Starting phenix.real_space_refine on Sat Aug 8 21:31:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9say_54704/08_2026/9say_54704.cif Found real_map, /net/cci-nas-00/data/ceres_data/9say_54704/08_2026/9say_54704.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9say_54704/08_2026/9say_54704.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9say_54704/08_2026/9say_54704.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9say_54704/08_2026/9say_54704.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9say_54704/08_2026/9say_54704.map" } resolution = 3.44 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= -0.001 sd= 0.035 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 8 6.06 5 P 65 5.49 5 Mg 1 5.21 5 S 171 5.16 5 C 18497 2.51 5 N 5177 2.21 5 O 5721 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 29640 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 10859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1379, 10859 Classifications: {'peptide': 1379} Link IDs: {'PCIS': 1, 'PTRANS': 61, 'TRANS': 1316} Chain breaks: 10 Chain: "B" Number of atoms: 9142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1148, 9142 Classifications: {'peptide': 1148} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 1098} Chain breaks: 6 Chain: "C" Number of atoms: 2095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2095 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 11, 'TRANS': 254} Chain: "E" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1744 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 200} Chain: "F" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 670 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 6, 'TRANS': 76} Chain: "H" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1077 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 129} Chain breaks: 1 Chain: "I" Number of atoms: 909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 909 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 5, 'TRANS': 106} Chain breaks: 1 Chain: "J" Number of atoms: 532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 532 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "K" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 904 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 5, 'TRANS': 106} Chain: "L" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 359 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "N" Number of atoms: 489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 489 Classifications: {'DNA': 23} Link IDs: {'rna3p': 22} Chain: "R" Number of atoms: 198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 198 Classifications: {'RNA': 9} Modifications used: {'rna3p_pur': 7, 'rna3p_pyr': 2} Link IDs: {'rna3p': 8} Chain: "T" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 653 Classifications: {'DNA': 33} Link IDs: {'rna3p': 32} Chain: "A" 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} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 457 SG CYS A 67 112.425 72.533 85.605 1.00134.08 S ATOM 479 SG CYS A 70 112.265 75.602 87.951 1.00134.68 S ATOM 532 SG CYS A 77 109.093 73.699 87.073 1.00120.72 S ATOM 762 SG CYS A 107 95.602 81.493 41.685 1.00156.03 S ATOM 786 SG CYS A 110 98.252 84.172 41.831 1.00155.48 S ATOM 1091 SG CYS A 148 95.186 84.682 39.659 1.00165.80 S ATOM 1105 SG CYS A 167 97.804 81.996 38.704 1.00162.99 S ATOM 19507 SG CYS B1163 109.894 88.293 77.896 1.00123.74 S ATOM 19525 SG CYS B1166 107.574 85.797 76.325 1.00115.52 S ATOM 19650 SG CYS B1182 111.079 84.785 77.636 1.00122.54 S ATOM 19669 SG CYS B1185 110.601 86.755 74.379 1.00120.17 S ATOM 20657 SG CYS C 86 81.645 59.132 147.260 1.00123.45 S ATOM 20674 SG CYS C 88 83.726 56.924 145.210 1.00129.23 S ATOM 20707 SG CYS C 92 81.635 55.351 147.869 1.00109.48 S ATOM 20730 SG CYS C 95 79.940 56.727 144.723 1.00108.35 S ATOM 25648 SG CYS I 7 39.359 45.595 29.863 1.00158.93 S ATOM 25673 SG CYS I 10 42.959 44.755 30.503 1.00164.62 S ATOM 25839 SG CYS I 29 42.147 48.263 29.254 1.00174.01 S ATOM 25863 SG CYS I 32 41.732 45.318 26.939 1.00172.22 S ATOM 26190 SG CYS I 75 12.431 51.640 65.169 1.00164.26 S ATOM 26212 SG CYS I 78 11.558 48.012 65.969 1.00159.75 S ATOM 26428 SG CYS I 103 14.892 49.367 67.012 1.00150.59 S ATOM 26448 SG CYS I 106 14.182 48.884 63.299 1.00141.39 S ATOM 26550 SG CYS J 7 53.256 55.228 127.147 1.00 90.03 S ATOM 26573 SG CYS J 10 52.835 56.799 130.611 1.00 90.33 S ATOM 26853 SG CYS J 45 50.193 57.196 127.941 1.00 90.49 S ATOM 26859 SG CYS J 46 50.651 53.899 129.771 1.00 99.89 S ATOM 27982 SG CYS L 31 81.850 26.852 111.306 1.00128.76 S ATOM 28002 SG CYS L 34 81.356 24.373 114.036 1.00139.35 S ATOM 28106 SG CYS L 48 84.848 24.948 112.319 1.00141.98 S ATOM 28129 SG CYS L 51 82.176 22.986 110.603 1.00146.22 S Time building chain proxies: 6.01, per 1000 atoms: 0.20 Number of scatterers: 29640 At special positions: 0 Unit cell: (129.479, 152.329, 167.562, 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 8 29.99 S 171 16.00 P 65 15.00 Mg 1 11.99 O 5721 8.00 N 5177 7.00 C 18497 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: 2.41 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1802 " pdb="ZN ZN A1802 " - pdb=" NE2 HIS A 80 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 77 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 70 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 67 " pdb=" ZN A1803 " pdb="ZN ZN A1803 " - pdb=" SG CYS A 107 " pdb="ZN ZN A1803 " - pdb=" SG CYS A 110 " pdb="ZN ZN A1803 " - pdb=" SG CYS A 167 " pdb="ZN ZN A1803 " - pdb=" SG CYS A 148 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1166 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1163 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1182 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1185 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 86 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 92 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 95 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 10 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 32 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 7 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 29 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 106 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 