Starting phenix.real_space_refine on Sun Sep 13 18:02:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6m6c_30119/09_2026/6m6c_30119.cif Found real_map, /net/cci-nas-00/data/ceres_data/6m6c_30119/09_2026/6m6c_30119.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6m6c_30119/09_2026/6m6c_30119.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6m6c_30119/09_2026/6m6c_30119.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6m6c_30119/09_2026/6m6c_30119.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6m6c_30119/09_2026/6m6c_30119.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6m6c_30119/09_2026/6m6c_30119.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6m6c_30119/09_2026/6m6c_30119.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.016 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 58 5.49 5 Mg 1 5.21 5 S 64 5.16 5 C 15380 2.51 5 N 4362 2.21 5 O 4716 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 233 residue(s): 0.22s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24583 Number of models: 1 Model: "" Number of chains: 9 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: 10300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1305, 10300 Classifications: {'peptide': 1305} Link IDs: {'PCIS': 2, 'PTRANS': 62, 'TRANS': 1240} Chain breaks: 2 Chain: "E" Number of atoms: 761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 761 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 6, 'TRANS': 87} Chain: "R" Number of atoms: 221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 221 Classifications: {'RNAv2': 10} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 8, 'rna3p_pyr': 1} Link IDs: {'rna2p': 1, 'rna3p': 8} Chain: "N" Number of atoms: 413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 413 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain breaks: 1 Chain: "T" Number of atoms: 583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 583 Classifications: {'DNA': 29} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 28} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 19686 SG CYS D1112 84.043 65.037 103.462 1.00116.18 S ATOM 20330 SG CYS D1194 83.244 65.269 99.635 1.00113.44 S ATOM 20386 SG CYS D1201 82.157 62.149 101.536 1.00109.81 S ATOM 20410 SG CYS D1204 80.510 65.312 102.376 1.00109.29 S ATOM 12771 SG CYS D 58 112.562 45.724 44.929 1.00182.15 S ATOM 12782 SG CYS D 60 114.388 47.085 42.144 1.00185.70 S ATOM 12893 SG CYS D 73 116.459 47.364 44.938 1.00180.59 S ATOM 12919 SG CYS D 76 113.687 49.792 44.980 1.00177.15 S Time building chain proxies: 5.11, per 1000 atoms: 0.21 Number of scatterers: 24583 At special positions: 0 Unit cell: (159.454, 138.542, 138.542, 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 64 16.00 P 58 15.00 Mg 1 11.99 O 4716 8.00 N 4362 7.00 C 15380 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.78 Conformation dependent library (CDL) restraints added in 889.8 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D2001 " pdb="ZN ZN D2001 " - pdb=" SG CYS D1112 " pdb="ZN ZN D2001 " - pdb=" SG CYS D1194 " pdb="ZN ZN D2001 " - pdb=" SG CYS D1201 " pdb="ZN ZN D2001 " - pdb=" SG CYS D1204 " pdb=" ZN D2002 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 58 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 76 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 73 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 60 " Number of angles added : 12 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5462 Finding SS restraints... Secondary structure from input PDB file: 113 helices and 48 sheets defined 40.6% alpha, 19.1% beta 27 base pairs and 43 stacking pairs defined. Time for finding SS restraints: 3.18 Creating SS restraints... Processing helix chain 'A' and resid 31 through 47 removed outlier: 3.620A 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: 3.635A pdb=" N HIS A 156 " --> pdb=" O PRO A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 224 removed outlier: 3.793A pdb=" N TYR A 224 " --> pdb=" O GLU A 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 48 removed outlier: 3.748A pdb=" N THR B 35 " --> pdb=" O GLY B 31 " (cutoff:3.500A) Proline residue: B 39 - end of helix removed outlier: 4.351A pdb=" N ILE B 48 " --> pdb=" O LEU B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 84 removed outlier: 3.715A pdb=" N GLU B 84 " --> pdb=" O LEU B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 114 No H-bonds generated for 'chain 'B' and resid 112 through 114' Processing helix chain 'B' and resid 152 through 157 removed outlier: 3.718A 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: 3.970A pdb=" N SER C 25 " --> pdb=" O ILE C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 39 removed outlier: 3.591A pdb=" N ARG C 39 " --> pdb=" O PRO C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 52 Processing helix chain 'C' and resid 79 through 87 Processing helix chain 'C' and resid 193 through 200 Processing helix chain 'C' and resid 203 through 212 Processing helix chain 'C' and resid 214 through 222 removed outlier: 3.644A pdb=" N VAL C 218 " --> pdb=" O TYR C 214 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N GLY C 220 " --> pdb=" O GLU C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 229 removed outlier: 3.927A 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 261 Processing helix chain 'C' and resid 270 through 282 Processing helix chain 'C' and resid 302 through 316 removed outlier: 3.516A pdb=" N ALA C 315 " --> pdb=" O PHE C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 359 Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 375 through 389 removed outlier: 3.530A pdb=" N SER C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 407 Processing helix chain 'C' and resid 424 through 429 removed outlier: 3.827A pdb=" N ARG C 428 " --> pdb=" O GLY C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 435 removed outlier: 4.023A 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 543 through 547 Processing helix chain 'C' and resid 549 through 553 Processing helix chain 'C' and resid 554 through 565 removed outlier: 3.963A pdb=" N MET C 560 " --> pdb=" O ASN C 556 " (cutoff:3.500A) Processing helix chain 'C' and resid 566 through 568 No H-bonds generated for 'chain 'C' and resid 566 through 568' Processing helix chain 'C' and resid 583 through 591 Processing helix chain 'C' and resid 692 through 697 Processing helix chain 'C' and resid 730 through 735 Processing helix chain 'C' and resid 768 through 779 Processing helix chain 'C' and resid 854 through 858 removed outlier: 3.536A pdb=" N MET C 858 " --> pdb=" O VAL C 855 " (cutoff:3.500A) Processing helix chain 'C' and resid 872 through 874 No H-bonds generated for 'chain 'C' and resid 872 through 874' Processing helix chain 'C' and resid 875 through 880 removed outlier: 3.562A pdb=" N ARG C 879 " --> pdb=" O GLY C 875 " (cutoff:3.500A) Processing helix chain 'C' and resid 882 through 898 Processing helix chain 'C' and resid 910 through 932 removed outlier: 3.722A pdb=" N LYS C 928 " --> pdb=" O VAL C 924 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ARG C 929 " --> pdb=" O TYR C 925 " (cutoff:3.500A) Processing helix chain 'C' and resid 937 through 949 Processing helix chain 'C' and resid 958 through 968 Processing helix chain 'C' and resid 1000 through 1004 Processing helix chain 'C' and resid 1033 through 1043 Processing helix chain 'C' and resid 1045 through 1054 removed outlier: 3.684A pdb=" N LEU C1049 " --> pdb=" O ALA C1045 " (cutoff:3.500A) Processing helix chain 'C' and resid 1059 through 1073 Processing helix chain 'C' and resid 1082 through 1094 removed outlier: 3.697A 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 removed outlier: 3.704A pdb=" N PHE D 50 " --> pdb=" O ASP D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 88 Processing helix chain 'D' and resid 102 through 107 removed outlier: 3.684A pdb=" N ASP D 107 " --> pdb=" O TRP D 103 " (cutoff:3.500A) 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 removed outlier: 3.531A pdb=" N GLU D 467 " --> pdb=" O GLN D 463 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 481 removed outlier: 3.540A pdb=" N LEU D 473 " --> pdb=" O ASP D 469 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LYS D 475 " --> pdb=" O GLU D 471 " (cutoff:3.500A) Processing helix chain 'D' and resid 485 through 506 removed outlier: 3.782A pdb=" N ARG D 489 " --> pdb=" O SER D 485 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY D 506 " --> pdb=" O PHE D 502 " (cutoff:3.500A) 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 561 removed outlier: 3.759A 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 602 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 678 Processing helix chain 'D' and resid 679 through 683 removed outlier: 3.561A pdb=" N ASP D 682 " --> pdb=" O ARG D 679 " (cutoff:3.500A) Processing helix chain 'D' and resid 685 through 695 removed outlier: 3.569A 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 762 Processing helix chain 'D' and resid 764 through 768 Processing helix chain 'D' and resid 782 through 793 Processing helix chain 'D' and resid 808 through 819 removed outlier: 3.664A pdb=" N ALA D 812 " --> pdb=" O THR D 808 " (cutoff:3.500A) 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: 3.664A pdb=" N ALA D 896 " --> pdb=" O ASP D 892 " (cutoff:3.500A) Processing helix chain 'D' and resid 907 through 923 Processing helix chain 'D' and resid 923 through 944 removed outlier: 3.729A pdb=" N THR D 944 " --> pdb=" O THR D 940 " (cutoff:3.500A) Processing helix chain 'D' and resid 950 through 954 removed outlier: 3.855A pdb=" N ALA D 954 " --> pdb=" O ILE D 951 " (cutoff:3.500A) Processing helix chain 'D' and resid 958 through 980 removed outlier: 4.027A pdb=" N GLN D 962 " --> pdb=" O GLU D 958 " (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: 3.982A pdb=" N HIS D1075 " --> pdb=" O PHE D1071 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N GLY D1076 " --> pdb=" O ILE D1072 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N ALA D1089 " --> pdb=" O ALA D1085 " (cutoff:3.500A) removed outlier: 4.166A 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 1179 Processing helix chain 'D' and resid 1202 through 1206 Processing helix chain 'D' and resid 1220 through 1231 removed outlier: 3.811A 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: 3.531A pdb=" N VAL D1344 " --> pdb=" O GLY D1340 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N VAL D1355 " --> pdb=" O GLU D1351 