachandran restraints generated. 3350 Oldfield, 0 Emsley, 3350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6700 Ramachandran restraints generated. 3350 Oldfield, 0 Emsley, 3350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 257 time to evaluate : 3.061 Fit side-chains REVERT: A 96 THR cc_start: 0.8547 (t) cc_final: 0.8210 (m) REVERT: A 191 ASP cc_start: 0.5890 (m-30) cc_final: 0.5607 (t0) REVERT: B 100 LEU cc_start: 0.6777 (OUTLIER) cc_final: 0.6270 (pp) REVERT: B 102 LYS cc_start: 0.7100 (ptpt) cc_final: 0.6712 (mmtt) REVERT: C 49 ARG cc_start: 0.7377 (mmt-90) cc_final: 0.7176 (mtp85) REVERT: C 524 VAL cc_start: 0.8266 (OUTLIER) cc_final: 0.8006 (p) REVERT: C 560 MET cc_start: 0.7468 (OUTLIER) cc_final: 0.6919 (mtp) REVERT: C 1034 GLU cc_start: 0.6962 (OUTLIER) cc_final: 0.6361 (mp0) REVERT: D 30 GLU cc_start: 0.6625 (mt-10) cc_final: 0.6184 (mt-10) REVERT: D 54 LYS cc_start: 0.7730 (mmtt) cc_final: 0.7312 (mmmm) REVERT: D 455 ARG cc_start: 0.7928 (OUTLIER) cc_final: 0.7508 (mtp180) REVERT: D 966 GLU cc_start: 0.6133 (OUTLIER) cc_final: 0.5741 (tp30) REVERT: D 979 GLU cc_start: 0.6819 (mm-30) cc_final: 0.6463 (tp30) REVERT: D 986 ARG cc_start: 0.6869 (mmm-85) cc_final: 0.6538 (tpp-160) REVERT: D 1325 LEU cc_start: 0.7544 (mp) cc_final: 0.7171 (mp) REVERT: E 8 LYS cc_start: 0.8393 (ttmm) cc_final: 0.8020 (tttp) REVERT: E 68 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8195 (tp) REVERT: F 120 THR cc_start: 0.5873 (OUTLIER) cc_final: 0.5642 (p) outliers start: 56 outliers final: 22 residues processed: 299 average time/residue: 1.5777 time to fit residues: 544.4697 Evaluate side-chains 272 residues out of total 2872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 242 time to evaluate : 3.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 560 MET Chi-restraints excluded: chain C residue 848 VAL Chi-restraints excluded: chain C residue 1034 GLU Chi-restraints excluded: chain D residue 8 VAL Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 428 LYS Chi-restraints excluded: chain D residue 455 ARG Chi-restraints excluded: chain D residue 632 VAL Chi-restraints excluded: chain D residue 864 VAL Chi-restraints excluded: chain D residue 966 GLU Chi-restraints excluded: chain D residue 995 LEU Chi-restraints excluded: chain D residue 1139 ASP Chi-restraints excluded: chain D residue 1207 TYR Chi-restraints excluded: chain D residue 1344 VAL Chi-restraints excluded: chain D residue 1471 LEU Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 287 THR Chi-restraints excluded: chain F residue 305 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 318 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 187 optimal weight: 7.9990 chunk 240 optimal weight: 5.9990 chunk 186 optimal weight: 5.9990 chunk 277 optimal weight: 2.9990 chunk 184 optimal weight: 7.9990 chunk 328 optimal weight: 20.0000 chunk 205 optimal weight: 0.8980 chunk 200 optimal weight: 0.7980 chunk 151 optimal weight: 4.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 ASN B 16 GLN C 187 ASN ** D 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 28870 Z= 0.284 Angle : 0.585 9.031 39370 Z= 0.306 Chirality : 0.044 0.173 4437 Planarity : 0.005 0.051 4892 Dihedral : 14.886 172.379 4604 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.44 % Allowed : 15.88 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.45 (0.14), residues: 3350 helix: 1.36 (0.14), residues: 1312 sheet: -0.16 (0.23), residues: 465 loop : -0.40 (0.15), residues: 1573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 200 HIS 0.008 0.001 HIS A 156 PHE 0.023 0.002 PHE C 114 TYR 0.014 0.001 TYR C 458 ARG 0.013 0.001 ARG D 486 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6700 Ramachandran restraints generated. 3350 Oldfield, 0 Emsley, 3350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6700 Ramachandran restraints generated. 