78 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 103 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 75 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 46 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 48 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 31 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 34 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 51 " Number of angles added : 45 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6684 Finding SS restraints... Secondary structure from input PDB file: 125 helices and 42 sheets defined 37.9% alpha, 18.8% beta 30 base pairs and 56 stacking pairs defined. Time for finding SS restraints: 4.00 Creating SS restraints... Processing helix chain 'A' and resid 23 through 31 Processing helix chain 'A' and resid 92 through 94 No H-bonds generated for 'chain 'A' and resid 92 through 94' Processing helix chain 'A' and resid 95 through 106 Processing helix chain 'A' and resid 119 through 127 Processing helix chain 'A' and resid 130 through 143 Processing helix chain 'A' and resid 203 through 213 removed outlier: 3.552A pdb=" N HIS A 213 " --> pdb=" O ASN A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 221 Processing helix chain 'A' and resid 230 through 235 Processing helix chain 'A' and resid 260 through 283 removed outlier: 3.664A pdb=" N GLY A 283 " --> pdb=" O LEU A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 305 Processing helix chain 'A' and resid 324 through 330 Processing helix chain 'A' and resid 334 through 340 Processing helix chain 'A' and resid 368 through 374 Processing helix chain 'A' and resid 384 through 395 Processing helix chain 'A' and resid 451 through 453 No H-bonds generated for 'chain 'A' and resid 451 through 453' Processing helix chain 'A' and resid 474 through 479 removed outlier: 3.691A pdb=" N TYR A 478 " --> pdb=" O VAL A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 505 Processing helix chain 'A' and resid 507 through 510 Processing helix chain 'A' and resid 525 through 535 removed outlier: 3.673A pdb=" N ARG A 532 " --> pdb=" O LEU A 528 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS A 533 " --> pdb=" O CYS A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 552 Processing helix chain 'A' and resid 574 through 579 Processing helix chain 'A' and resid 618 through 623 Processing helix chain 'A' and resid 628 through 637 Processing helix chain 'A' and resid 638 through 659 Processing helix chain 'A' and resid 665 through 670 Processing helix chain 'A' and resid 672 through 699 Processing helix chain 'A' and resid 709 through 737 Processing helix chain 'A' and resid 741 through 750 Processing helix chain 'A' and resid 754 through 763 removed outlier: 3.573A pdb=" N ILE A 758 " --> pdb=" O SER A 754 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 797 Processing helix chain 'A' and resid 809 through 845 removed outlier: 3.582A pdb=" N GLU A 822 " --> pdb=" O MET A 818 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLY A 823 " --> pdb=" O GLY A 819 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ALA A 832 " --> pdb=" O ALA A 828 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 871 Processing helix chain 'A' and resid 889 through 898 Processing helix chain 'A' and resid 909 through 913 Processing helix chain 'A' and resid 915 through 920 removed outlier: 3.601A pdb=" N LEU A 920 " --> pdb=" O GLY A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 947 Processing helix chain 'A' and resid 959 through 972 removed outlier: 3.547A pdb=" N ILE A 963 " --> pdb=" O ASN A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 994 removed outlier: 3.573A pdb=" N GLN A 994 " --> pdb=" O VAL A 990 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1015 removed outlier: 3.565A pdb=" N VAL A1015 " --> pdb=" O GLN A1011 " (cutoff:3.500A) Processing helix chain 'A' and resid 1015 through 1026 Processing helix chain 'A' and resid 1027 through 1034 Processing helix chain 'A' and resid 1038 through 1056 Processing helix chain 'A' and resid 1063 through 1078 Proline residue: A1075 - end of helix Processing helix chain 'A' and resid 1096 through 1107 Processing helix chain 'A' and resid 1130 through 1139 Processing helix chain 'A' and resid 1142 through 1145 Processing helix chain 'A' and resid 1166 through 1174 removed outlier: 3.710A pdb=" N PHE A1174 " --> pdb=" O ILE A1170 " (cutoff:3.500A) Processing helix chain 'A' and resid 1198 through 1206 Processing helix chain 'A' and resid 1208 through 1221 Processing helix chain 'A' and resid 1257 through 1270 Processing helix chain 'A' and resid 1312 through 1317 removed outlier: 3.655A pdb=" N MET A1317 " --> pdb=" O LEU A1313 " (cutoff:3.500A) Processing helix chain 'A' and resid 1331 through 1340 Processing helix chain 'A' and resid 1340 through 1357 Processing helix chain 'A' and resid 1364 through 1376 removed outlier: 3.981A pdb=" N MET A1368 " --> pdb=" O ASN A1364 " (cutoff:3.500A) Processing helix chain 'A' and resid 1395 through 1401 Processing helix chain 'A' and resid 1404 through 1416 Processing helix chain 'A' and resid 1423 through 1430 removed outlier: 3.768A pdb=" N ASN A1427 " --> pdb=" O GLY A1423 " (cutoff:3.500A) Processing helix chain 'A' and resid 1447 through 1452 Processing helix chain 'B' and resid 29 through 37 removed outlier: 4.050A pdb=" N VAL B 33 " --> pdb=" O ASP B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 64 removed outlier: 3.756A pdb=" N LEU B 48 " --> pdb=" O VAL B 44 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N LEU B 59 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N GLN B 60 " --> pdb=" O ASP B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 121 Processing helix chain 'B' and resid 160 through 164 removed outlier: 3.705A pdb=" N LYS B 164 " --> pdb=" O GLU B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 192 Processing helix chain 'B' and resid 282 through 289 Processing helix chain 'B' and resid 293 through 303 removed outlier: 3.545A pdb=" N ILE B 297 " --> pdb=" O PRO B 293 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N TYR B 303 " --> pdb=" O GLU B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 Proline residue: B 316 - end of helix Processing helix chain 