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N TYR D1356 " --> pdb=" O ILE D1352 " (cutoff:3.500A) Processing helix chain 'D' and resid 1364 through 1376 removed outlier: 4.355A pdb=" N ILE D1368 " --> pdb=" O HIS D1364 " (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: 3.625A 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 1462 through 1468 Processing helix chain 'D' and resid 1474 through 1478 Processing helix chain 'D' and resid 1489 through 1501 Processing helix chain 'E' and resid 5 through 13 removed outlier: 3.873A pdb=" N VAL E 13 " --> pdb=" O LEU E 9 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 33 Processing helix chain 'E' and resid 41 through 45 removed outlier: 3.760A pdb=" N ARG E 45 " --> pdb=" O PRO E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 71 removed outlier: 3.623A pdb=" N TRP E 63 " --> pdb=" O ASN E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 93 Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 16 removed outlier: 6.644A 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: 7.462A pdb=" N ASN A 139 " --> pdb=" O ILE A 58 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N ILE A 58 " --> pdb=" O ASN A 139 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N GLU A 141 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N VAL A 56 " --> pdb=" O GLU A 141 " (cutoff:3.500A) removed outlier: 6.606A 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: 3.635A pdb=" N ALA A 130 " --> pdb=" O VAL A 109 " (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: 5.797A pdb=" N TYR B 20 " --> pdb=" O THR B 201 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N THR B 201 " --> pdb=" O TYR B 20 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N GLU B 22 " --> pdb=" O ILE B 199 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N ILE B 199 " --> pdb=" O GLU B 22 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N VAL B 24 " --> pdb=" O LEU B 197 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N LEU B 197 " --> pdb=" O VAL B 24 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N GLU B 26 " --> pdb=" O LEU B 195 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N LEU B 195 " --> pdb=" O GLU B 26 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N THR B 190 " --> pdb=" O LEU B 186 " (cutoff:3.500A) removed outlier: 6.469A 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: 7.533A pdb=" N ASN B 139 " --> pdb=" O ILE B 58 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N ILE B 58 " --> pdb=" O ASN B 139 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N GLU B 141 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N VAL B 56 " --> pdb=" O GLU B 141 " (cutoff:3.500A) removed outlier: 6.781A 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 110 removed outlier: 3.885A 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 2 through 5 Processing sheet with id=AB3, first strand: chain 'C' and resid 65 through 73 removed outlier: 7.033A pdb=" N ARG C 97 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N TYR C 71 " --> pdb=" O TYR C 95 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N TYR C 95 " --> pdb=" O TYR C 71 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N LEU C 73 " --> pdb=" O PRO C 93 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N ALA C 92 " --> pdb=" O HIS C 117 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N HIS C 117 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 5.930A 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: 3.844A pdb=" N SER C 138 " --> pdb=" O ARG C 409 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 145 through 150 removed outlier: 6.413A pdb=" N TYR C 158 " --> pdb=" O VAL C 176 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N VAL C 176 " --> pdb=" O TYR C 158 " (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: 3.527A pdb=" N ARG C 473 " --> pdb=" O GLU C 482 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N GLU C 482 " --> pdb=" O ARG C 473 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N VAL C 475 " --> pdb=" O THR C 480 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N THR C 480 " --> pdb=" O VAL C 475 " (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: 6.717A 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: 7.009A pdb=" N ARG C 610 " --> pdb=" O VAL C 606 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N VAL C 606 " --> pdb=" O ARG C 610 " (cutoff:3.500A) removed outlier: 6.606A 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: 7.042A pdb=" N ILE C 688 " --> pdb=" O ALA C 850 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ILE C 852 " --> pdb=" O ILE C 688 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ILE C 690 " --> pdb=" O ILE C 852 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL C 689 " --> pdb=" O ILE C 870 " (cutoff:3.500A) removed outlier: 4.450A 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: 6.519A pdb=" N ASP C 714 " --> pdb=" O VAL C 819 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N VAL C 819 " --> pdb=" O ASP C 714 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ARG C 802 " --> pdb=" O TYR C 826 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ALA C 828 " --> pdb=" O VAL C 800 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N VAL C 800 " --> pdb=" O ALA C 828 " (cutoff:3.500A) removed outlier: 8.686A pdb=" N LYS C 830 " --> pdb=" O GLY C 798 " (cutoff:3.500A) removed outlier: 9.386A pdb=" N GLY C 798 " --> pdb=" O LYS C 830 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 721 through 722 Processing sheet with id=AC9, first strand: chain 'C' and resid 754 through 756 removed outlier: 6.730A pdb=" N LEU C 790 " --> pdb=" O LEU C 755 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 1006 through 1008 removed outlier: 7.909A pdb=" N ILE D 726 " --> pdb=" O ARG D 628 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N VAL D 630 " --> pdb=" O ILE D 726 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N LEU D 728 " --> pdb=" O VAL D 630 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N VAL D 632 " --> pdb=" O LEU D 728 " (cutoff:3.500A) 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: 7.818A pdb=" N HIS D 92 " --> pdb=" O TYR D 23 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLU D 25 " --> pdb=" O HIS D 92 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N GLU D 94 " --> pdb=" O GLU D 25 " (cutoff:3.500A) removed outlier: 10.185A pdb=" N LEU D 95 " --> pdb=" O PRO D 518 " (cutoff:3.500A) removed outlier: 10.545A pdb=" N THR D 97 " --> pdb=" O ALA D 516 " (cutoff:3.500A) removed outlier: 7.305A 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: 7.012A pdb=" N ASP D 453 " --> pdb=" O LEU D 135 " (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 Processing sheet with id=AD9, first strand: chain 'D' and resid 398 through 402 Processing sheet with id=AE1, first strand: chain 'D' and resid 420 through 422 removed outlier: 7.125A pdb=" N VAL D 427 " --> pdb=" O LEU D 421 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 527 through 529 Processing sheet with id=AE3, first strand: chain 'D' and resid 805 through 806 Processing sheet with id=AE4, first strand: chain 'D' and resid 842 through 843 Processing sheet with id=AE5, first strand: chain 'D' and resid 1106 through 1109 Processing sheet with id=AE6, first strand: chain 'D' and resid 1118 through 1121 Processing sheet with id=AE7, first strand: chain 'D' and resid 1123 through 1126 Processing sheet with id=AE8, first strand: chain 'D' and resid 1153 through 1155 Processing sheet with id=AE9, first strand: chain 'D' and resid 1300 through 1305 removed outlier: 4.110A pdb=" N LEU D1290 " --> pdb=" O LEU D1305 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLY D1279 " --> pdb=" O VAL D1319 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 1394 through 1396 removed outlier: 6.830A pdb=" N ALA D1416 " --> pdb=" O THR D1382 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 1485 through 1488 Processing sheet with id=AF3, first strand: chain 'E' and resid 47 through 49 1053 hydrogen bonds defined for protein. 2895 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 71 hydrogen bonds 142 hydrogen bond angles 0 basepair planarities 27 basepair parallelities 43 stacking parallelities Total time for adding SS restraints: 7.98 Time building geometry restraints manager: 2.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7864 1.34 - 1.45: 3186 1.45 - 1.57: 13865 1.57 - 1.69: 113 1.69 - 1.81: 115 Bond restraints: 25143 Sorted by residual: bond pdb=" C3' DC N 28 " pdb=" C2' DC N 28 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.14e+01 bond pdb=" C3' DC N 18 " pdb=" C2' DC N 18 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.76e+00 bond pdb=" C3' DC T 22 " pdb=" C2' DC T 22 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.51e+00 bond pdb=" N THR C 335 " pdb=" CA THR C 335 " ideal model delta sigma weight residual 1.453 1.488 -0.035 1.31e-02 5.83e+03 7.20e+00 bond pdb=" C3' DT T 21 " pdb=" C2' DT T 21 " ideal model delta sigma weight residual 1.516 1.535 -0.019 8.00e-03 1.56e+04 5.42e+00 ... (remaining 25138 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.07: 31999 1.07 - 2.14: 1828 2.14 - 3.20: 373 3.20 - 4.27: 48 4.27 - 5.34: 18 Bond angle restraints: 34266 Sorted by residual: angle pdb=" O4' DG N 1 " pdb=" C4' DG N 1 " pdb=" C3' DG N 1 " ideal model delta sigma weight residual 106.00 102.97 3.03 6.00e-01 2.78e+00 2.55e+01 angle pdb=" O4' DA T 16 " pdb=" C4' DA T 16 " pdb=" C3' DA T 16 " ideal model delta sigma weight residual 106.00 103.34 2.66 6.00e-01 2.78e+00 1.97e+01 angle pdb=" N3 DT T 21 " pdb=" C4 DT T 21 " pdb=" O4 DT T 21 " ideal model delta sigma weight residual 119.90 122.44 -2.54 6.00e-01 2.78e+00 1.80e+01 angle pdb=" O4' DG T 12 " pdb=" C4' DG T 12 " pdb=" C3' DG T 12 " ideal model delta sigma weight residual 106.00 103.52 2.48 6.00e-01 2.78e+00 1.71e+01 angle pdb=" N3 DT N 25 " pdb=" C4 DT N 25 " pdb=" O4 DT N 25 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.71e+01 ... (remaining 34261 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.78: 14692 30.78 - 61.56: 535 61.56 - 92.34: 51 92.34 - 123.12: 0 123.12 - 153.90: 1 Dihedral angle restraints: 15279 sinusoidal: 6782 harmonic: 8497 Sorted by residual: dihedral pdb=" C4' C R 11 " pdb=" C3' C R 11 " pdb=" C2' C R 11 " pdb=" C1' C R 11 " ideal model delta sinusoidal sigma weight residual 36.34 -35.05 71.39 1 3.10e+00 1.04e-01 6.80e+02 dihedral pdb=" O4' C R 11 " pdb=" C4' C R 11 " pdb=" C3' C R 11 " pdb=" C2' C R 11 " ideal model delta sinusoidal sigma weight residual -35.15 23.61 -58.76 1 4.00e+00 6.25e-02 2.89e+02 dihedral pdb=" O4' C R 11 " pdb=" C2' C R 11 " pdb=" C1' C R 11 " pdb=" C3' C R 11 " ideal model delta sinusoidal sigma weight residual -94.41 -35.34 -59.07 3 3.80e+00 6.93e-02 1.48e+02 ... (remaining 15276 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 3213 0.055 - 0.109: 569 0.109 - 0.164: 79 0.164 - 0.219: 2 0.219 - 0.274: 10 Chirality restraints: 3873 Sorted by residual: chirality pdb=" C2' C R 11 " pdb=" C3' C R 11 " pdb=" O2' C R 11 " pdb=" C1' C R 11 " both_signs ideal model delta sigma weight residual False -2.79 -2.52 -0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" C3' C R 11 " pdb=" C4' C R 11 " pdb=" O3' C R 11 " pdb=" C2' C R 11 " both_signs ideal model delta sigma weight residual False -2.50 -2.75 0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" P C R 11 " pdb=" OP1 C R 11 " pdb=" OP2 C R 11 " pdb=" O5' C R 11 " both_signs ideal model delta sigma weight residual True 2.17 -2.41 -0.23 2.00e-01 2.50e+01 1.36e+00 ... (remaining 3870 not shown) Planarity restraints: 4287 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY D 634 " 0.031 5.00e-02 4.00e+02 4.74e-02 3.60e+00 pdb=" N PRO D 635 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO D 635 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 635 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 469 " -0.027 5.00e-02 4.00e+02 4.13e-02 2.73e+00 pdb=" N PRO C 470 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO C 470 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 470 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 865 " -0.024 5.00e-02 4.00e+02 3.60e-02 2.07e+00 pdb=" N PRO C 866 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO C 866 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 866 " -0.020 5.00e-02 4.00e+02 ... (remaining 4284 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 214 2.59 - 3.17: 19943 3.17 - 3.75: 37228 3.75 - 4.32: 51727 4.32 - 4.90: 85777 Nonbonded interactions: 194889 Sorted by model distance: nonbonded pdb=" OD1 ASP D 739 " pdb="MG MG D2003 " model vdw 2.016 2.170 nonbonded pdb=" O3' A R 20 " pdb="MG MG D2003 " model vdw 2.035 2.170 nonbonded pdb=" OD1 ASP D 741 " pdb="MG MG D2003 " model vdw 2.080 2.170 nonbonded pdb=" OG SER D1190 " pdb=" OE1 GLU D1369 " model vdw 2.215 3.040 nonbonded pdb=" NE2 GLN E 49 " pdb=" O THR E 50 " model vdw 2.240 3.120 ... (remaining 194884 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 7 through 228) selection = chain 'B' } 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=0.50 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: 0.540 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: 0.030 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 30.600 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6653 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 0.082 25151 Z= 0.202 Angle : 0.610 16.798 34278 Z= 0.393 Chirality : 0.044 0.274 3873 Planarity : 0.004 0.047 4287 Dihedral : 15.173 153.902 9817 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.51 (0.14), residues: 2942 helix: -0.22 (0.15), residues: 1039 sheet: -1.40 (0.21), residues: 451 loop : -1.40 (0.14), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 88 TYR 0.013 0.001 TYR D1207 PHE 0.010 0.001 PHE C 896 TRP 0.010 0.001 TRP B 200 HIS 0.003 0.001 HIS C 552 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.20 (25143) covalent geometry : angle 0.58322 / 0.39 (34266) hydrogen bonds : bond 0.13455 / 8.99 ( 1122) hydrogen bonds : angle 5.97341 / 4.20 ( 3037) metal coordination : bond 0.04933 / 2.56 ( 8) metal coordination : angle 9.59313 / 5.43 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 2516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 438 time to evaluate : 0.895 Fit side-chains revert: symmetry clash REVERT: A 47 SER cc_start: 0.8254 (t) cc_final: 0.8045 (p) REVERT: A 57 TYR cc_start: 0.7859 (t80) cc_final: 0.7525 (t80) REVERT: A 66 SER cc_start: 0.7946 (t) cc_final: 0.7709 (p) REVERT: A 102 LYS cc_start: 0.8332 (mttp) cc_final: 0.7920 (mtpp) REVERT: A 113 ASP cc_start: 0.8684 (m-30) cc_final: 0.8453 (m-30) REVERT: A 175 ARG cc_start: 0.7118 (mtt-85) cc_final: 0.6542 (mmt90) REVERT: B 29 GLU cc_start: 0.6650 (tp30) cc_final: 0.6307 (mp0) REVERT: B 47 SER cc_start: 0.8277 (m) cc_final: 0.7967 (p) REVERT: B 137 ARG cc_start: 0.8401 (mtp85) cc_final: 0.7978 (ttm110) REVERT: B 160 ASP cc_start: 0.7961 (t0) cc_final: 0.7619 (t0) REVERT: B 220 GLU cc_start: 0.7425 (tt0) cc_final: 0.7074 (tp30) REVERT: C 24 GLU cc_start: 0.6566 (tp30) cc_final: 0.5786 (mm-30) REVERT: C 27 ARG cc_start: 0.7218 (ttp80) cc_final: 0.6781 (ttm170) REVERT: C 64 LEU cc_start: 0.7605 (mp) cc_final: 0.7088 (tt) REVERT: C 229 MET cc_start: 0.8116 (ptt) cc_final: 0.7573 (ptp) REVERT: C 288 ARG cc_start: 0.7316 (mtm-85) cc_final: 0.6519 (mtp-110) REVERT: C 384 GLU cc_start: 0.6123 (tp30) cc_final: 0.5761 (tt0) REVERT: C 426 ASP cc_start: 0.6859 (p0) cc_final: 0.6561 (m-30) REVERT: C 504 GLU cc_start: 0.6474 (pt0) cc_final: 0.6071 (pt0) REVERT: C 512 ARG cc_start: 0.8014 (ptm160) cc_final: 0.7608 (ptm-80) REVERT: C 599 GLU cc_start: 0.7201 (tp30) cc_final: 0.6598 (mt-10) REVERT: C 605 LYS cc_start: 0.7246 (mttt) cc_final: 0.6735 (mtmt) REVERT: C 626 ARG cc_start: 0.7395 (ttm110) cc_final: 0.7004 (ttp-170) REVERT: C 677 MET cc_start: 0.8033 (ptm) cc_final: 0.7707 (ptp) REVERT: C 706 GLU cc_start: 0.7100 (tp30) cc_final: 0.6819 (tp30) REVERT: C 736 ASP cc_start: 0.7442 (p0) cc_final: 0.7233 (p0) REVERT: C 754 ILE cc_start: 0.8219 (mt) cc_final: 0.8000 (mp) REVERT: C 821 GLU cc_start: 0.6407 (pt0) cc_final: 0.6205 (pt0) REVERT: C 916 GLU cc_start: 0.5807 (tp30) cc_final: 0.5582 (pt0) REVERT: C 1000 MET cc_start: 0.8266 (mtm) cc_final: 0.8058 (mtm) REVERT: C 1005 MET cc_start: 0.8108 (ttp) cc_final: 0.7875 (ttt) REVERT: C 1106 ASP cc_start: 0.7033 (m-30) cc_final: 0.6340 (t0) REVERT: C 1107 ASN cc_start: 0.6360 (m-40) cc_final: 0.6152 (m-40) REVERT: D 27 GLU cc_start: 0.8183 (pt0) cc_final: 0.7862 (pt0) REVERT: D 38 LYS cc_start: 0.6524 (mmtp) cc_final: 0.6171 (mtmm) REVERT: D 40 GLU cc_start: 0.6433 (tp30) cc_final: 0.6103 (mt-10) REVERT: D 46 ASP cc_start: 0.8971 (t0) cc_final: 0.8212 (t70) REVERT: D 54 LYS cc_start: 0.6900 (mttp) cc_final: 0.6384 (mtpp) REVERT: D 464 LEU cc_start: 0.6366 (mt) cc_final: 0.6152 (mt) REVERT: D 476 GLU cc_start: 0.7134 (mm-30) cc_final: 0.6900 (tm-30) REVERT: D 491 LYS cc_start: 0.6391 (tmmt) cc_final: 0.5839 (mtmm) REVERT: D 512 MET cc_start: 0.8333 (mtm) cc_final: 0.8019 (mtm) REVERT: D 601 ARG cc_start: 0.6366 (ttt-90) cc_final: 0.6152 (mmm-85) REVERT: D 797 LYS cc_start: 0.7808 (tptt) cc_final: 0.6892 (mttp) REVERT: D 799 LYS cc_start: 0.8156 (mttt) cc_final: 0.7887 (mttp) REVERT: D 845 ASN cc_start: 0.7171 (p0) cc_final: 0.6809 (p0) REVERT: D 847 ASP cc_start: 0.6034 (m-30) cc_final: 0.5650 (m-30) REVERT: D 871 LYS cc_start: 0.7010 (pttt) cc_final: 0.6579 (pttt) REVERT: D 1012 GLU cc_start: 0.7378 (tm-30) cc_final: 0.6231 (mt-10) REVERT: D 1046 GLN cc_start: 0.7011 (pm20) cc_final: 0.5865 (mp10) REVERT: D 1079 LYS cc_start: 0.6163 (tptt) cc_final: 0.5655 (tppt) REVERT: D 1159 ARG cc_start: 0.7886 (ttm110) cc_final: 0.7455 (ttm170) REVERT: D 1184 GLN cc_start: 0.7970 (mt0) cc_final: 0.7573 (mt0) REVERT: D 1211 MET cc_start: 0.7073 (mtm) cc_final: 0.6818 (mtp) REVERT: D 1269 LYS cc_start: 0.7919 (mmmt) cc_final: 0.7649 (mttt) REVERT: D 1301 LYS cc_start: 0.7702 (mmmt) cc_final: 0.7475 (mmtm) REVERT: D 1327 ARG cc_start: 0.8130 (mtt90) cc_final: 0.7838 (mtp85) REVERT: D 1350 GLU cc_start: 0.6454 (tp30) cc_final: 0.6016 (tt0) REVERT: D 1455 LYS cc_start: 0.7437 (mtpp) cc_final: 0.6998 (mttt) REVERT: D 1490 LYS cc_start: 0.7977 (ttmt) cc_final: 0.7735 (ttmm) REVERT: E 32 ARG cc_start: 0.7093 (ttp-110) cc_final: 0.6869 (ttp-110) REVERT: E 48 MET cc_start: 0.6978 (ttt) cc_final: 0.5650 (ttp) REVERT: E 56 ASP cc_start: 0.8450 (m-30) cc_final: 0.8198 (m-30) REVERT: E 59 ASN cc_start: 0.7788 (t0) cc_final: 0.7343 (t0) REVERT: E 86 GLN cc_start: 0.8467 (tp40) cc_final: 0.8185 (tp40) outliers start: 0 outliers final: 0 residues processed: 438 average time/residue: 0.2109 time to fit residues: 134.1070 Evaluate side-chains 287 residues out of total 2516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 287 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.0980 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 6.9990 chunk 298 optimal weight: 9.9990 overall best weight: 3.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 128 HIS ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 130 ASN C 187 ASN C 390 GLN C 434 HIS C 543 ASN C 565 GLN C 860 HIS C1107 ASN D 507 ASN D 552 ASN ** D 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 762 GLN ** D1359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 59 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.164876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.116144 restraints weight = 28047.760| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 2.96 r_work: 0.2690 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2693 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2693 r_free = 0.2693 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2693 r_free = 0.2693 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.2693 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 25151 Z= 0.233 Angle : 0.645 20.863 34278 Z= 0.331 Chirality : 0.050 0.945 3873 Planarity : 0.005 0.050 4287 Dihedral : 12.645 149.560 3910 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.03 % Allowed : 8.23 % Favored : 90.