3350 Oldfield, 0 Emsley, 3350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 239 time to evaluate : 3.534 Fit side-chains revert: symmetry clash REVERT: A 96 THR cc_start: 0.8549 (t) cc_final: 0.8223 (m) REVERT: A 191 ASP cc_start: 0.5839 (m-30) cc_final: 0.5555 (t0) REVERT: B 102 LYS cc_start: 0.7108 (OUTLIER) cc_final: 0.6795 (mmtt) REVERT: C 28 ARG cc_start: 0.7804 (OUTLIER) cc_final: 0.7421 (ttt90) REVERT: C 49 ARG cc_start: 0.7318 (mmt-90) cc_final: 0.7092 (mtp85) REVERT: C 342 ASP cc_start: 0.6930 (t70) cc_final: 0.6603 (t0) REVERT: C 524 VAL cc_start: 0.8419 (OUTLIER) cc_final: 0.8111 (p) REVERT: C 560 MET cc_start: 0.7509 (OUTLIER) cc_final: 0.6953 (mtp) REVERT: C 1034 GLU cc_start: 0.7049 (OUTLIER) cc_final: 0.6364 (mp0) REVERT: C 1035 MET cc_start: 0.7807 (mtt) cc_final: 0.7551 (mtt) REVERT: D 30 GLU cc_start: 0.6528 (mt-10) cc_final: 0.6181 (mt-10) REVERT: D 54 LYS cc_start: 0.7778 (mmtt) cc_final: 0.7359 (mmmm) REVERT: D 455 ARG cc_start: 0.7914 (OUTLIER) cc_final: 0.7397 (mtp180) REVERT: D 966 GLU cc_start: 0.6277 (OUTLIER) cc_final: 0.5757 (tp30) REVERT: D 1176 LYS cc_start: 0.7253 (OUTLIER) cc_final: 0.6966 (mtmm) REVERT: D 1325 LEU cc_start: 0.7567 (mp) cc_final: 0.7298 (mp) REVERT: F 120 THR cc_start: 0.5836 (OUTLIER) cc_final: 0.5611 (p) outliers start: 70 outliers final: 39 residues processed: 291 average time/residue: 1.6129 time to fit residues: 541.8218 Evaluate side-chains 283 residues out of total 2872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 235 time to evaluate : 3.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 102 LYS Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 182 GLU Chi-restraints excluded: chain B residue 185 ARG Chi-restraints excluded: chain C residue 28 ARG Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 209 ARG Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 560 MET Chi-restraints excluded: chain C residue 710 ILE Chi-restraints excluded: chain C residue 848 VAL Chi-restraints excluded: chain C residue 1005 MET Chi-restraints excluded: chain C residue 1034 GLU Chi-restraints excluded: chain C residue 1048 THR Chi-restraints excluded: chain D residue 8 VAL Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 428 LYS Chi-restraints excluded: chain D residue 455 ARG Chi-restraints excluded: chain D residue 632 VAL Chi-restraints excluded: chain D residue 676 MET Chi-restraints excluded: chain D residue 966 GLU Chi-restraints excluded: chain D residue 995 LEU Chi-restraints excluded: chain D residue 1108 ARG Chi-restraints excluded: chain D residue 1139 ASP Chi-restraints excluded: chain D residue 1154 GLU Chi-restraints excluded: chain D residue 1176 LYS Chi-restraints excluded: chain D residue 1207 TYR Chi-restraints excluded: chain D residue 1344 VAL Chi-restraints excluded: chain D residue 1471 LEU Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 150 THR Chi-restraints excluded: chain F residue 287 THR Chi-restraints excluded: chain F residue 305 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 203 optimal weight: 7.9990 chunk 131 optimal weight: 3.9990 chunk 196 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 63 optimal weight: 9.9990 chunk 208 optimal weight: 3.9990 chunk 223 optimal weight: 3.9990 chunk 162 optimal weight: 4.9990 chunk 30 optimal weight: 10.0000 chunk 258 optimal weight: 0.0980 overall best weight: 3.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 337 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 28870 Z= 0.272 Angle : 0.580 8.991 39370 Z= 0.304 Chirality : 0.044 0.177 4437 Planarity : 0.005 0.051 4892 Dihedral : 14.861 171.852 4604 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.47 % Allowed : 16.30 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.43 (0.14), residues: 3350 helix: 1.35 (0.14), residues: 1306 sheet: -0.18 (0.23), residues: 465 loop : -0.41 (0.15), residues: 1579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 200 HIS 0.007 0.001 HIS A 156 PHE 0.039 0.002 PHE C 191 TYR 0.013 0.001 TYR D 128 ARG 0.015 0.001 ARG B 137 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6700 Ramachandran restraints generated. 