'B' and resid 326 through 338 Processing helix chain 'B' and resid 344 through 359 Processing helix chain 'B' and resid 370 through 390 Processing helix chain 'B' and resid 400 through 402 No H-bonds generated for 'chain 'B' and resid 400 through 402' Processing helix chain 'B' and resid 408 through 437 removed outlier: 3.712A pdb=" N GLU B 437 " --> pdb=" O GLN B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 448 Processing helix chain 'B' and resid 450 through 464 removed outlier: 3.579A pdb=" N THR B 454 " --> pdb=" O ALA B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 495 Processing helix chain 'B' and resid 515 through 519 Processing helix chain 'B' and resid 551 through 561 Processing helix chain 'B' and resid 565 through 569 Processing helix chain 'B' and resid 592 through 606 Processing helix chain 'B' and resid 654 through 667 Processing helix chain 'B' and resid 680 through 687 Processing helix chain 'B' and resid 696 through 701 removed outlier: 3.829A pdb=" N ILE B 701 " --> pdb=" O GLU B 698 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 710 removed outlier: 3.584A pdb=" N LEU B 710 " --> pdb=" O PRO B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 744 through 749 removed outlier: 3.669A pdb=" N LEU B 749 " --> pdb=" O SER B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 752 through 756 removed outlier: 3.604A pdb=" N ILE B 755 " --> pdb=" O ALA B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 762 removed outlier: 3.880A pdb=" N ASN B 762 " --> pdb=" O PRO B 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 763 through 774 Processing helix chain 'B' and resid 775 through 777 No H-bonds generated for 'chain 'B' and resid 775 through 777' Processing helix chain 'B' and resid 843 through 849 Processing helix chain 'B' and resid 1015 through 1021 removed outlier: 4.587A pdb=" N SER B1019 " --> pdb=" O HIS B1015 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ARG B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) Processing helix chain 'B' and resid 1022 through 1039 removed outlier: 3.758A pdb=" N LEU B1026 " --> pdb=" O THR B1022 " (cutoff:3.500A) Processing helix chain 'B' and resid 1051 through 1061 removed outlier: 3.714A pdb=" N GLU B1061 " --> pdb=" O LYS B1057 " (cutoff:3.500A) Processing helix chain 'B' and resid 1098 through 1102 Processing helix chain 'B' and resid 1131 through 1142 Processing helix chain 'B' and resid 1143 through 1152 Processing helix chain 'B' and resid 1197 through 1210 Processing helix chain 'C' and resid 26 through 40 Processing helix chain 'C' and resid 59 through 69 Processing helix chain 'C' and resid 76 through 80 removed outlier: 3.538A pdb=" N GLN C 79 " --> pdb=" O ASP C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 118 No H-bonds generated for 'chain 'C' and resid 116 through 118' Processing helix chain 'C' and resid 167 through 171 Processing helix chain 'C' and resid 196 through 201 Processing helix chain 'C' and resid 206 through 210 Processing helix chain 'C' and resid 239 through 266 removed outlier: 3.636A pdb=" N ASP C 266 " --> pdb=" O LEU C 262 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 27 removed outlier: 3.504A pdb=" N GLY E 27 " --> pdb=" O VAL E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 36 Processing helix chain 'E' and resid 38 through 44 Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 92 through 104 Processing helix chain 'E' and resid 117 through 124 removed outlier: 3.525A pdb=" N MET E 121 " --> pdb=" O THR E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 141 removed outlier: 3.587A pdb=" N VAL E 141 " --> pdb=" O ALA E 138 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 138 through 141' Processing helix chain 'E' and resid 157 through 169 Processing helix chain 'E' and resid 182 through 189 Processing helix chain 'F' and resid 86 through 103 Processing helix chain 'F' and resid 116 through 128 Processing helix chain 'H' and resid 88 through 93 Processing helix chain 'H' and resid 129 through 133 Processing helix chain 'I' and resid 61 through 65 Processing helix chain 'J' and resid 14 through 17 Processing helix chain 'J' and resid 18 through 27 Processing helix chain 'J' and resid 31 through 39 Processing helix chain 'J' and resid 43 through 53 removed outlier: 3.842A pdb=" N HIS J 53 " --> pdb=" O MET J 49 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 61 Processing helix chain 'K' and resid 5 through 10 Processing helix chain 'K' and resid 39 through 53 removed outlier: 4.358A pdb=" N LEU K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU K 49 " --> pdb=" O LEU K 45 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASN K 52 " --> pdb=" O ALA K 48 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 110 Processing sheet with id=AA1, first strand: chain 'A' and resid 1418 through 1419 Processing sheet with id=AA2, first strand: chain 'A' and resid 82 through 90 removed outlier: 9.871A pdb=" N LEU A 86 " --> pdb=" O PRO A 240 " (cutoff:3.500A) removed outlier: 11.030A pdb=" N LYS A 88 " --> pdb=" O CYS A 238 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N CYS A 238 " --> pdb=" O LYS A 88 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 173 through 177 removed outlier: 4.733A pdb=" N LEU A 181 " --> pdb=" O LEU A 202 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 250 through 252 removed outlier: 3.743A pdb=" N PHE A 252 " --> pdb=" O GLN A 256 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 343 through 345 removed outlier: 3.611A pdb=" N LEU B1128 " --> pdb=" O VAL A 345 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1104 through 1106 removed outlier: 3.554A pdb=" N HIS B1104 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N THR A 351 " --> pdb=" O MET A 487 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N MET A 487 " --> pdb=" O THR A 351 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N MET A 456 " --> pdb=" O PHE A 444 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N PHE A 468 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N VAL A 352 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N LEU A 470 " --> pdb=" O VAL A 352 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N SER A 354 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 