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.14), residues: 2942 helix: 0.56 (0.16), residues: 1054 sheet: -0.78 (0.23), residues: 429 loop : -0.84 (0.15), residues: 1459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 550 TYR 0.031 0.002 TYR C1043 PHE 0.014 0.002 PHE A 179 TRP 0.011 0.002 TRP B 200 HIS 0.010 0.002 HIS C 434 Details of bonding type rmsd/Z covalent geometry : bond 0.00568 / 0.23 (25143) covalent geometry : angle 0.64234 / 0.33 (34266) hydrogen bonds : bond 0.05356 / 3.55 ( 1122) hydrogen bonds : angle 4.97765 / 3.52 ( 3037) metal coordination : bond 0.01323 / 0.73 ( 8) metal coordination : angle 2.93220 / 1.64 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 300 time to evaluate : 0.929 Fit side-chains REVERT: A 57 TYR cc_start: 0.8896 (t80) cc_final: 0.8642 (t80) REVERT: A 159 LYS cc_start: 0.8850 (mtpt) cc_final: 0.8548 (mtmt) REVERT: A 175 ARG cc_start: 0.8582 (mtt-85) cc_final: 0.8226 (mmt90) REVERT: A 202 ASP cc_start: 0.8642 (p0) cc_final: 0.8183 (p0) REVERT: B 29 GLU cc_start: 0.8103 (tp30) cc_final: 0.7824 (mp0) REVERT: C 24 GLU cc_start: 0.7989 (tp30) cc_final: 0.7623 (mm-30) REVERT: C 229 MET cc_start: 0.8497 (ptt) cc_final: 0.8286 (ptp) REVERT: C 288 ARG cc_start: 0.8276 (mtm-85) cc_final: 0.7604 (mtp-110) REVERT: C 361 MET cc_start: 0.7431 (mmp) cc_final: 0.7096 (mmm) REVERT: C 384 GLU cc_start: 0.7759 (tp30) cc_final: 0.7494 (tt0) REVERT: C 388 ARG cc_start: 0.8623 (mtt90) cc_final: 0.8350 (mtt90) REVERT: C 429 ASP cc_start: 0.8446 (OUTLIER) cc_final: 0.8152 (t0) REVERT: C 504 GLU cc_start: 0.7109 (pt0) cc_final: 0.6761 (pt0) REVERT: C 605 LYS cc_start: 0.8619 (mttt) cc_final: 0.8277 (mtmt) REVERT: C 788 THR cc_start: 0.7569 (p) cc_final: 0.7152 (p) REVERT: C 960 GLU cc_start: 0.7846 (tt0) cc_final: 0.7542 (mp0) REVERT: C 1005 MET cc_start: 0.9259 (ttp) cc_final: 0.8914 (ttt) REVERT: D 38 LYS cc_start: 0.7424 (mmtp) cc_final: 0.7089 (mtmm) REVERT: D 46 ASP cc_start: 0.8985 (t0) cc_final: 0.8718 (t0) REVERT: D 54 LYS cc_start: 0.8212 (mttp) cc_final: 0.7632 (mtpp) REVERT: D 464 LEU cc_start: 0.8049 (mt) cc_final: 0.7798 (mt) REVERT: D 488 ARG cc_start: 0.7731 (mmm-85) cc_final: 0.7436 (mmm-85) REVERT: D 491 LYS cc_start: 0.7802 (tmmt) cc_final: 0.7088 (mtmm) REVERT: D 512 MET cc_start: 0.9414 (mtm) cc_final: 0.9149 (mtm) REVERT: D 515 GLU cc_start: 0.7959 (mt-10) cc_final: 0.7722 (mt-10) REVERT: D 797 LYS cc_start: 0.8379 (tptt) cc_final: 0.7903 (mttt) REVERT: D 799 LYS cc_start: 0.8453 (mttt) cc_final: 0.8208 (mttp) REVERT: D 811 GLU cc_start: 0.7692 (mt-10) cc_final: 0.7301 (mt-10) REVERT: D 828 LYS cc_start: 0.8220 (mttt) cc_final: 0.8018 (mttm) REVERT: D 847 ASP cc_start: 0.7241 (m-30) cc_final: 0.6830 (m-30) REVERT: D 1012 GLU cc_start: 0.8542 (tm-30) cc_final: 0.7881 (mt-10) REVERT: D 1079 LYS cc_start: 0.8468 (tptt) cc_final: 0.7868 (tppt) REVERT: D 1184 GLN cc_start: 0.8573 (mt0) cc_final: 0.8312 (mt0) REVERT: D 1188 VAL cc_start: 0.8564 (OUTLIER) cc_final: 0.8292 (m) REVERT: D 1327 ARG cc_start: 0.8718 (mtt90) cc_final: 0.8451 (mtp85) REVERT: D 1350 GLU cc_start: 0.8137 (tp30) cc_final: 0.7753 (tt0) REVERT: D 1455 LYS cc_start: 0.8702 (mtpp) cc_final: 0.8501 (mttt) REVERT: D 1490 LYS cc_start: 0.8612 (ttmt) cc_final: 0.8313 (ttmm) REVERT: E 32 ARG cc_start: 0.8345 (ttp-110) cc_final: 0.8068 (ttp-110) REVERT: E 48 MET cc_start: 0.8369 (ttt) cc_final: 0.7566 (ttp) REVERT: E 59 ASN cc_start: 0.9023 (t160) cc_final: 0.8555 (t0) REVERT: E 86 GLN cc_start: 0.8619 (tp40) cc_final: 0.8321 (tp40) outliers start: 26 outliers final: 20 residues processed: 311 average time/residue: 0.2074 time to fit residues: 93.9267 Evaluate side-chains 283 residues out of total 2516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 261 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ARG Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain C residue 2 GLU Chi-restraints excluded: chain C residue 8 ARG Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 429 ASP Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 950 LEU Chi-restraints excluded: chain C residue 974 LEU Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain D residue 452 ILE Chi-restraints excluded: chain D residue 538 SER Chi-restraints excluded: chain D residue 677 LEU Chi-restraints excluded: chain D residue 684 LYS Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain D residue 1090 ASP Chi-restraints excluded: chain D residue 1132 LEU Chi-restraints excluded: chain D residue 1188 VAL Chi-restraints excluded: chain D residue 1415 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 291 optimal weight: 0.9980 chunk 140 optimal weight: 1.9990 chunk 6 optimal weight: 0.0170 chunk 297 optimal weight: 50.0000 chunk 249 optimal weight: 0.0970 chunk 276 optimal weight: 5.9990 chunk 7 optimal weight: 0.9990 chunk 151 optimal weight: 3.9990 chunk 268 optimal weight: 4.9990 chunk 18 optimal weight: 9.9990 chunk 12 optimal weight: 6.9990 overall best weight: 0.8220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1107 ASN ** D 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1359 GLN E 28 GLN E 33 HIS E 49 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.167479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.120179 restraints weight = 27975.629| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 2.82 r_work: 0.2744 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2763 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2763 r_free = 0.2763 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2763 r_free = 0.2763 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2763 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 25151 Z= 0.113 Angle : 0.511 10.539 34278 Z= 0.269 Chirality : 0.044 0.438 3873 Planarity : 0.004 0.045 4287 Dihedral : 12.570 153.515 3910 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.27 % Allowed : 9.42 % Favored : 89.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.15), residues: 2942 helix: 0.95 (0.16), residues: 1069 sheet: -0.46 (0.23), residues: 426 loop : -0.48 (0.15), residues: 1447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG D 553 TYR 0.010 0.001 TYR C 925 PHE 0.012 0.001 PHE C 114 TRP 0.009 0.001 TRP D1434 HIS 0.004 0.001 HIS C 434 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (25143) covalent geometry : angle 0.50879 / 0.27 (34266) hydrogen bonds : bond 0.04192 / 2.79 ( 1122) hydrogen bonds : angle 4.64659 / 3.30 ( 3037) metal coordination : bond 0.00466 / 0.26 ( 8) metal coordination : angle 2.77451 / 1.62 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 279 time to evaluate : 0.901 Fit side-chains REVERT: A 57 TYR cc_start: 0.8847 (t80) cc_final: 0.8560 (t80) REVERT: A 159 LYS cc_start: 0.8842 (mtpt) cc_final: 0.8540 (mtmt) REVERT: A 175 ARG cc_start: 0.8497 (mtt-85) cc_final: 0.8093 (mmt90) REVERT: A 202 ASP cc_start: 0.8645 (p0) cc_final: 0.8143 (p0) REVERT: B 29 GLU cc_start: 0.8049 (tp30) cc_final: 0.7813 (mp0) REVERT: B 137 ARG cc_start: 0.8733 (ttm110) cc_final: 0.8297 (ttm110) REVERT: C 24 GLU cc_start: 0.7872 (tp30) cc_final: 0.7512 (mm-30) REVERT: C 191 PHE cc_start: 0.7839 (p90) cc_final: 0.7413 (p90) REVERT: C 229 MET cc_start: 0.8462 (ptt) cc_final: 0.8192 (ptp) REVERT: C 288 ARG cc_start: 0.8216 (mtm-85) cc_final: 0.7583 (mtp-110) REVERT: C 361 MET cc_start: 0.7270 (mmp) cc_final: 0.6861 (mmm) REVERT: C 388 ARG cc_start: 0.8577 (mtt90) cc_final: 0.8211 (mtp85) REVERT: C 429 ASP cc_start: 0.8421 (OUTLIER) cc_final: 0.8120 (t0) REVERT: C 504 GLU cc_start: 0.7170 (pt0) cc_final: 0.6824 (pt0) REVERT: C 605 LYS cc_start: 0.8616 (mttt) cc_final: 0.8264 (mtmt) REVERT: C 683 ASN cc_start: 0.8793 (m110) cc_final: 0.8585 (m110) REVERT: C 788 THR cc_start: 0.7544 (p) cc_final: 0.7097 (p) REVERT: C 960 GLU cc_start: 0.7777 (tt0) cc_final: 0.7457 (mp0) REVERT: C 1005 MET cc_start: 0.9157 (ttp) cc_final: 0.8881 (ttt) REVERT: D 38 LYS cc_start: 0.7343 (mmtp) cc_final: 0.7072 (mtmm) REVERT: D 46 ASP cc_start: 0.8936 (t0) cc_final: 0.8617 (t0) REVERT: D 54 LYS cc_start: 0.8198 (mttp) cc_final: 0.7635 (mtpp) REVERT: D 157 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.8234 (mp0) REVERT: D 453 ASP cc_start: 0.8403 (t0) cc_final: 0.7981 (t0) REVERT: D 464 LEU cc_start: 0.8047 (mt) cc_final: 0.7810 (mt) REVERT: D 491 LYS cc_start: 0.7729 (tmmt) cc_final: 0.7029 (mtmm) REVERT: D 512 MET cc_start: 0.9399 (mtm) cc_final: 0.9125 (mtm) REVERT: D 797 LYS cc_start: 0.8316 (tptt) cc_final: 0.7826 (mttt) REVERT: D 799 LYS cc_start: 0.8439 (mttt) cc_final: 0.8203 (mttp) REVERT: D 811 GLU cc_start: 0.7547 (mt-10) cc_final: 0.7163 (mt-10) REVERT: D 832 ARG cc_start: 0.7949 (mtm180) cc_final: 0.7689 (ptt180) REVERT: D 845 ASN cc_start: 0.7947 (p0) cc_final: 0.7628 (p0) REVERT: D 847 ASP cc_start: 0.7284 (m-30) cc_final: 0.6907 (m-30) REVERT: D 1012 GLU cc_start: 0.8432 (tm-30) cc_final: 0.7801 (mt-10) REVERT: D 1051 GLU cc_start: 0.7934 (tt0) cc_final: 0.7688 (tt0) REVERT: D 1079 LYS cc_start: 0.8457 (tptt) cc_final: 0.7833 (tppt) REVERT: D 1184 GLN cc_start: 0.8482 (mt0) cc_final: 0.8237 (mt0) REVERT: D 1327 ARG cc_start: 0.8670 (mtt90) cc_final: 0.8404 (mtp85) REVERT: D 1350 GLU cc_start: 0.7974 (tp30) cc_final: 0.7550 (tt0) REVERT: D 1490 LYS cc_start: 0.8580 (ttmt) cc_final: 0.8284 (ttmm) REVERT: E 32 ARG cc_start: 0.8224 (ttp-110) cc_final: 0.7934 (ttp-110) REVERT: E 48 MET cc_start: 0.8439 (ttt) cc_final: 0.7632 (ttp) REVERT: E 65 MET cc_start: 0.8941 (mtm) cc_final: 0.8718 (mtt) REVERT: E 72 ARG cc_start: 0.8759 (mtt90) cc_final: 0.8425 (mtt180) REVERT: E 86 GLN cc_start: 0.8603 (tp40) cc_final: 0.8300 (tp40) outliers start: 32 outliers final: 21 residues processed: 296 average time/residue: 0.2018 time to fit residues: 88.3989 Evaluate side-chains 273 residues out of total 2516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 250 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 185 ARG Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain C residue 2 GLU Chi-restraints excluded: chain C residue 8 ARG Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 289 THR Chi-restraints excluded: chain C residue 429 ASP Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 974 LEU Chi-restraints excluded: chain D residue 157 GLU Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain D residue 452 ILE Chi-restraints excluded: chain D residue 632 VAL Chi-restraints excluded: chain D residue 677 LEU Chi-restraints excluded: chain D residue 684 LYS Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain D residue 1090 ASP Chi-restraints excluded: chain D residue 1400 VAL Chi-restraints excluded: chain D residue 1415 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 298 optimal weight: 9.9990 chunk 268 optimal weight: 6.9990 chunk 241 optimal weight: 4.9990 chunk 205 optimal weight: 0.9990 chunk 104 optimal weight: 5.9990 chunk 57 optimal weight: 4.9990 chunk 133 optimal weight: 2.9990 chunk 157 optimal weight: 9.9990 chunk 247 optimal weight: 4.9990 chunk 132 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 703 ASN ** D 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 901 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.162669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.114069 restraints weight = 27912.405| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.91 r_work: 0.2804 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2758 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2758 r_free = 0.2758 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2758 r_free = 0.2758 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2758 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 25151 Z= 0.237 Angle : 0.613 9.242 34278 Z= 0.318 Chirality : 0.048 0.397 3873 Planarity : 0.005 0.049 4287 Dihedral : 12.570 147.356 3910 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.83 % Allowed : 10.57 % Favored : 87.