3350 Oldfield, 0 Emsley, 3350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6700 Ramachandran restraints generated. 3350 Oldfield, 0 Emsley, 3350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 239 time to evaluate : 3.306 Fit side-chains revert: symmetry clash REVERT: A 96 THR cc_start: 0.8548 (t) cc_final: 0.8220 (m) REVERT: A 191 ASP cc_start: 0.5843 (m-30) cc_final: 0.5556 (t0) REVERT: C 28 ARG cc_start: 0.7801 (OUTLIER) cc_final: 0.7434 (ttt90) REVERT: C 49 ARG cc_start: 0.7378 (mmt-90) cc_final: 0.7173 (mtp85) REVERT: C 342 ASP cc_start: 0.6908 (t70) cc_final: 0.6589 (t0) REVERT: C 524 VAL cc_start: 0.8421 (OUTLIER) cc_final: 0.8106 (p) REVERT: C 560 MET cc_start: 0.7517 (OUTLIER) cc_final: 0.6983 (mtp) REVERT: C 580 MET cc_start: 0.8147 (mtt) cc_final: 0.7892 (mtt) REVERT: C 984 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7468 (mt-10) REVERT: C 1034 GLU cc_start: 0.7108 (OUTLIER) cc_final: 0.6394 (mp0) REVERT: C 1035 MET cc_start: 0.7808 (mtt) cc_final: 0.7553 (mtt) REVERT: D 30 GLU cc_start: 0.6593 (mt-10) cc_final: 0.6251 (mt-10) REVERT: D 41 ARG cc_start: 0.7154 (mmm-85) cc_final: 0.6830 (mmm-85) REVERT: D 54 LYS cc_start: 0.7712 (mmtt) cc_final: 0.7274 (mmmm) REVERT: D 455 ARG cc_start: 0.7907 (OUTLIER) cc_final: 0.7381 (mtp180) REVERT: D 534 ARG cc_start: 0.6870 (OUTLIER) cc_final: 0.6554 (mtp85) REVERT: D 966 GLU cc_start: 0.6244 (OUTLIER) cc_final: 0.5723 (tp30) REVERT: D 1176 LYS cc_start: 0.7210 (OUTLIER) cc_final: 0.6928 (mtmm) REVERT: D 1325 LEU cc_start: 0.7563 (mp) cc_final: 0.7286 (mp) REVERT: D 1366 LYS cc_start: 0.7762 (OUTLIER) cc_final: 0.7461 (ptpt) REVERT: E 8 LYS cc_start: 0.8428 (ttmm) cc_final: 0.8071 (tttp) REVERT: E 68 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8171 (mt) REVERT: F 120 THR cc_start: 0.5838 (OUTLIER) cc_final: 0.5603 (p) outliers start: 71 outliers final: 47 residues processed: 291 average time/residue: 1.6890 time to fit residues: 564.4362 Evaluate side-chains 285 residues out of total 2872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 226 time to evaluate : 3.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 140 MET Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 182 GLU Chi-restraints excluded: chain B residue 185 ARG Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 28 ARG Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 209 ARG Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 560 MET Chi-restraints excluded: chain C residue 710 ILE Chi-restraints excluded: chain C residue 848 VAL Chi-restraints excluded: chain C residue 984 GLU Chi-restraints excluded: chain C residue 1005 MET Chi-restraints excluded: chain C residue 1034 GLU Chi-restraints excluded: chain C residue 1048 THR Chi-restraints excluded: chain D residue 8 VAL Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 428 LYS Chi-restraints excluded: chain D residue 455 ARG Chi-restraints excluded: chain D residue 534 ARG Chi-restraints excluded: chain D residue 632 VAL Chi-restraints excluded: chain D residue 676 MET Chi-restraints excluded: chain D residue 682 ASP Chi-restraints excluded: chain D residue 821 VAL Chi-restraints excluded: chain D residue 864 VAL Chi-restraints excluded: chain D residue 966 GLU Chi-restraints excluded: chain D residue 995 LEU Chi-restraints excluded: chain D residue 1086 LEU Chi-restraints excluded: chain D residue 1102 THR Chi-restraints excluded: chain D residue 1108 ARG Chi-restraints excluded: chain D residue 1139 ASP Chi-restraints excluded: chain D residue 1154 GLU Chi-restraints excluded: chain D residue 1176 LYS Chi-restraints excluded: chain D residue 1207 TYR Chi-restraints excluded: chain D residue 1344 VAL Chi-restraints excluded: chain D residue 1366 LYS Chi-restraints excluded: chain D residue 1471 LEU Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 150 THR Chi-restraints excluded: chain F residue 253 ASP Chi-restraints excluded: chain F residue 287 THR Chi-restraints excluded: chain F residue 305 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 298 optimal weight: 10.0000 chunk 314 optimal weight: 4.9990 chunk 287 optimal weight: 6.9990 chunk 306 optimal weight: 30.0000 chunk 184 optimal weight: 8.9990 chunk 133 optimal weight: 3.9990 chunk 240 optimal weight: 9.9990 chunk 93 optimal weight: 0.5980 chunk 276 optimal weight: 6.9990 chunk 289 optimal weight: 0.9980 chunk 305 optimal weight: 3.