375 through 379 removed outlier: 6.339A pdb=" N LYS A 431 " --> pdb=" O VAL A 405 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N VAL A 405 " --> pdb=" O LYS A 431 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N GLU A 433 " --> pdb=" O LYS A 403 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 512 through 513 removed outlier: 3.730A pdb=" N LYS A 518 " --> pdb=" O SER A 513 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 540 through 541 Processing sheet with id=AB1, first strand: chain 'A' and resid 588 through 590 removed outlier: 7.058A pdb=" N LEU A 606 " --> pdb=" O ILE A 613 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 766 through 767 Processing sheet with id=AB3, first strand: chain 'A' and resid 849 through 850 removed outlier: 6.888A pdb=" N THR A 856 " --> pdb=" O ILE A 864 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 878 through 882 Processing sheet with id=AB5, first strand: chain 'A' and resid 1282 through 1292 removed outlier: 3.721A pdb=" N LEU A1116 " --> pdb=" O THR A1308 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1224 through 1228 removed outlier: 4.223A pdb=" N LEU A1236 " --> pdb=" O LEU A1197 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N VAL A1242 " --> pdb=" O TRP A1191 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N TRP A1191 " --> pdb=" O VAL A1242 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LEU A1192 " --> pdb=" O ILE A1152 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ILE A1152 " --> pdb=" O LEU A1192 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ARG A1194 " --> pdb=" O SER A1150 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N SER A1150 " --> pdb=" O ARG A1194 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N GLU A1196 " --> pdb=" O ILE A1148 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N SER A1150 " --> pdb=" O HIS I 46 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N HIS I 46 " --> pdb=" O SER A1150 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TYR I 44 " --> pdb=" O ILE A1152 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1441 through 1445 Processing sheet with id=AB8, first strand: chain 'B' and resid 69 through 73 removed outlier: 5.214A pdb=" N ARG B 86 " --> pdb=" O ALA B 139 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ALA B 139 " --> pdb=" O ARG B 86 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N TYR B 88 " --> pdb=" O TYR B 137 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N TYR B 137 " --> pdb=" O TYR B 88 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N ILE B 90 " --> pdb=" O ARG B 135 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ARG B 135 " --> pdb=" O ILE B 90 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N PHE B 92 " --> pdb=" O LYS B 133 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N LYS B 133 " --> pdb=" O PHE B 92 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N LYS B 94 " --> pdb=" O ASP B 131 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N GLY B 127 " --> pdb=" O THR B 98 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N SER B 125 " --> pdb=" O PRO B 100 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LYS B 134 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N GLU B 154 " --> pdb=" O LYS B 134 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N THR B 136 " --> pdb=" O ILE B 152 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ILE B 152 " --> pdb=" O THR B 136 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU B 150 " --> pdb=" O GLU B 138 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 109 through 111 removed outlier: 5.214A pdb=" N ARG B 86 " --> pdb=" O ALA B 139 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ALA B 139 " --> pdb=" O ARG B 86 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N TYR B 88 " --> pdb=" O TYR B 137 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N TYR B 137 " --> pdb=" O TYR B 88 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N ILE B 90 " --> pdb=" O ARG B 135 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ARG B 135 " --> pdb=" O ILE B 90 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N PHE B 92 " --> pdb=" O LYS B 133 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N LYS B 133 " --> pdb=" O PHE B 92 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N LYS B 94 " --> pdb=" O ASP B 131 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N GLY B 127 " --> pdb=" O THR B 98 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N SER B 125 " --> pdb=" O PRO B 100 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N GLY B 168 " --> pdb=" O LEU B 128 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N VAL B 130 " --> pdb=" O PHE B 166 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N PHE B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 203 through 205 Processing sheet with id=AC2, first strand: chain 'B' and resid 404 through 407 removed outlier: 5.982A pdb=" N ALA B 214 " --> pdb=" O ASN B 499 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 223 through 227 removed outlier: 4.020A pdb=" N HIS B 236 " --> pdb=" O LEU B 258 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 544 through 545 Processing sheet with id=AC5, first strand: chain 'B' and resid 650 through 651 removed outlier: 3.756A pdb=" N CYS B 741 " --> pdb=" O PHE B 638 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 585 through 590 removed outlier: 5.228A pdb=" N TRP B 586 " --> pdb=" O VAL B 582 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N VAL B 582 " --> pdb=" O TRP B 586 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLY B 588 " --> pdb=" O VAL B 580 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 792 through 793 removed outlier: 7.084A pdb=" N PHE B 963 " --> pdb=" O VAL B 954 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N VAL B 954 " --> pdb=" O PHE B 963 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N LYS B 965 " --> pdb=" O VAL B 952 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N VAL B 952 " --> pdb=" O LYS B 965 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ARG B 967 " --> pdb=" O ASP B 950 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 792 through 793 removed