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.15), residues: 2942 helix: 0.85 (0.16), residues: 1063 sheet: -0.39 (0.23), residues: 430 loop : -0.38 (0.15), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 627 TYR 0.019 0.002 TYR C 925 PHE 0.015 0.002 PHE A 179 TRP 0.012 0.002 TRP B 200 HIS 0.010 0.002 HIS D 709 Details of bonding type rmsd/Z covalent geometry : bond 0.00591 / 0.24 (25143) covalent geometry : angle 0.61136 / 0.32 (34266) hydrogen bonds : bond 0.05358 / 3.55 ( 1122) hydrogen bonds : angle 4.69512 / 3.33 ( 3037) metal coordination : bond 0.00643 / 0.42 ( 8) metal coordination : angle 2.49627 / 1.50 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 273 time to evaluate : 0.895 Fit side-chains REVERT: A 159 LYS cc_start: 0.8948 (mtpt) cc_final: 0.8601 (mtmt) REVERT: A 175 ARG cc_start: 0.8672 (mtt-85) cc_final: 0.8144 (mtt180) REVERT: A 202 ASP cc_start: 0.8678 (p0) cc_final: 0.8353 (p0) REVERT: B 137 ARG cc_start: 0.8799 (ttm110) cc_final: 0.8387 (ttm110) REVERT: C 24 GLU cc_start: 0.8122 (tp30) cc_final: 0.7778 (mm-30) REVERT: C 191 PHE cc_start: 0.8038 (p90) cc_final: 0.7602 (p90) REVERT: C 229 MET cc_start: 0.8508 (ptt) cc_final: 0.8272 (ptp) REVERT: C 288 ARG cc_start: 0.8356 (mtm-85) cc_final: 0.7733 (mtp-110) REVERT: C 429 ASP cc_start: 0.8499 (OUTLIER) cc_final: 0.8271 (t0) REVERT: C 504 GLU cc_start: 0.7211 (pt0) cc_final: 0.6857 (pt0) REVERT: C 605 LYS cc_start: 0.8714 (mttt) cc_final: 0.8384 (mtmt) REVERT: C 750 LYS cc_start: 0.8822 (mttt) cc_final: 0.8420 (mttm) REVERT: C 788 THR cc_start: 0.7889 (p) cc_final: 0.7449 (p) REVERT: C 960 GLU cc_start: 0.7919 (tt0) cc_final: 0.7650 (mp0) REVERT: C 1005 MET cc_start: 0.9084 (ttp) cc_final: 0.8870 (ttt) REVERT: D 38 LYS cc_start: 0.7449 (mmtp) cc_final: 0.7160 (mtmm) REVERT: D 46 ASP cc_start: 0.8989 (t0) cc_final: 0.8691 (t0) REVERT: D 54 LYS cc_start: 0.8312 (mttp) cc_final: 0.7773 (mtpp) REVERT: D 129 PHE cc_start: 0.8652 (m-80) cc_final: 0.8411 (m-80) REVERT: D 453 ASP cc_start: 0.8420 (t0) cc_final: 0.8089 (t0) REVERT: D 456 MET cc_start: 0.8001 (mtm) cc_final: 0.7508 (mtp) REVERT: D 491 LYS cc_start: 0.7996 (tmmt) cc_final: 0.7270 (mtmm) REVERT: D 512 MET cc_start: 0.9426 (mtm) cc_final: 0.9208 (mtm) REVERT: D 550 ARG cc_start: 0.8224 (tpp-160) cc_final: 0.7984 (tpp-160) REVERT: D 553 ARG cc_start: 0.7945 (ttp80) cc_final: 0.7712 (ttp80) REVERT: D 797 LYS cc_start: 0.8492 (tptt) cc_final: 0.8038 (mttt) REVERT: D 799 LYS cc_start: 0.8441 (mttt) cc_final: 0.8225 (mttp) REVERT: D 811 GLU cc_start: 0.7727 (mt-10) cc_final: 0.7322 (mt-10) REVERT: D 832 ARG cc_start: 0.7971 (mtm180) cc_final: 0.7672 (ptt180) REVERT: D 847 ASP cc_start: 0.7340 (m-30) cc_final: 0.6935 (m-30) REVERT: D 1012 GLU cc_start: 0.8622 (tm-30) cc_final: 0.8036 (mt-10) REVERT: D 1051 GLU cc_start: 0.7933 (tt0) cc_final: 0.7731 (tt0) REVERT: D 1079 LYS cc_start: 0.8588 (tptt) cc_final: 0.8055 (tppt) REVERT: D 1133 ARG cc_start: 0.8247 (ptm160) cc_final: 0.7384 (ptm-80) REVERT: D 1184 GLN cc_start: 0.8623 (mt0) cc_final: 0.8383 (mt0) REVERT: D 1327 ARG cc_start: 0.8838 (mtt90) cc_final: 0.8591 (mtp85) REVERT: D 1346 ARG cc_start: 0.8221 (ttm110) cc_final: 0.7890 (mtm-85) REVERT: D 1350 GLU cc_start: 0.8142 (tp30) cc_final: 0.7768 (tt0) REVERT: D 1490 LYS cc_start: 0.8640 (ttmt) cc_final: 0.8348 (ttmm) REVERT: E 32 ARG cc_start: 0.8350 (ttp-110) cc_final: 0.8097 (ttp-110) REVERT: E 48 MET cc_start: 0.8563 (ttt) cc_final: 0.7875 (ttp) REVERT: E 59 ASN cc_start: 0.9052 (t160) cc_final: 0.8564 (t0) outliers start: 46 outliers final: 34 residues processed: 301 average time/residue: 0.2043 time to fit residues: 90.0538 Evaluate side-chains 286 residues out of total 2516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 251 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 185 ARG Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain C residue 2 GLU Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 289 THR Chi-restraints excluded: chain C residue 345 ARG Chi-restraints excluded: chain C residue 429 ASP Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 950 LEU Chi-restraints excluded: chain C residue 974 LEU Chi-restraints excluded: chain C residue 1107 ASN Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain D residue 452 ILE Chi-restraints excluded: chain D residue 538 SER Chi-restraints excluded: chain D residue 632 VAL Chi-restraints excluded: chain D residue 677 LEU Chi-restraints excluded: chain D residue 684 LYS Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain D residue 875 THR Chi-restraints excluded: chain D residue 940 THR Chi-restraints excluded: chain D residue 1086 LEU Chi-restraints excluded: chain D residue 1090 ASP Chi-restraints excluded: chain D residue 1132 LEU Chi-restraints excluded: chain D residue 1188 VAL Chi-restraints excluded: chain D residue 1275 SER Chi-restraints excluded: chain D residue 1400 VAL Chi-restraints excluded: chain D residue 1415 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 134 optimal weight: 2.9990 chunk 263 optimal weight: 30.0000 chunk 185 optimal weight: 9.9990 chunk 202 optimal weight: 0.7980 chunk 118 optimal weight: 0.9990 chunk 218 optimal weight: 6.9990 chunk 131 optimal weight: 2.9990 chunk 181 optimal weight: 50.0000 chunk 186 optimal weight: 2.9990 chunk 58 optimal weight: 8.9990 chunk 187 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 575 GLN C 670 GLN ** D 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.165350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.116269 restraints weight = 27759.310| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 2.76 r_work: 0.2686 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.2534 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2534 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2599 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2599 r_free = 0.2599 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2599 r_free = 0.2599 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2599 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 25151 Z= 0.172 Angle : 0.547 8.716 34278 Z= 0.286 Chirality : 0.046 0.313 3873 Planarity : 0.005 0.050 4287 Dihedral : 12.522 150.113 3910 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.07 % Allowed : 11.25 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.15), residues: 2942 helix: 1.01 (0.16), residues: 1068 sheet: -0.10 (0.25), residues: 415 loop : -0.28 (0.15), residues: 1459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 388 TYR 0.015 0.001 TYR C 925 PHE 0.012 0.001 PHE C 239 TRP 0.012 0.001 TRP B 200 HIS 0.006 0.001 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.17 (25143) covalent geometry : angle 0.54475 / 0.29 (34266) hydrogen bonds : bond 0.04678 / 3.11 ( 1122) hydrogen bonds : angle 4.52935 / 3.22 ( 3037) metal coordination : bond 0.00401 / 0.27 ( 8) metal coordination : angle 2.42963 / 1.42 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 266 time to evaluate : 0.786 Fit side-chains REVERT: A 175 ARG cc_start: 0.8713 (mtt-85) cc_final: 0.8165 (mtt180) REVERT: A 202 ASP cc_start: 0.8770 (p0) cc_final: 0.8504 (p0) REVERT: A 229 GLN cc_start: 0.7405 (mm110) cc_final: 0.7194 (mm110) REVERT: B 137 ARG cc_start: 0.8840 (ttm110) cc_final: 0.8460 (ttm110) REVERT: C 24 GLU cc_start: 0.8266 (tp30) cc_final: 0.7841 (mm-30) REVERT: C 64 LEU cc_start: 0.8524 (mm) cc_final: 0.8246 (mt) REVERT: C 191 PHE cc_start: 0.7961 (p90) cc_final: 0.7538 (p90) REVERT: C 229 MET cc_start: 0.8478 (ptt) cc_final: 0.8271 (ptp) REVERT: C 288 ARG cc_start: 0.8301 (mtm-85) cc_final: 0.7698 (mtp-110) REVERT: C 361 MET cc_start: 0.7337 (mmp) cc_final: 0.6872 (mmm) REVERT: C 429 ASP cc_start: 0.8620 (OUTLIER) cc_final: 0.8361 (t0) REVERT: C 605 LYS cc_start: 0.8790 (mttt) cc_final: 0.8349 (mtmt) REVERT: C 788 THR cc_start: 0.7849 (p) cc_final: 0.7389 (p) REVERT: C 960 GLU cc_start: 0.8042 (tt0) cc_final: 0.7547 (mp0) REVERT: C 1005 MET cc_start: 0.9342 (ttp) cc_final: 0.9114 (ttt) REVERT: D 38 LYS cc_start: 0.7405 (mmtp) cc_final: 0.7076 (mtmm) REVERT: D 46 ASP cc_start: 0.9095 (t0) cc_final: 0.8727 (t0) REVERT: D 54 LYS cc_start: 0.8238 (mttp) cc_final: 0.7687 (mtpp) REVERT: D 129 PHE cc_start: 0.8699 (m-80) cc_final: 0.8346 (m-80) REVERT: D 157 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.8230 (mp0) REVERT: D 453 ASP cc_start: 0.8296 (t0) cc_final: 0.7932 (t0) REVERT: D 491 LYS cc_start: 0.7962 (tmmt) cc_final: 0.7203 (mtmm) REVERT: D 550 ARG cc_start: 0.8202 (tpp-160) cc_final: 0.7874 (mmt-90) REVERT: D 553 ARG cc_start: 0.7989 (ttp80) cc_final: 0.7757 (ttp80) REVERT: D 797 LYS cc_start: 0.8491 (tptt) cc_final: 0.7878 (mttt) REVERT: D 799 LYS cc_start: 0.8504 (mttt) cc_final: 0.8253 (mttp) REVERT: D 811 GLU cc_start: 0.7776 (mt-10) cc_final: 0.7296 (mt-10) REVERT: D 847 ASP cc_start: 0.7537 (m-30) cc_final: 0.7127 (m-30) REVERT: D 1012 GLU cc_start: 0.8766 (tm-30) cc_final: 0.7894 (mt-10) REVERT: D 1051 GLU cc_start: 0.8163 (tt0) cc_final: 0.7922 (tt0) REVERT: D 1079 LYS cc_start: 0.8561 (tptt) cc_final: 0.7968 (tppt) REVERT: D 1100 ASP cc_start: 0.8696 (OUTLIER) cc_final: 0.8425 (m-30) REVERT: D 1133 ARG cc_start: 0.8207 (ptm160) cc_final: 0.7215 (ptm-80) REVERT: D 1184 GLN cc_start: 0.8575 (mt0) cc_final: 0.8297 (mt0) REVERT: D 1188 VAL cc_start: 0.8577 (OUTLIER) cc_final: 0.8344 (m) REVERT: D 1327 ARG cc_start: 0.8777 (mtt90) cc_final: 0.8550 (mtp85) REVERT: D 1350 GLU cc_start: 0.8287 (tp30) cc_final: 0.7744 (tt0) REVERT: D 1490 LYS cc_start: 0.8612 (ttmt) cc_final: 0.8327 (ttmm) REVERT: E 28 GLN cc_start: 0.7958 (mt0) cc_final: 0.7580 (mt0) REVERT: E 32 ARG cc_start: 0.8360 (ttp-110) cc_final: 0.8078 (ttp-110) REVERT: E 48 MET cc_start: 0.8466 (ttt) cc_final: 0.7604 (ttp) REVERT: E 59 ASN cc_start: 0.9050 (t160) cc_final: 0.8591 (t0) REVERT: E 65 MET cc_start: 0.9106 (mtm) cc_final: 0.8877 (mtt) outliers start: 52 outliers final: 42 residues processed: 300 average time/residue: 0.2000 time to fit residues: 89.2186 Evaluate side-chains 299 residues out of total 2516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 253 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 185 