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 HIS ** D 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 337 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 28870 Z= 0.267 Angle : 0.580 9.547 39370 Z= 0.304 Chirality : 0.044 0.173 4437 Planarity : 0.005 0.051 4892 Dihedral : 14.838 171.618 4604 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.51 % Allowed : 16.75 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.44 (0.14), residues: 3350 helix: 1.37 (0.14), residues: 1306 sheet: -0.21 (0.23), residues: 468 loop : -0.40 (0.15), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 200 HIS 0.007 0.001 HIS A 156 PHE 0.036 0.002 PHE C 191 TYR 0.017 0.001 TYR F 329 ARG 0.014 0.001 ARG C 650 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6700 Ramachandran restraints generated. 3350 Oldfield, 0 Emsley, 3350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6700 Ramachandran restraints generated. 3350 Oldfield, 0 Emsley, 3350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 235 time to evaluate : 3.156 Fit side-chains revert: symmetry clash REVERT: A 96 THR cc_start: 0.8544 (t) cc_final: 0.8216 (m) REVERT: A 191 ASP cc_start: 0.5845 (m-30) cc_final: 0.5552 (t0) REVERT: B 14 ARG cc_start: 0.6063 (mmp80) cc_final: 0.5855 (mmp80) REVERT: C 28 ARG cc_start: 0.7804 (OUTLIER) cc_final: 0.7437 (ttt90) REVERT: C 49 ARG cc_start: 0.7312 (mmt-90) cc_final: 0.7099 (mtp85) REVERT: C 342 ASP cc_start: 0.6899 (t70) cc_final: 0.6583 (t0) REVERT: C 524 VAL cc_start: 0.8418 (OUTLIER) cc_final: 0.8104 (p) REVERT: C 560 MET cc_start: 0.7540 (OUTLIER) cc_final: 0.7004 (mtp) REVERT: C 580 MET cc_start: 0.8114 (mtt) cc_final: 0.7872 (mtt) REVERT: C 788 THR cc_start: 0.8330 (OUTLIER) cc_final: 0.8080 (t) REVERT: C 984 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7486 (mt-10) REVERT: C 1034 GLU cc_start: 0.7113 (OUTLIER) cc_final: 0.6389 (mp0) REVERT: C 1035 MET cc_start: 0.7805 (mtt) cc_final: 0.7546 (mtt) REVERT: D 30 GLU cc_start: 0.6602 (mt-10) cc_final: 0.6299 (mt-10) REVERT: D 54 LYS cc_start: 0.7707 (mmtt) cc_final: 0.7280 (mmmm) REVERT: D 455 ARG cc_start: 0.7902 (OUTLIER) cc_final: 0.7358 (mtp180) REVERT: D 534 ARG cc_start: 0.6860 (OUTLIER) cc_final: 0.6534 (mtp85) REVERT: D 966 GLU cc_start: 0.6222 (OUTLIER) cc_final: 0.5687 (tp30) REVERT: D 1176 LYS cc_start: 0.7211 (OUTLIER) cc_final: 0.6922 (mtmm) REVERT: D 1366 LYS cc_start: 0.7763 (OUTLIER) cc_final: 0.7463 (ptpt) REVERT: E 8 LYS cc_start: 0.8420 (ttmm) cc_final: 0.8044 (tttp) REVERT: E 68 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8413 (tp) REVERT: F 120 THR cc_start: 0.5831 (OUTLIER) cc_final: 0.5611 (p) outliers start: 72 outliers final: 46 residues processed: 289 average time/residue: 1.6291 time to fit residues: 541.1823 Evaluate side-chains 288 residues out of total 2872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 229 time to evaluate : 3.