outlier: 7.084A pdb=" N PHE B 963 " --> pdb=" O VAL B 954 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N VAL B 954 " --> pdb=" O PHE B 963 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N LYS B 965 " --> pdb=" O VAL B 952 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N VAL B 952 " --> pdb=" O LYS B 965 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ARG B 967 " --> pdb=" O ASP B 950 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N VAL B 952 " --> pdb=" O LYS L 58 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU L 27 " --> pdb=" O LEU L 40 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 804 through 805 Processing sheet with id=AD1, first strand: chain 'B' and resid 1069 through 1070 removed outlier: 6.979A pdb=" N MET B 839 " --> pdb=" O GLY B 991 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N THR B 993 " --> pdb=" O MET B 839 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N MET B 841 " --> pdb=" O THR B 993 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N PHE B1086 " --> pdb=" O ILE B 827 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 873 through 874 Processing sheet with id=AD3, first strand: chain 'B' and resid 910 through 912 removed outlier: 3.780A pdb=" N ILE B 912 " --> pdb=" O THR B 939 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1158 through 1163 Processing sheet with id=AD5, first strand: chain 'B' and resid 1172 through 1174 Processing sheet with id=AD6, first strand: chain 'C' and resid 7 through 13 removed outlier: 5.312A pdb=" N VAL C 8 " --> pdb=" O SER C 23 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N SER C 23 " --> pdb=" O VAL C 8 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N ILE C 10 " --> pdb=" O ILE C 21 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ILE C 21 " --> pdb=" O ILE C 10 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU C 12 " --> pdb=" O ASP C 19 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 119 through 120 removed outlier: 6.534A pdb=" N GLU C 152 " --> pdb=" O THR C 53 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N THR C 53 " --> pdb=" O GLU C 152 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N LYS C 154 " --> pdb=" O VAL C 51 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N VAL C 51 " --> pdb=" O LYS C 154 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N THR C 156 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N VAL C 49 " --> pdb=" O THR C 156 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N VAL C 158 " --> pdb=" O ASP C 47 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA C 45 " --> pdb=" O LYS C 160 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N VAL L 65 " --> pdb=" O VAL C 51 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 72 through 74 removed outlier: 4.570A pdb=" N HIS C 131 " --> pdb=" O GLN C 73 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 111 through 114 Processing sheet with id=AE1, first strand: chain 'E' and resid 60 through 62 removed outlier: 6.532A pdb=" N TRP E 79 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N VAL E 111 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N GLU E 81 " --> pdb=" O VAL E 111 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 152 through 156 removed outlier: 3.709A pdb=" N LYS E 152 " --> pdb=" O ILE E 199 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N VAL E 195 " --> pdb=" O LEU E 156 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 4 through 16 removed outlier: 5.356A pdb=" N VAL H 12 " --> pdb=" O ALA H 29 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ALA H 29 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU H 121 " --> pdb=" O PHE H 118 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA H 60 " --> pdb=" O TYR H 141 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 15 through 19 Processing sheet with id=AE5, first strand: chain 'I' and resid 70 through 71 removed outlier: 4.301A pdb=" N ASN I 83 " --> pdb=" O SER I 71 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 19 through 23 1179 hydrogen bonds defined for protein. 3267 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 79 hydrogen bonds 158 hydrogen bond angles 0 basepair planarities 30 basepair parallelities 56 stacking parallelities Total time for adding SS restraints: 8.98 Time building geometry restraints manager: 3.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9583 1.34 - 1.46: 4794 1.46 - 1.58: 15528 1.58 - 1.70: 127 1.70 - 1.82: 275 Bond restraints: 30307 Sorted by residual: bond pdb=" C1' DC N 67 " pdb=" N1 DC N 67 " ideal model delta sigma weight residual 1.468 1.544 -0.076 1.40e-02 5.10e+03 2.92e+01 bond pdb=" C1' DG T 23 " pdb=" N9 DG T 23 " ideal model delta sigma weight residual 1.468 1.393 0.075 1.40e-02 5.10e+03 2.90e+01 bond pdb=" C3' DA N 54 " pdb=" C2' DA N 54 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.15e+01 bond pdb=" N9 G R 9 " pdb=" C4 G R 9 " ideal model delta sigma weight residual 1.375 1.401 -0.026 8.00e-03 1.56e+04 1.07e+01 bond pdb=" C3' DG N 51 " pdb=" C2' DG N 51 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.01e+01 ... (remaining 30302 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.86: 40613 1.86 - 3.72: 524 3.72 - 5.58: 47 5.58 - 7.44: 7 7.44 - 9.31: 2 Bond angle restraints: 41193 Sorted by residual: angle pdb=" C LEU I 14 " pdb=" N TYR I 15 " pdb=" CA TYR I 15 " ideal model delta sigma weight residual 120.94 129.10 -8.16 1.90e+00 2.77e-01 1.84e+01 angle pdb=" N3 DT T 33 " pdb=" C4 DT T 33 " pdb=" O4 DT T 33 " ideal model delta sigma weight residual 119.90 122.46 -2.56 6.00e-01 2.78e+00 1.83e+01 angle pdb=" N3 DT T 34 " pdb=" C4 DT T 34 " pdb=" O4 DT T 34 " ideal model delta sigma weight residual 119.90 122.45 -2.55 6.00e-01 2.78e+00 1.81e+01 angle pdb=" N3 DT T 25 " pdb=" C4 DT T 25 " pdb=" O4 DT T 25 " ideal model delta sigma weight residual 119.90 122.44 -2.54 6.00e-01 2.78e+00 1.79e+01 angle pdb=" N3 DT T 30 " pdb=" C4 DT T 30 " pdb=" O4 DT T 30 " ideal model delta sigma weight residual 119.90 122.42 -2.52 6.00e-01 2.78e+00 1.77e+01 ... (remaining 41188 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.90: 17826 30.90 - 61.80: 503 61.80 - 92.70: 44 92.70 - 123.60: 0 123.60 - 154.50: 1 Dihedral angle restraints: 