ARG Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain C residue 2 GLU Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 289 THR Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 345 ARG Chi-restraints excluded: chain C residue 429 ASP Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 583 LEU Chi-restraints excluded: chain C residue 670 GLN Chi-restraints excluded: chain C residue 698 ASP Chi-restraints excluded: chain C residue 950 LEU Chi-restraints excluded: chain C residue 954 THR Chi-restraints excluded: chain C residue 974 LEU Chi-restraints excluded: chain C residue 1107 ASN Chi-restraints excluded: chain D residue 157 GLU Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain D residue 452 ILE Chi-restraints excluded: chain D residue 538 SER Chi-restraints excluded: chain D residue 632 VAL Chi-restraints excluded: chain D residue 677 LEU Chi-restraints excluded: chain D residue 684 LYS Chi-restraints excluded: chain D residue 694 VAL Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain D residue 875 THR Chi-restraints excluded: chain D residue 904 VAL Chi-restraints excluded: chain D residue 940 THR Chi-restraints excluded: chain D residue 1003 VAL Chi-restraints excluded: chain D residue 1083 ASP Chi-restraints excluded: chain D residue 1086 LEU Chi-restraints excluded: chain D residue 1100 ASP Chi-restraints excluded: chain D residue 1132 LEU Chi-restraints excluded: chain D residue 1188 VAL Chi-restraints excluded: chain D residue 1275 SER Chi-restraints excluded: chain D residue 1400 VAL Chi-restraints excluded: chain D residue 1415 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 73 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 chunk 29 optimal weight: 7.9990 chunk 224 optimal weight: 0.4980 chunk 111 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 203 optimal weight: 0.0770 chunk 201 optimal weight: 2.9990 chunk 163 optimal weight: 4.9990 overall best weight: 1.5142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 95 GLN C 575 GLN ** D 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 49 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.166167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.117229 restraints weight = 27787.910| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 2.97 r_work: 0.2702 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2689 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2689 r_free = 0.2689 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2689 r_free = 0.2689 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2689 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25151 Z= 0.139 Angle : 0.519 7.881 34278 Z= 0.273 Chirality : 0.044 0.268 3873 Planarity : 0.004 0.050 4287 Dihedral : 12.463 151.247 3910 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.63 % Allowed : 11.80 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.15), residues: 2942 helix: 1.16 (0.16), residues: 1068 sheet: -0.00 (0.25), residues: 416 loop : -0.17 (0.15), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 507 TYR 0.013 0.001 TYR C 925 PHE 0.015 0.001 PHE C 298 TRP 0.011 0.001 TRP B 200 HIS 0.005 0.001 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (25143) covalent geometry : angle 0.51755 / 0.27 (34266) hydrogen bonds : bond 0.04341 / 2.88 ( 1122) hydrogen bonds : angle 4.45104 / 3.17 ( 3037) metal coordination : bond 0.00331 / 0.22 ( 8) metal coordination : angle 2.37769 / 1.39 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 262 time to evaluate : 0.732 Fit side-chains revert: symmetry clash REVERT: A 175 ARG cc_start: 0.8526 (mtt-85) cc_final: 0.8157 (mmt90) REVERT: A 202 ASP cc_start: 0.8659 (p0) cc_final: 0.8441 (p0) REVERT: B 137 ARG cc_start: 0.8843 (ttm110) cc_final: 0.8477 (ttm110) REVERT: C 24 GLU cc_start: 0.7995 (tp30) cc_final: 0.7629 (mm-30) REVERT: C 191 PHE cc_start: 0.7941 (p90) cc_final: 0.7549 (p90) REVERT: C 288 ARG cc_start: 0.8353 (mtm-85) cc_final: 0.8119 (mtp180) REVERT: C 361 MET cc_start: 0.7221 (mmp) cc_final: 0.6816 (mtt) REVERT: C 429 ASP cc_start: 0.8430 (OUTLIER) cc_final: 0.8183 (t0) REVERT: C 504 GLU cc_start: 0.6969 (pt0) cc_final: 0.6678 (pt0) REVERT: C 560 MET cc_start: 0.8707 (mtt) cc_final: 0.8335 (mtp) REVERT: C 605 LYS cc_start: 0.8692 (mttt) cc_final: 0.8259 (mtmt) REVERT: C 788 THR cc_start: 0.7784 (p) cc_final: 0.7336 (p) REVERT: C 960 GLU cc_start: 0.7849 (tt0) cc_final: 0.7485 (mp0) REVERT: C 1005 MET cc_start: 0.9106 (ttp) cc_final: 0.8900 (ttt) REVERT: D 38 LYS cc_start: 0.7394 (mmtp) cc_final: 0.7079 (mtmm) REVERT: D 46 ASP cc_start: 0.8955 (t0) cc_final: 0.8625 (t70) REVERT: D 54 LYS cc_start: 0.8203 (mttp) cc_final: 0.7653 (mtpp) REVERT: D 157 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.8176 (mp0) REVERT: D 453 ASP cc_start: 0.8144 (t0) cc_final: 0.7798 (t0) REVERT: D 491 LYS cc_start: 0.7823 (tmmt) cc_final: 0.7093 (mtmm) REVERT: D 662 GLU cc_start: 0.8076 (tp30) cc_final: 0.7854 (tp30) REVERT: D 797 LYS cc_start: 0.8421 (tptt) cc_final: 0.7862 (mttt) REVERT: D 799 LYS cc_start: 0.8455 (mttt) cc_final: 0.8198 (mttp) REVERT: D 811 GLU cc_start: 0.7774 (mt-10) cc_final: 0.7512 (mt-10) REVERT: D 847 ASP cc_start: 0.7294 (m-30) cc_final: 0.6865 (m-30) REVERT: D 976 GLN cc_start: 0.7926 (tt0) cc_final: 0.7708 (tm-30) REVERT: D 1012 GLU cc_start: 0.8550 (tm-30) cc_final: 0.7861 (mt-10) REVERT: D 1051 GLU cc_start: 0.7978 (tt0) cc_final: 0.7746 (tt0) REVERT: D 1079 LYS cc_start: 0.8473 (tptt) cc_final: 0.7909 (tppt) REVERT: D 1100 ASP cc_start: 0.8412 (OUTLIER) cc_final: 0.8123 (m-30) REVERT: D 1184 GLN cc_start: 0.8428 (mt0) cc_final: 0.8195 (mt0) REVERT: D 1327 ARG cc_start: 0.8703 (mtt90) cc_final: 0.8490 (mtp85) REVERT: D 1350 GLU cc_start: 0.7954 (tp30) cc_final: 0.7528 (tt0) REVERT: D 1490 LYS cc_start: 0.8551 (ttmt) cc_final: 0.8251 (ttmm) REVERT: E 28 GLN cc_start: 0.7699 (mt0) cc_final: 0.7296 (mt0) REVERT: E 48 MET cc_start: 0.8414 (ttt) cc_final: 0.7631 (ttp) REVERT: E 59 ASN cc_start: 0.8937 (t160) cc_final: 0.8403 (t0) REVERT: E 65 MET cc_start: 0.9004 (mtm) cc_final: 0.8737 (mtt) outliers start: 41 outliers final: 35 residues processed: 289 average time/residue: 0.1917 time to fit residues: 82.5175 Evaluate side-chains 293 residues out of total 2516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 255 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 185 ARG Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain C residue 2 GLU Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 289 THR Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 429 ASP Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 583 LEU Chi-restraints excluded: chain C residue 653 ASP Chi-restraints excluded: chain C residue 950 LEU Chi-restraints excluded: chain C residue 974 LEU Chi-restraints excluded: chain C residue 1107 ASN Chi-restraints excluded: chain D residue 157 GLU Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain D residue 452 ILE Chi-restraints excluded: chain D residue 632 VAL Chi-restraints excluded: chain D residue 684 LYS Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain D residue 875 THR Chi-restraints excluded: chain D residue 904 VAL Chi-restraints excluded: chain D residue 940 THR Chi-restraints excluded: chain D residue 1086 LEU Chi-restraints excluded: chain D residue 1100 ASP Chi-restraints excluded: chain D residue 1132 LEU Chi-restraints excluded: chain D residue 1275 SER Chi-restraints excluded: chain D residue 1400 VAL Chi-restraints excluded: chain D residue 1415 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 223 optimal weight: 0.8980 chunk 58 optimal weight: 9.9990 chunk 1 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 130 optimal weight: 0.9980 chunk 185 optimal weight: 9.9990 chunk 249 optimal weight: 0.0980 chunk 57 optimal weight: 1.9990 chunk 174 optimal weight: 7.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 GLN B 95 GLN ** D 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.167203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.117971 restraints weight = 27768.196| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.73 r_work: 0.2863 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2792 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2792 r_free = 0.2792 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2792 r_free = 0.2792 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2792 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 25151 Z= 0.121 Angle : 0.500 7.201 34278 Z= 0.263 Chirality : 0.043 0.248 3873 Planarity : 0.004 0.051 4287 Dihedral : 12.389 152.969 3910 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.91 % Allowed : 12.00 % Favored : 86.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.15), residues: 2942 helix: 1.31 (0.16), residues: 1067 sheet: 0.05 (0.25), residues: 423 loop : -0.05 (0.16), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 507 TYR 0.014 0.001 TYR B 224 PHE 0.014 0.001 PHE C 239 TRP 0.011 0.001 TRP B 200 HIS 0.004 0.001 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (25143) covalent geometry : angle 0.49852 / 0.26 (34266) hydrogen bonds : bond 0.04026 / 2.67 ( 1122) hydrogen bonds : angle 4.34203 / 3.09 ( 3037) metal coordination : bond 0.00251 / 0.17 ( 8) metal coordination : angle 2.39939 / 1.39 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 266 time to evaluate : 0.949 Fit side-chains REVERT: A 175 ARG cc_start: 0.8533 (mtt-85) cc_final: 0.8214 (mmt90) REVERT: B 137 ARG cc_start: 0.8854 (ttm110) cc_final: 0.8497 (ttm110) REVERT: C 24 GLU cc_start: 0.8090 (tp30) cc_final: 0.7741 (mm-30) REVERT: C 191 PHE cc_start: 0.7996 (p90) cc_final: 0.7629 (p90) REVERT: C 361 MET cc_start: 0.7010 (mmp) cc_final: 0.6565 (mtt) REVERT: C 429 ASP cc_start: 0.8466 (OUTLIER) cc_final: 0.8254 (t0) REVERT: C 504 GLU cc_start: 0.7024 (pt0) cc_final: 0.6767 (pt0) REVERT: C 560 MET cc_start: 0.8804 (mtt) cc_final: 0.8432 (mtp) REVERT: C 605 LYS cc_start: 0.8673 (mttt) cc_final: 0.8346 (mtmt) REVERT: C 788 THR cc_start: 0.7958 (p) cc_final: 0.7504 (p) REVERT: C 960 GLU cc_start: 0.7951 (tt0) cc_final: 0.7678 (mp0) REVERT: C 1005 MET cc_start: 0.8999 (ttp) cc_final: 0.8797 (ttt) REVERT: D 38 LYS cc_start: 0.7430 (mmtp) cc_final: 0.7140 (mtmm) REVERT: D 46 ASP cc_start: 0.8909 (t0) cc_final: 0.8635 (t0) REVERT: D 54 LYS cc_start: 0.8313 (mttp) cc_final: 0.7837 (mtpp) REVERT: D 157 GLU cc_start: 0.8482 (OUTLIER) cc_final: 0.8242 (mp0) REVERT: D 453 ASP cc_start: 0.8232 (t0) cc_final: 0.7963 (t0) REVERT: D 491 LYS cc_start: 0.7916 (tmmt) cc_final: 0.7219 (mtmm) REVERT: D 553 ARG cc_start: 0.8053 (ttp80) cc_final: 0.7785 (ttp-110) REVERT: D 797 LYS cc_start: 0.8478 (tptt) cc_final: 0.8000 (mttt) REVERT: D 799 LYS cc_start: 0.8424 (mttt) cc_final: 0.8188 (mttp) REVERT: D 811 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7533 (mt-10) REVERT: D 847 ASP cc_start: 0.7358 (m-30) cc_final: 0.6948 (m-30) REVERT: D 1012 GLU cc_start: 0.8573 (tm-30) cc_final: 0.8007 (mt-10) REVERT: D 1051 GLU cc_start: 0.8057 (tt0) cc_final: 0.7831 (tt0) REVERT: D 1079 LYS cc_start: 0.8559 (tptt) cc_final: 0.8047 (tppt) REVERT: D 1100 ASP cc_start: 0.8367 (OUTLIER) cc_final: 0.8070 (m-30) REVERT: D 1327 ARG cc_start: 0.8754 (mtt90) cc_final: 0.8546 (mtp85) REVERT: D 1350 GLU cc_start: 0.7990 (tp30) cc_final: 0.7628 (tt0) REVERT: D 1490 LYS cc_start: 0.8629 (ttmt) cc_final: 0.8347 (ttmm) REVERT: E 28 GLN cc_start: 0.7781 (mt0) cc_final: 0.7400 (mt0) REVERT: E 48 MET cc_start: 0.8419 (ttt) cc_final: 0.7746 (ttp) REVERT: E 59 ASN cc_start: 0.8931 (t160) cc_final: 0.8398 (t0) REVERT: E 65 MET cc_start: 0.9003 (mtm) cc_final: 0.8742 (mtt) REVERT: E 88 GLU cc_start: 0.7800 (mm-30) cc_final: 0.7486 (tp30) outliers start: 48 outliers final: 39 residues processed: 297 average time/residue: 0.1936 time to fit residues: 85.9262 Evaluate side-chains 292 residues out of total 2516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 250 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 185 ARG Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain C residue 2 GLU Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 289 THR Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 429 ASP Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 583 LEU Chi-restraints excluded: chain C residue 653 ASP Chi-restraints excluded: chain C residue 698 ASP Chi-restraints excluded: chain C residue 950 LEU Chi-restraints excluded: chain C residue 954 THR Chi-restraints excluded: chain C residue 1107 ASN Chi-restraints excluded: chain D residue 157 GLU Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain D residue 452 ILE Chi-restraints excluded: chain D residue 538 SER Chi-restraints excluded: chain D residue 632 VAL Chi-restraints excluded: chain D residue 684 LYS Chi-restraints excluded: chain D residue 694 VAL Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain D residue 875 THR Chi-restraints excluded: chain D residue 904 VAL Chi-restraints excluded: chain D residue 940 THR Chi-restraints excluded: chain D residue 1086 LEU Chi-restraints excluded: chain D residue 1100 ASP Chi-restraints excluded: chain D residue 1132 LEU Chi-restraints excluded: chain D residue 1275 SER Chi-restraints excluded: chain D residue 1400 VAL Chi-restraints excluded: chain D residue 1415 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 21 optimal weight: 5.9990 chunk 83 optimal weight: 0.9990 chunk 95 optimal weight: 4.9990 chunk 226 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 chunk 198 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 266 optimal weight: 6.9990 chunk 281 optimal weight: 5.9990 chunk 141 optimal weight: 2.9990 chunk 224 optimal weight: 4.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 GLN D 593 ASN D 744 GLN D 901 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.164902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.116035 restraints weight = 27696.519| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 3.08 r_work: 0.2724 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2699 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2699 r_free = 0.2699 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2699 r_free = 0.2699 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2699 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 25151 Z= 0.224 Angle : 0.587 9.539 34278 Z= 0.306 Chirality : 0.047 0.320 3873 Planarity : 0.005 0.051 4287 Dihedral : 12.429 148.110 3910 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.95 % Allowed : 12.28 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.15), residues: 2942 helix: 1.12 (0.16), residues: 1065 sheet: 0.09 (0.25), residues: 421 loop : -0.13 (0.16), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 388 TYR 0.028 0.002 TYR B 224 PHE 0.015 0.002 PHE C 896 TRP 0.010 0.002 TRP B 200 HIS 0.009 0.002 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00558 / 0.22 (25143) covalent geometry : angle 0.58577 / 0.31 (34266) hydrogen bonds : bond 0.05040 / 3.34 ( 1122) hydrogen bonds : angle 4.48944 / 3.19 ( 3037) metal coordination : bond 0.00583 / 0.39 ( 8) metal coordination : angle 2.44712 / 1.44 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 257 time to evaluate : 0.649 Fit side-chains REVERT: A 175 ARG cc_start: 0.8678 (mtt-85) cc_final: 0.8178 (mtt180) REVERT: C 24 GLU cc_start: 0.8098 (tp30) cc_final: 0.7762 (mm-30) REVERT: C 191 PHE cc_start: 0.8001 (p90) cc_final: 0.7654 (p90) REVERT: C 361 MET cc_start: 0.7217 (mmp) cc_final: 0.6821 (mtt) REVERT: C 560 MET cc_start: 0.8833 (mtt) cc_final: 0.8446 (mtp) REVERT: C 605 LYS cc_start: 0.8777 (mttt) cc_final: 0.8494 (mtmt) REVERT: C 788 THR cc_start: 0.7978 (p) cc_final: 0.7531 (p) REVERT: D 38 LYS cc_start: 0.7554 (mmtp) cc_final: 0.7272 (mtmm) REVERT: D 46 ASP cc_start: 0.8950 (t0) cc_final: 0.8683 (t0) REVERT: D 54 LYS cc_start: 0.8330 (mttp) cc_final: 0.7840 (mtpp) REVERT: D 157 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.8213 (mp0) REVERT: D 453 ASP cc_start: 0.8286 (t0) cc_final: 0.7988 (t0) REVERT: D 491 LYS cc_start: 0.8012 (tmmt) cc_final: 0.7299 (mtmm) REVERT: D 553 ARG cc_start: 0.8155 (ttp80) cc_final: 0.7803 (ttp-110) REVERT: D 797 LYS cc_start: 0.8495 (tptt) cc_final: 0.8046 (mttt) REVERT: D 799 LYS cc_start: 0.8496 (mttt) cc_final: 0.8242 (mttp) REVERT: D 832 ARG cc_start: 0.7856 (mtm180) cc_final: 0.7464 (ptt180) REVERT: D 847 ASP cc_start: 0.7380 (m-30) cc_final: 0.6965 (m-30) REVERT: D 1005 GLN cc_start: 0.7840 (mm-40) cc_final: 0.7580 (mt0) REVERT: D 1012 GLU cc_start: 0.8666 (tm-30) cc_final: 0.8007 (mt-10) REVERT: D 1051 GLU cc_start: 0.8059 (tt0) cc_final: 0.7824 (tt0) REVERT: D 1079 LYS cc_start: 0.8534 (tptt) cc_final: 0.8072 (ttmt) REVERT: D 1100 ASP cc_start: 0.8478 (OUTLIER) cc_final: 0.8194 (m-30) REVERT: D 1327 ARG cc_start: 0.8747 (mtt90) cc_final: 0.8537 (mtp85) REVERT: D 1350 GLU cc_start: 0.8032 (tp30) cc_final: 0.7676 (tt0) REVERT: D 1490 LYS cc_start: 0.8608 (ttmt) cc_final: 0.8311 (ttmm) REVERT: E 48 MET cc_start: 0.8426 (ttt) cc_final: 0.7763 (ttp) REVERT: E 59 ASN cc_start: 0.8963 (OUTLIER) cc_final: 0.8425 (t0) REVERT: E 65 MET cc_start: 0.9060 (mtm) cc_final: 0.8778 (mtt) outliers start: 49 outliers final: 41 residues processed: 288 average time/residue: 0.1924 time to fit residues: 82.4105 Evaluate side-chains 293 residues out of total 2516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 249 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 185 ARG Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain C residue 2 GLU Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 289 THR Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 583 LEU Chi-restraints excluded: chain C residue 653 ASP Chi-restraints excluded: chain C residue 950 LEU Chi-restraints excluded: chain C residue 954 THR Chi-restraints excluded: chain C residue 974 LEU Chi-restraints excluded: chain C residue 1107 ASN Chi-restraints excluded: chain D residue 157 GLU Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain D residue 452 ILE Chi-restraints excluded: chain D residue 538 SER Chi-restraints excluded: chain D residue 632 VAL Chi-restraints excluded: chain D residue 684 LYS Chi-restraints excluded: chain D residue 694 VAL Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain D residue 875 THR Chi-restraints excluded: chain D residue 904 VAL Chi-restraints excluded: chain D residue 940 THR Chi-restraints excluded: chain D residue 1083 ASP Chi-restraints excluded: chain D residue 1086 LEU Chi-restraints excluded: chain D residue 1100 ASP Chi-restraints excluded: chain D residue 1132 LEU Chi-restraints excluded: chain D residue 1275 SER Chi-restraints excluded: chain D residue 1400 VAL Chi-restraints excluded: chain D residue 1415 VAL Chi-restraints excluded: chain E residue 59 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 141 optimal weight: 2.9990 chunk 280 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 150 optimal weight: 0.9990 chunk 62 optimal weight: 9.9990 chunk 33 optimal weight: 0.8980 chunk 188 optimal weight: 2.9990 chunk 112 optimal weight: 0.6980 chunk 69 optimal weight: 10.0000 chunk 228 optimal weight: 1.9990 chunk 115 optimal weight: 3.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 GLN D 901 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.167087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.118476 restraints weight = 27754.663| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 2.97 r_work: 0.2850 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2759 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2759 r_free = 0.2759 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2759 r_free = 0.2759 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2759 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 25151 Z= 0.120 Angle : 0.501 7.583 34278 Z= 0.265 Chirality : 0.043 0.242 3873 Planarity : 0.004 0.050 4287 Dihedral : 12.366 153.028 3910 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.59 % Allowed : 12.88 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.15), residues: 2942 helix: 1.36 (0.16), residues: 1066 sheet: 0.16 (0.25), residues: 420 loop : -0.02 (0.16), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 388 TYR 0.018 0.001 TYR B 224 PHE 0.013 0.001 PHE C 114 TRP 0.012 0.001 TRP B 200 HIS 0.004 0.001 HIS C 552 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (25143) covalent geometry : angle 0.49872 / 0.26 (34266) hydrogen bonds : bond 0.04026 / 2.67 ( 1122) hydrogen bonds : angle 4.33276 / 3.09 ( 3037) metal coordination : bond 0.00226 / 0.16 ( 8) metal coordination : angle 2.35079 / 1.36 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 256 time to evaluate : 0.865 Fit side-chains REVERT: A 175 ARG cc_start: 0.8576 (mtt-85) cc_final: 0.8239 (mmt90) REVERT: B 137 ARG cc_start: 0.8812 (ttm110) cc_final: 0.8318 (ttm110) REVERT: C 24 GLU cc_start: 0.8083 (tp30) cc_final: 0.7740 (mm-30) REVERT: C 191 PHE cc_start: 0.7976 (p90) cc_final: 0.7637 (p90) REVERT: C 361 MET cc_start: 0.7133 (mmp) cc_final: 0.6716 (mtt) REVERT: C 504 GLU cc_start: 0.7146 (pt0) cc_final: 0.6890 (pt0) REVERT: C 560 MET cc_start: 0.8826 (mtt) cc_final: 0.8455 (mtp) REVERT: C 605 LYS cc_start: 0.8730 (mttt) cc_final: 0.8472 (mtmt) REVERT: C 788 THR cc_start: 0.8012 (p) cc_final: 0.7560 (p) REVERT: D 38 LYS cc_start: 0.7530 (mmtp) cc_final: 0.7237 (mtmm) REVERT: D 46 ASP cc_start: 0.8934 (t0) cc_final: 0.8654 (t0) REVERT: D 54 LYS cc_start: 0.8303 (mttp) cc_final: 0.7829 (mtpp) REVERT: D 157 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.8237 (mp0) REVERT: D 453 ASP cc_start: 0.8268 (t0) cc_final: 0.8006 (t0) REVERT: D 491 LYS cc_start: 0.7931 (tmmt) cc_final: 0.7222 (mtmm) REVERT: D 553 ARG cc_start: 0.8137 (ttp80) cc_final: 0.7790 (ttp-110) REVERT: D 797 LYS cc_start: 0.8467 (tptt) cc_final: 0.7994 (mttt) REVERT: D 799 LYS cc_start: 0.8459 (mttt) cc_final: 0.8206 (mttp) REVERT: D 811 GLU cc_start: 0.7865 (mt-10) cc_final: 0.7549 (mt-10) REVERT: D 832 ARG cc_start: 0.7735 (mtm180) cc_final: 0.7361 (ptt180) REVERT: D 847 ASP cc_start: 0.7369 (m-30) cc_final: 0.6958 (m-30) REVERT: D 976 GLN cc_start: 0.7750 (tm-30) cc_final: 0.7339 (tm-30) REVERT: D 1005 GLN cc_start: 0.7814 (mm-40) cc_final: 0.7588 (mt0) REVERT: D 1012 GLU cc_start: 0.8570 (tm-30) cc_final: 0.7999 (mt-10) REVERT: D 1051 GLU cc_start: 0.8075 (tt0) cc_final: 0.7844 (tt0) REVERT: D 1079 LYS cc_start: 0.8566 (tptt) cc_final: 0.8065 (tppt) REVERT: D 1100 ASP cc_start: 0.8403 (OUTLIER) cc_final: 0.8120 (m-30) REVERT: D 1327 ARG cc_start: 0.8753 (mtt90) cc_final: 0.8536 (mtp85) REVERT: D 1346 ARG cc_start: 0.8226 (ttm110) cc_final: 0.7807 (mtp180) REVERT: D 1350 GLU cc_start: 0.8030 (tp30) cc_final: 0.7668 (tt0) REVERT: D 1490 LYS cc_start: 0.8602 (ttmt) cc_final: 0.8316 (ttmm) REVERT: E 12 MET cc_start: 0.8514 (mtp) cc_final: 0.8240 (mtp) REVERT: E 28 GLN cc_start: 0.7783 (mt0) cc_final: 0.7412 (mt0) REVERT: E 48 MET cc_start: 0.8431 (ttt) cc_final: 0.8187 (ptm) REVERT: E 59 ASN cc_start: 0.8917 (t160) cc_final: 0.8347 (t0) REVERT: E 65 MET cc_start: 0.9011 (mtm) cc_final: 0.8771 (mtt) outliers start: 40 outliers final: 34 residues processed: 281 average time/residue: 0.1906 time to fit residues: 79.8894 Evaluate side-chains 283 residues out of total 2516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 247 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 185 ARG Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain C residue 2 GLU Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 289 THR Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 583 LEU Chi-restraints excluded: chain C residue 653 ASP Chi-restraints excluded: chain C residue 950 LEU Chi-restraints excluded: chain C residue 954 THR Chi-restraints excluded: chain C residue 1107 ASN Chi-restraints excluded: chain D residue 157 GLU Chi-restraints excluded: chain D residue 452 ILE Chi-restraints excluded: chain D residue 538 SER Chi-restraints excluded: chain D residue 632 VAL Chi-restraints excluded: chain D residue 684 LYS Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain D residue 904 VAL Chi-restraints excluded: chain D residue 1067 VAL Chi-restraints excluded: chain D residue 1086 LEU Chi-restraints excluded: chain D residue 1100 ASP Chi-restraints excluded: chain D residue 1132 LEU Chi-restraints excluded: chain D residue 1275 SER Chi-restraints excluded: chain D residue 1400 VAL Chi-restraints excluded: chain D residue 1415 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 219 optimal weight: 8.9990 chunk 36 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 chunk 239 optimal weight: 4.9990 chunk 29 optimal weight: 6.9990 chunk 71 optimal weight: 8.9990 chunk 27 optimal weight: 8.9990 chunk 47 optimal weight: 1.9990 chunk 190 optimal weight: 9.9990 chunk 244 optimal weight: 4.9990 chunk 236 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 GLN D 901 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.165171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.118580 restraints weight = 27467.149| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 2.66 r_work: 0.2689 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2749 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2749 r_free = 0.2749 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2749 r_free = 0.2749 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2749 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.077 25151 Z= 0.314 Angle : 0.658 10.984 34278 Z= 0.340 Chirality : 0.050 0.388 3873 Planarity : 0.006 0.056 4287 Dihedral : 12.466 144.178 3910 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.71 % Allowed : 12.92 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.15), residues: 2942 helix: 1.02 (0.16), residues: 1053 sheet: 0.09 (0.25), residues: 432 loop : -0.16 (0.16), residues: 1457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 388 TYR 0.022 0.002 TYR C 925 PHE 0.020 0.002 PHE C 896 TRP 0.009 0.002 TRP B 200 HIS 0.012 0.002 HIS D 709 Details of bonding type rmsd/Z covalent geometry : bond 0.00797 / 0.31 (25143) covalent geometry : angle 0.65634 / 0.34 (34266) hydrogen bonds : bond 0.05763 / 3.81 ( 1122) hydrogen bonds : angle 4.61676 / 3.28 ( 3037) metal coordination : bond 0.00901 / 0.61 ( 8) metal coordination : angle 2.52158 / 1.48 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 255 time to evaluate : 0.779 Fit side-chains REVERT: A 175 ARG cc_start: 0.8678 (mtt-85) cc_final: 0.8196 (mtt180) REVERT: B 137 ARG cc_start: 0.8735 (ttm110) cc_final: 0.8244 (ttm110) REVERT: C 24 GLU cc_start: 0.8159 (tp30) cc_final: 0.7804 (mm-30) REVERT: C 191 PHE cc_start: 0.7924 (p90) cc_final: 0.7619 (p90) REVERT: C 229 MET cc_start: 0.8347 (OUTLIER) cc_final: 0.8006 (tmm) REVERT: C 560 MET cc_start: 0.8862 (mtt) cc_final: 0.8472 (mtp) REVERT: C 605 LYS cc_start: 0.8697 (mttt) cc_final: 0.8451 (mtmt) REVERT: C 750 LYS cc_start: 0.8864 (mttt) cc_final: 0.8467 (mttm) REVERT: C 788 THR cc_start: 0.8068 (p) cc_final: 0.7618 (p) REVERT: D 38 LYS cc_start: 0.7661 (mmtp) cc_final: 0.7423 (mtmm) REVERT: D 46 ASP cc_start: 0.9002 (t0) cc_final: 0.8735 (t0) REVERT: D 54 LYS cc_start: 0.8295 (mttp) cc_final: 0.7786 (mtpp) REVERT: D 453 ASP cc_start: 0.8314 (t0) cc_final: 0.8015 (t0) REVERT: D 491 LYS cc_start: 0.8077 (tmmt) cc_final: 0.7339 (mtmm) REVERT: D 553 ARG cc_start: 0.8124 (ttp80) cc_final: 0.7886 (ttp-170) REVERT: D 797 LYS cc_start: 0.8534 (tptt) cc_final: 0.8115 (mttt) REVERT: D 799 LYS cc_start: 0.8575 (mttt) cc_final: 0.8260 (mttp) REVERT: D 847 ASP cc_start: 0.7404 (m-30) cc_final: 0.6992 (m-30) REVERT: D 1005 GLN cc_start: 0.7854 (mm-40) cc_final: 0.7606 (mt0) REVERT: D 1012 GLU cc_start: 0.8706 (tm-30) cc_final: 0.8015 (mt-10) REVERT: D 1051 GLU cc_start: 0.8085 (tt0) cc_final: 0.7843 (tt0) REVERT: D 1079 LYS cc_start: 0.8547 (tptt) cc_final: 0.8101 (ttmt) REVERT: D 1100 ASP cc_start: 0.8463 (OUTLIER) cc_final: 0.8202 (m-30) REVERT: D 1327 ARG cc_start: 0.8787 (mtt90) cc_final: 0.8566 (mtp85) REVERT: D 1346 ARG cc_start: 0.8264 (ttm110) cc_final: 0.7882 (mtp180) REVERT: D 1350 GLU cc_start: 0.8177 (tp30) cc_final: 0.7831 (tt0) REVERT: D 1490 LYS cc_start: 0.8630 (ttmt) cc_final: 0.8330 (ttmm) REVERT: E 48 MET cc_start: 0.8466 (ttt) cc_final: 0.7839 (ttp) REVERT: E 59 ASN cc_start: 0.8978 (t160) cc_final: 0.8397 (t0) outliers start: 43 outliers final: 38 residues processed: 282 average time/residue: 0.1992 time to fit residues: 83.5034 Evaluate side-chains 287 residues out of total 2516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 247 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 185 ARG Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain C residue 2 GLU Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain C residue 289 THR Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 583 LEU Chi-restraints excluded: chain C residue 653 ASP Chi-restraints excluded: chain C residue 950 LEU Chi-restraints excluded: chain C residue 954 THR Chi-restraints excluded: chain C residue 1107 ASN Chi-restraints excluded: chain D residue 452 ILE Chi-restraints excluded: chain D residue 538 SER Chi-restraints excluded: chain D residue 632 VAL Chi-restraints excluded: chain D residue 684 LYS Chi-restraints excluded: chain D residue 694 VAL Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain D residue 904 VAL Chi-restraints excluded: chain D residue 940 THR Chi-restraints excluded: chain D residue 1083 ASP Chi-restraints excluded: chain D residue 1086 LEU Chi-restraints excluded: chain D residue 1100 ASP Chi-restraints excluded: chain D residue 1132 LEU Chi-restraints excluded: chain D residue 1159 ARG Chi-restraints excluded: chain D residue 1275 SER Chi-restraints excluded: chain D residue 1400 VAL Chi-restraints excluded: chain D residue 1415 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 127 optimal weight: 0.8980 chunk 230 optimal weight: 0.9990 chunk 74 optimal weight: 10.0000 chunk 98 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 123 optimal weight: 7.9990 chunk 75 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 296 optimal weight: 30.0000 chunk 91 optimal weight: 1.9990 chunk 188 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 GLN D 901 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.167296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.118403 restraints weight = 27741.156| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.96 r_work: 0.2861 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2747 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2747 r_free = 0.2747 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2747 r_free = 0.2747 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2747 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 25151 Z= 0.111 Angle : 0.509 8.068 34278 Z= 0.269 Chirality : 0.043 0.236 3873 Planarity : 0.004 0.051 4287 Dihedral : 12.376 152.546 3910 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.51 % Allowed : 13.43 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.15), residues: 2942 helix: 1.35 (0.16), residues: 1066 sheet: 0.25 (0.25), residues: 423 loop : -0.00 (0.16), residues: 1453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 388 TYR 0.014 0.001 TYR C 925 PHE 0.014 0.001 PHE C 114 TRP 0.013 0.001 TRP B 200 HIS 0.006 0.001 HIS C 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (25143) covalent geometry : angle 0.50750 / 0.27 (34266) hydrogen bonds : bond 0.04041 / 2.67 ( 1122) hydrogen bonds : angle 4.35696 / 3.10 ( 3037) metal coordination : bond 0.00191 / 0.14 ( 8) metal coordination : angle 2.29002 / 1.31 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6062.81 seconds wall clock time: 104 minutes 13.32 seconds (6253.32 seconds total)