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 185 ARG Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 28 ARG Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 209 ARG Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 560 MET Chi-restraints excluded: chain C residue 710 ILE Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 848 VAL Chi-restraints excluded: chain C residue 984 GLU Chi-restraints excluded: chain C residue 1005 MET Chi-restraints excluded: chain C residue 1034 GLU Chi-restraints excluded: chain C residue 1048 THR Chi-restraints excluded: chain D residue 8 VAL Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 428 LYS Chi-restraints excluded: chain D residue 455 ARG Chi-restraints excluded: chain D residue 534 ARG Chi-restraints excluded: chain D residue 632 VAL Chi-restraints excluded: chain D residue 676 MET Chi-restraints excluded: chain D residue 682 ASP Chi-restraints excluded: chain D residue 821 VAL Chi-restraints excluded: chain D residue 864 VAL Chi-restraints excluded: chain D residue 904 VAL Chi-restraints excluded: chain D residue 966 GLU Chi-restraints excluded: chain D residue 995 LEU Chi-restraints excluded: chain D residue 1102 THR Chi-restraints excluded: chain D residue 1108 ARG Chi-restraints excluded: chain D residue 1139 ASP Chi-restraints excluded: chain D residue 1154 GLU Chi-restraints excluded: chain D residue 1176 LYS Chi-restraints excluded: chain D residue 1207 TYR Chi-restraints excluded: chain D residue 1366 LYS Chi-restraints excluded: chain D residue 1471 LEU Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 150 THR Chi-restraints excluded: chain F residue 253 ASP Chi-restraints excluded: chain F residue 287 THR Chi-restraints excluded: chain F residue 305 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 201 optimal weight: 3.9990 chunk 323 optimal weight: 3.9990 chunk 197 optimal weight: 3.9990 chunk 153 optimal weight: 3.9990 chunk 225 optimal weight: 9.9990 chunk 339 optimal weight: 20.0000 chunk 312 optimal weight: 5.9990 chunk 270 optimal weight: 20.0000 chunk 28 optimal weight: 9.9990 chunk 208 optimal weight: 4.9990 chunk 165 optimal weight: 0.7980 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 337 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 28870 Z= 0.295 Angle : 0.600 10.396 39370 Z= 0.313 Chirality : 0.045 0.172 4437 Planarity : 0.006 0.070 4892 Dihedral : 14.865 171.376 4604 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.40 % Allowed : 16.89 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.14), residues: 3350 helix: 1.30 (0.14), residues: 1306 sheet: -0.24 (0.24), residues: 458 loop : -0.41 (0.15), residues: 1586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 200 HIS 0.008 0.001 HIS A 156 PHE 0.031 0.002 PHE C 191 TYR 0.015 0.001 TYR D 128 ARG 0.013 0.001 ARG C 650 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6700 Ramachandran restraints generated. 3350 Oldfield, 0 Emsley, 3350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6700 Ramachandran restraints generated. 3350 Oldfield, 0 Emsley, 3350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 232 time to evaluate : 3.203 Fit side-chains revert: symmetry clash REVERT: A 96 THR cc_start: 0.8552 (t) cc_final: 0.8226 (m) REVERT: A 191 ASP cc_start: 0.5848 (m-30) cc_final: 0.5554 (t0) REVERT: B 139 ASN cc_start: 0.6738 (t0) cc_final: 0.6322 (t0) REVERT: C 28 ARG cc_start: 0.7806 (OUTLIER) cc_final: 0.7439 (ttt90) REVERT: C 49 ARG cc_start: 0.7406 (mmt-90) cc_final: 0.7205 (mtp85) REVERT: C 342 ASP cc_start: 0.6949 (t70) cc_final: 0.6640 (t0) REVERT: C 524 VAL cc_start: 0.8421 (OUTLIER) cc_final: 0.8098 (p) REVERT: C 560 MET cc_start: 0.7534 (OUTLIER) cc_final: 0.6999 (mtp) REVERT: C 580 MET cc_start: 0.8120 (mtt) cc_final: 0.7869 (mtt) REVERT: C 788 THR cc_start: 0.8350 (OUTLIER) cc_final: 0.8116 (t) REVERT: C 984 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7510 (mt-10) REVERT: C 1034 GLU cc_start: 0.7132 (OUTLIER) cc_final: 0.6408 (mp0) REVERT: C 1035 MET cc_start: 0.7825 (mtt) cc_final: 0.7574 (mtt) REVERT: D 30 GLU cc_start: 0.6581 (mt-10) cc_final: 0.6317 (mm-30) REVERT: D 54 LYS cc_start: 0.7735 (mmtt) cc_final: 0.7290 (mmmm) REVERT: D 455 ARG cc_start: 0.7932 (OUTLIER) cc_final: 0.7402 (mtp180) REVERT: D 966 GLU cc_start: 0.6238 (OUTLIER) cc_final: 0.5687 (tp30) REVERT: D 986 ARG cc_start: 0.6772 (mmm-85) cc_final: 0.6537 (tpp-160) REVERT: D 1176 LYS cc_start: 0.7217 (OUTLIER) cc_final: 0.6931 (mtmm) REVERT: D 1366 LYS cc_start: 0.7830 (OUTLIER) cc_final: 0.7510 (ptpt) REVERT: E 68 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8072 (mt) REVERT: F 79 ASP cc_start: 0.7137 (OUTLIER) cc_final: 0.6814 (t0) REVERT: F 120 THR cc_start: 0.5837 (OUTLIER) cc_final: 0.5623 (p) outliers start: 69 outliers final: 47 residues processed: 284 average time/residue: 1.6646 time to fit residues: 547.0320 Evaluate side-chains 284 residues out of total 2872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 224 time to evaluate : 3.