18374 sinusoidal: 8055 harmonic: 10319 Sorted by residual: dihedral pdb=" CA THR A 69 " pdb=" C THR A 69 " pdb=" N CYS A 70 " pdb=" CA CYS A 70 " ideal model delta harmonic sigma weight residual 180.00 157.07 22.93 0 5.00e+00 4.00e-02 2.10e+01 dihedral pdb=" CA TRP B 561 " pdb=" C TRP B 561 " pdb=" N GLY B 562 " pdb=" CA GLY B 562 " ideal model delta harmonic sigma weight residual 180.00 159.58 20.42 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA ILE C 38 " pdb=" C ILE C 38 " pdb=" N ALA C 39 " pdb=" CA ALA C 39 " ideal model delta harmonic sigma weight residual -180.00 -160.34 -19.66 0 5.00e+00 4.00e-02 1.55e+01 ... (remaining 18371 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 3030 0.034 - 0.069: 1092 0.069 - 0.103: 336 0.103 - 0.137: 158 0.137 - 0.172: 7 Chirality restraints: 4623 Sorted by residual: chirality pdb=" CB VAL A 474 " pdb=" CA VAL A 474 " pdb=" CG1 VAL A 474 " pdb=" CG2 VAL A 474 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.37e-01 chirality pdb=" C1' DC N 67 " pdb=" O4' DC N 67 " pdb=" C2' DC N 67 " pdb=" N1 DC N 67 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.94e-01 chirality pdb=" CA HIS A 287 " pdb=" N HIS A 287 " pdb=" C HIS A 287 " pdb=" CB HIS A 287 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.64e-01 ... (remaining 4620 not shown) Planarity restraints: 5103 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A1434 " 0.030 5.00e-02 4.00e+02 4.57e-02 3.34e+00 pdb=" N PRO A1435 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO A1435 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A1435 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS I 75 " 0.029 5.00e-02 4.00e+02 4.35e-02 3.02e+00 pdb=" N PRO I 76 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO I 76 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO I 76 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 244 " 0.028 5.00e-02 4.00e+02 4.21e-02 2.83e+00 pdb=" N PRO A 245 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO A 245 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 245 " 0.024 5.00e-02 4.00e+02 ... (remaining 5100 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 269 2.59 - 3.17: 24730 3.17 - 3.75: 46629 3.75 - 4.32: 64152 4.32 - 4.90: 106437 Nonbonded interactions: 242217 Sorted by model distance: nonbonded pdb=" OD1 ASP A 481 " pdb="MG MG A1801 " model vdw 2.013 2.170 nonbonded pdb=" OD1 ASP A 485 " pdb="MG MG A1801 " model vdw 2.119 2.170 nonbonded pdb=" OE1 GLU A1062 " pdb=" OH TYR F 88 " model vdw 2.165 3.040 nonbonded pdb=" NH1 ARG B 996 " pdb=" O CYS J 10 " model vdw 2.210 3.120 nonbonded pdb=" OD1 ASP B 998 " pdb=" NH2 ARG C 35 " model vdw 2.225 3.120 ... (remaining 242212 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.360 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: 0.500 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 36.110 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.060 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:1.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 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 0.076 30339 Z= 0.190 Angle : 0.534 9.305 41238 Z= 0.330 Chirality : 0.042 0.172 4623 Planarity : 0.003 0.046 5103 Dihedral : 13.599 154.503 11690 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.68 % Favored : 96.20 % Rotamer: Outliers : 0.00 % Allowed : 0.03 % Favored : 99.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: 0.43 (0.15), residues: 3502 helix: 1.48 (0.16), residues: 1201 sheet: 0.04 (0.24), residues: 523 loop : -0.43 (0.15), residues: 1778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1366 TYR 0.024 0.001 TYR B 797 PHE 0.017 0.001 PHE B 37 TRP 0.016 0.001 TRP A 552 HIS 0.010 0.001 HIS A1173 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.19 (30307) covalent geometry : angle 0.52653 / 0.33 (41193) hydrogen bonds : bond 0.18831 / 12.57 ( 1243) hydrogen bonds : angle 6.94781 / 5.01 ( 3425) metal coordination : bond 0.00366 / 0.25 ( 32) metal coordination : angle 2.75210 / 1.83 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 755 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 755 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.7679 (ptt90) cc_final: 0.7250 (mtp180) REVERT: A 72 GLU cc_start: 0.8070 (mm-30) cc_final: 0.7782 (mm-30) REVERT: A 100 LYS cc_start: 0.6995 (tttm) cc_final: 0.6774 (ttpp) REVERT: A 182 VAL cc_start: 0.8148 (t) cc_final: 0.7865 (m) REVERT: A 341 MET cc_start: 0.9446 (mmm) cc_final: 0.9228 (mmt) REVERT: A 383 TYR cc_start: 0.8051 (m-80) cc_final: 0.7768 (m-80) REVERT: A 386 ASP cc_start: 0.8406 (p0) cc_final: 0.8040 (t0) REVERT: A 542 GLU cc_start: 0.7858 (mt-10) cc_final: 0.7504 (pt0) REVERT: A 559 VAL cc_start: 0.9187 (t) cc_final: 0.8964 (p) REVERT: A 584 ASN cc_start: 0.7407 (m-40) cc_final: 0.7161 (p0) REVERT: A 605 MET cc_start: 0.8896 (tpp) cc_final: 0.8679 (tpt) REVERT: A 897 TYR cc_start: 0.8273 (m-80) cc_final: 0.7491 (m-80) REVERT: A 931 GLU cc_start: 0.8541 (tt0) cc_final: 0.8318 (tp30) REVERT: A 977 LYS cc_start: 0.9104 (tttp) cc_final: 0.8557 (ttpt) REVERT: A 1005 GLU cc_start: 0.8698 (mm-30) cc_final: 0.8220 (mp0) REVERT: A 1151 GLU cc_start: 0.8360 (pm20) cc_final: 0.7949 (pm20) REVERT: A 1173 HIS cc_start: 0.5698 (p90) cc_final: 0.5353 (t-90) REVERT: A 1225 PHE cc_start: 0.7181 (t80) cc_final: 0.6451 (t80) REVERT: A 1234 GLU cc_start: 0.8419 (tm-30) cc_final: 0.8056 (mp0) REVERT: A 1285 MET cc_start: 0.8330 (mmt) cc_final: 0.8039 (mmm) REVERT: A 1299 VAL cc_start: 0.9024 (t) cc_final: 0.8773 (m) REVERT: A 1442 ASP cc_start: 0.8760 (m-30) cc_final: 0.8537 (m-30) REVERT: B 101 MET cc_start: 0.8979 (mtt) cc_final: 0.8686 (mpp) REVERT: B 194 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7426 (mm-30) REVERT: B 213 ILE cc_start: 0.8912 (mm) cc_final: 0.8684 (mm) REVERT: B 215 GLN cc_start: 0.8424 (mm110) cc_final: 0.8219 (mm-40) REVERT: B 241 ARG cc_start: 0.7781 (ttm-80) cc_final: 0.6478 (ttp-170) REVERT: B 302 CYS cc_start: 0.8550 (t) cc_final: 0.8294 (p) REVERT: B 303 TYR cc_start: 0.8251 (m-10) cc_final: 0.7998 (m-10) REVERT: B 358 LYS cc_start: 0.7322 (mmtm) cc_final: 0.6924 (mtpp) REVERT: B 393 LYS cc_start: 0.8096 (ttpt) cc_final: 0.7630 (mmtt) REVERT: B 396 ASP cc_start: 0.7815 (m-30) cc_final: 0.7425 (m-30) REVERT: B 397 ASP cc_start: 