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 185 ARG Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 28 ARG Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 209 ARG Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 560 MET Chi-restraints excluded: chain C residue 710 ILE Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 848 VAL Chi-restraints excluded: chain C residue 984 GLU Chi-restraints excluded: chain C residue 1005 MET Chi-restraints excluded: chain C residue 1034 GLU Chi-restraints excluded: chain C residue 1048 THR Chi-restraints excluded: chain D residue 8 VAL Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 428 LYS Chi-restraints excluded: chain D residue 455 ARG Chi-restraints excluded: chain D residue 632 VAL Chi-restraints excluded: chain D residue 676 MET Chi-restraints excluded: chain D residue 682 ASP Chi-restraints excluded: chain D residue 821 VAL Chi-restraints excluded: chain D residue 864 VAL Chi-restraints excluded: chain D residue 904 VAL Chi-restraints excluded: chain D residue 966 GLU Chi-restraints excluded: chain D residue 995 LEU Chi-restraints excluded: chain D residue 1102 THR Chi-restraints excluded: chain D residue 1108 ARG Chi-restraints excluded: chain D residue 1139 ASP Chi-restraints excluded: chain D residue 1154 GLU Chi-restraints excluded: chain D residue 1176 LYS Chi-restraints excluded: chain D residue 1207 TYR Chi-restraints excluded: chain D residue 1366 LYS Chi-restraints excluded: chain D residue 1471 LEU Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain F residue 79 ASP Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 150 THR Chi-restraints excluded: chain F residue 253 ASP Chi-restraints excluded: chain F residue 287 THR Chi-restraints excluded: chain F residue 305 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 214 optimal weight: 0.9980 chunk 288 optimal weight: 6.9990 chunk 82 optimal weight: 0.2980 chunk 249 optimal weight: 7.9990 chunk 39 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 chunk 270 optimal weight: 20.0000 chunk 113 optimal weight: 6.9990 chunk 278 optimal weight: 6.9990 chunk 34 optimal weight: 8.9990 chunk 49 optimal weight: 0.0670 overall best weight: 2.2722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 337 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.152802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.114612 restraints weight = 38036.790| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 1.82 r_work: 0.3279 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3142 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3142 r_free = 0.3142 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3142 r_free = 0.3142 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3142 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 28870 Z= 0.228 Angle : 0.565 10.204 39370 Z= 0.295 Chirality : 0.043 0.173 4437 Planarity : 0.005 0.057 4892 Dihedral : 14.783 171.433 4604 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.12 % Allowed : 17.38 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.54 (0.14), residues: 3350 helix: 1.46 (0.14), residues: 1307 sheet: -0.19 (0.23), residues: 470 loop : -0.35 (0.15), residues: 1573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 200 HIS 0.006 0.001 HIS A 156 PHE 0.032 0.002 PHE C 191 TYR 0.014 0.001 TYR D 432 ARG 0.014 0.000 ARG C 420 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9547.20 seconds wall clock time: 170 minutes 48.73 seconds (10248.73 seconds total)