0.9001 (p0) cc_final: 0.8761 (p0) REVERT: B 498 THR cc_start: 0.8221 (m) cc_final: 0.7604 (p) REVERT: B 542 MET cc_start: 0.8405 (mtm) cc_final: 0.8011 (mtp) REVERT: B 561 TRP cc_start: 0.6930 (m-90) cc_final: 0.6720 (m-90) REVERT: B 573 GLN cc_start: 0.8812 (tt0) cc_final: 0.8225 (mm-40) REVERT: B 595 ARG cc_start: 0.8082 (ttt180) cc_final: 0.7878 (tmt170) REVERT: B 775 LYS cc_start: 0.8849 (mtmt) cc_final: 0.8394 (mttm) REVERT: B 841 MET cc_start: 0.9210 (ttm) cc_final: 0.8892 (mtp) REVERT: B 864 LYS cc_start: 0.7258 (mtmt) cc_final: 0.6414 (pttp) REVERT: B 955 THR cc_start: 0.8425 (m) cc_final: 0.8096 (m) REVERT: B 1124 ARG cc_start: 0.7987 (mtm-85) cc_final: 0.7702 (mtt180) REVERT: B 1152 MET cc_start: 0.8068 (mmm) cc_final: 0.7266 (mmm) REVERT: B 1174 LYS cc_start: 0.7891 (mtmt) cc_final: 0.7646 (mttt) REVERT: C 29 MET cc_start: 0.8131 (ttm) cc_final: 0.7918 (ttp) REVERT: C 137 LYS cc_start: 0.8587 (tttm) cc_final: 0.8308 (mmtm) REVERT: C 195 GLN cc_start: 0.8331 (mp-120) cc_final: 0.7981 (mp10) REVERT: C 199 LYS cc_start: 0.8780 (ttmt) cc_final: 0.8370 (tptt) REVERT: C 211 ASP cc_start: 0.8454 (m-30) cc_final: 0.8237 (p0) REVERT: C 220 ASP cc_start: 0.8170 (t0) cc_final: 0.7732 (p0) REVERT: C 253 LYS cc_start: 0.8011 (mmtt) cc_final: 0.7707 (mtpt) REVERT: C 262 LEU cc_start: 0.7926 (tp) cc_final: 0.7705 (tt) REVERT: E 3 GLN cc_start: 0.8600 (mt0) cc_final: 0.7941 (tt0) REVERT: E 48 ASP cc_start: 0.7955 (t0) cc_final: 0.7651 (t0) REVERT: E 112 TYR cc_start: 0.7731 (p90) cc_final: 0.7358 (p90) REVERT: E 114 ASN cc_start: 0.9118 (m110) cc_final: 0.8911 (m-40) REVERT: E 124 VAL cc_start: 0.8628 (t) cc_final: 0.8248 (t) REVERT: E 215 MET cc_start: 0.7646 (ptt) cc_final: 0.7263 (ptt) REVERT: F 119 ARG cc_start: 0.7753 (tpp80) cc_final: 0.7550 (mtp85) REVERT: F 123 LYS cc_start: 0.8924 (tttm) cc_final: 0.8658 (tttm) REVERT: F 127 GLU cc_start: 0.8550 (mt-10) cc_final: 0.8343 (mt-10) REVERT: F 129 LYS cc_start: 0.8190 (mmtm) cc_final: 0.7921 (mmmm) REVERT: F 135 ARG cc_start: 0.8363 (ttm170) cc_final: 0.8146 (ttm110) REVERT: H 19 ARG cc_start: 0.7631 (mmt180) cc_final: 0.7324 (mtp85) REVERT: H 94 ASP cc_start: 0.8237 (m-30) cc_final: 0.8036 (m-30) REVERT: H 105 GLU cc_start: 0.8211 (tt0) cc_final: 0.7852 (mt-10) REVERT: H 134 ASN cc_start: 0.8407 (m-40) cc_final: 0.8204 (m-40) REVERT: I 34 TYR cc_start: 0.8110 (t80) cc_final: 0.7477 (t80) REVERT: I 83 ASN cc_start: 0.8665 (p0) cc_final: 0.8378 (p0) REVERT: I 109 ILE cc_start: 0.8572 (mt) cc_final: 0.8091 (mt) REVERT: K 12 LEU cc_start: 0.8473 (mt) cc_final: 0.8180 (mm) REVERT: K 22 ASP cc_start: 0.8205 (m-30) cc_final: 0.7967 (m-30) outliers start: 0 outliers final: 0 residues processed: 755 average time/residue: 0.2122 time to fit residues: 245.1073 Evaluate side-chains 430 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 430 time to evaluate : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 0.0170 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 7.9990 overall best weight: 2.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 358 ASN A 445 ASN ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 698 GLN A 996 ASN ** A1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 433 GLN ** B 740 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 770 GLN B1104 HIS E 99 HIS E 101 GLN E 146 HIS H 33 GLN H 131 ASN K 44 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.124662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.092326 restraints weight = 42725.875| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 2.16 r_work: 0.2973 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 30339 Z= 0.243 Angle : 0.637 10.199 41238 Z= 0.331 Chirality : 0.046 0.208 4623 Planarity : 0.005 0.049 5103 Dihedral : 14.227 148.814 4592 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.48 % Favored : 95.43 % Rotamer: Outliers : 1.63 % Allowed : 8.16 % Favored : 90.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: 0.06 (0.14), residues: 3502 helix: 1.16 (0.15), residues: 1231 sheet: -0.34 (0.23), residues: 525 loop : -0.60 (0.15), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 591 TYR 0.029 0.002 TYR E 46 PHE 0.023 0.002 PHE A 219 TRP 0.018 0.001 TRP B 561 HIS 0.013 0.001 HIS A1173 Details of bonding type rmsd/Z covalent geometry : bond 0.00576 / 0.24 (30307) covalent geometry : angle 0.62325 / 0.33 (41193) hydrogen bonds : bond 0.05082 / 3.42 ( 1243) hydrogen bonds : angle 5.39415 / 3.85 ( 3425) metal coordination : bond 0.00807 / 0.53 ( 32) metal coordination : angle 3.96980 / 2.61 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 453 time to evaluate : 1.114 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.7498 (ptt90) cc_final: 0.7251 (mtp180) REVERT: A 72 GLU cc_start: 0.8244 (mm-30) cc_final: 0.7991 (mm-30) REVERT: A 74 MET cc_start: 0.6863 (tpp) cc_final: 0.6644 (tpp) REVERT: A 100 LYS cc_start: 0.7297 (tttm) cc_final: 0.7090 (ttpp) REVERT: A 122 MET cc_start: 0.8690 (mmm) cc_final: 0.8297 (tpt) REVERT: A 175 ARG cc_start: 0.8076 (tmm160) cc_final: 0.7557 (tmm-80) REVERT: A 182 VAL cc_start: 0.8201 (t) cc_final: 0.7939 (m) REVERT: A 383 TYR cc_start: 0.8162 (m-80) cc_final: 0.7915 (m-80) REVERT: A 386 ASP cc_start: 0.8618 (p0) cc_final: 0.8226 (t0) REVERT: A 542 GLU cc_start: 0.8043 (mt-10) cc_final: 0.7790 (pt0) REVERT: A 897 TYR cc_start: 0.8433 (m-80) cc_final: 0.7742 (m-80) REVERT: A 931 GLU cc_start: 0.8632 (tt0) cc_final: 0.8373 (tp30) REVERT: A 977 LYS cc_start: 0.9123 (tttp) cc_final: 0.8616 (ttpt) REVERT: A 1005 GLU cc_start: 0.8625 (mm-30) cc_final: 0.8089 (mt-10) REVERT: A 1151 GLU cc_start: 0.8447 (pm20) cc_final: 0.8230 (pm20) REVERT: A 1171 GLN cc_start: 0.8682 (pp30) cc_final: 0.8442 (pp30) REVERT: A 1173 HIS cc_start: 0.5864 (p90) cc_final: 0.5416 (t-90) REVERT: A 1225 PHE cc_start: 0.7566 (t80) cc_final: 0.7290 (t80) REVERT: A 1234 GLU cc_start: 0.8303 (tm-30) cc_final: 0.7967 (mp0) REVERT: A 1285 MET cc_start: 0.8144 (mmt) cc_final: 0.7730 (mmm) REVERT: A 1299 VAL cc_start: 0.8881 (t) cc_final: 0.8561 (m) REVERT: A 1307 GLU cc_start: 0.8842 (mm-30) cc_final: 0.8396 (mp0) REVERT: A 1442 ASP cc_start: 0.8785 (m-30) cc_final: 0.8466 (m-30) REVERT: A 1444 MET cc_start: 0.8141 (mmt) cc_final: 0.7719 (mmm) REVERT: B 87 LYS cc_start: 0.7438 (ttpt) cc_final: 0.7175 (mtpt) REVERT: B 101 MET cc_start: 0.9104 (mtt) cc_final: 0.8855 (mpp) REVERT: B 169 ARG cc_start: 0.8696 (mtp85) cc_final: 0.8344 (mtt90) REVERT: B 241 ARG cc_start: 0.7871 (ttm-80) cc_final: 0.6610 (ttp-170) REVERT: B 272 THR cc_start: 0.8921 (m) cc_final: 0.8371 (p) REVERT: B 397 ASP cc_start: 0.9093 (p0) cc_final: 0.8828 (p0) REVERT: B 434 ARG cc_start: 0.7861 (OUTLIER) cc_final: 0.6819 (mtm-85) REVERT: B 471 LYS cc_start: 0.7306 (mptt) cc_final: 0.6936 (ttpt) REVERT: B 476 ARG cc_start: 0.6913 (ptp-170) cc_final: 0.6561 (ptt180) REVERT: B 573 GLN cc_start: 0.8871 (tt0) cc_final: 0.8203 (mm-40) REVERT: B 595 ARG cc_start: 0.8313 (ttt180) cc_final: 0.8037 (tmt170) REVERT: B 597 MET cc_start: 0.8432 (OUTLIER) cc_final: 0.7910 (tpt) REVERT: B 621 GLU cc_start: 0.8350 (tp30) cc_final: 0.7658 (tp30) REVERT: B 775 LYS cc_start: 0.8923 (mtmt) cc_final: 0.8538 (mttm) REVERT: B 809 MET cc_start: 0.8887 (mtt) cc_final: 0.8623 (mtt) REVERT: B 864 LYS cc_start: 0.7528 (mtmt) cc_final: 0.6626 (pttp) REVERT: B 885 MET cc_start: 0.4266 (mmt) cc_final: 0.4055 (mmt) REVERT: B 1152 MET cc_start: 0.8131 (mmm) cc_final: 0.7553 (mmm) REVERT: C 47 ASP cc_start: 0.8627 (t70) cc_final: 0.8360 (t70) REVERT: C 113 VAL cc_start: 0.8868 (t) cc_final: 0.8381 (p) REVERT: C 199 LYS cc_start: 0.8831 (ttmt) cc_final: 0.8481 (tptt) REVERT: C 209 TYR cc_start: 0.8847 (m-80) cc_final: 0.8348 (m-80) REVERT: C 220 ASP cc_start: 0.8429 (t0) cc_final: 0.7935 (p0) REVERT: C 253 LYS cc_start: 0.8001 (mmtt) cc_final: 0.7756 (mtpt) REVERT: C 265 MET cc_start: 0.7813 (tpt) cc_final: 0.7599 (tpt) REVERT: E 54 GLN cc_start: 0.8658 (mt0) cc_final: 0.8391 (mt0) REVERT: E 112 TYR cc_start: 0.7872 (p90) cc_final: 0.7543 (p90) REVERT: F 76 LYS cc_start: 0.8894 (tppt) cc_final: 0.8665 (tppt) REVERT: F 81 THR cc_start: 0.8904 (m) cc_final: 0.8599 (p) REVERT: F 111 LEU cc_start: 0.8968 (mm) cc_final: 0.8710 (mt) REVERT: F 119 ARG cc_start: 0.7938 (tpp80) cc_final: 0.7736 (mtp85) REVERT: F 127 GLU cc_start: 0.8480 (mt-10) cc_final: 0.8265 (mt-10) REVERT: F 129 LYS cc_start: 0.8298 (mmtm) cc_final: 0.8003 (mmmm) REVERT: F 135 ARG cc_start: 0.8427 (ttm170) cc_final: 0.8151 (ttm110) REVERT: H 19 ARG cc_start: 0.7672 (mmt180) cc_final: 0.7412 (mtp85) REVERT: H 129 TYR cc_start: 0.6887 (p90) cc_final: 0.6203 (p90) REVERT: H 131 ASN cc_start: 0.8344 (m110) cc_final: 0.7906 (m-40) REVERT: I 1 MET cc_start: 0.7227 (ppp) cc_final: 0.6532 (pmm) REVERT: I 34 TYR cc_start: 0.8060 (t80) cc_final: 0.7268 (t80) REVERT: I 109 ILE cc_start: 0.8734 (mt) cc_final: 0.8511 (mt) REVERT: K 12 LEU cc_start: 0.8560 (mt) cc_final: 0.8301 (mm) REVERT: K 38 GLU cc_start: 0.8529 (mm-30) cc_final: 0.8044 (mm-30) REVERT: L 62 LYS cc_start: 0.7983 (mmmt) cc_final: 0.7780 (mptt) outliers start: 51 outliers final: 36 residues processed: 487 average time/residue: 0.2018 time to fit residues: 154.5897 Evaluate side-chains 424 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 386 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 579 SER Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 708 MET Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1101 LEU Chi-restraints excluded: chain A residue 1238 ILE Chi-restraints excluded: chain A residue 1358 SER Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 398 ARG Chi-restraints excluded: chain B residue 434 ARG Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 529 GLU Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 550 ASP Chi-restraints excluded: chain B residue 597 MET Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 771 SER Chi-restraints excluded: chain B residue 805 THR Chi-restraints excluded: chain B residue 943 SER Chi-restraints excluded: chain B residue 1104 HIS Chi-restraints excluded: chain B residue 1169 MET Chi-restraints excluded: chain B residue 1210 MET Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 133 ILE Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain E residue 4 GLU Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 128 ASN Chi-restraints excluded: chain I residue 59 VAL Chi-restraints excluded: chain K residue 11 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 74 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 chunk 318 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 6 optimal weight: 0.0870 chunk 49 optimal weight: 2.9990 chunk 283 optimal weight: 2.9990 chunk 189 optimal weight: 0.9980 chunk 136 optimal weight: 0.8980 chunk 158 optimal weight: 0.0000 chunk 5 optimal weight: 4.9990 overall best weight: 0.7964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 659 HIS ** A1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 278 GLN ** B 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1117 GLN E 63 ASN ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 2 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.126991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.094573 restraints weight = 42355.618| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 2.17 r_work: 0.3001 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 30339 Z= 0.124 Angle : 0.537 8.666 41238 Z= 0.282 Chirality : 0.043 0.196 4623 Planarity : 0.004 0.048 5103 Dihedral : 14.180 150.630 4592 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.54 % Favored : 96.37 % Rotamer: Outliers : 1.57 % Allowed : 9.83 % Favored : 88.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: 0.20 (0.14), residues: 3502 helix: 1.31 (0.15), residues: 1234 sheet: -0.32 (0.22), residues: 527 loop : -0.53 (0.15), residues: 1741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG H 130 TYR 0.020 0.001 TYR H 129 PHE 0.023 0.001 PHE B 166 TRP 0.007 0.001 TRP C 201 HIS 0.012 0.001 HIS B1104 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (30307) covalent geometry : angle 0.52663 / 0.28 (41193) hydrogen bonds : bond 0.04090 / 2.74 ( 1243) hydrogen bonds : angle 4.93486 / 3.53 ( 3425) metal coordination : bond 0.00453 / 0.29 ( 32) metal coordination : angle 3.17585 / 1.98 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 428 time to evaluate : 1.171 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.5297 (mmm) cc_final: 0.4593 (ttt) REVERT: A 63 ARG cc_start: 0.7575 (ptt90) cc_final: 0.7253 (mtp180) REVERT: A 72 GLU cc_start: 0.8150 (mm-30) cc_final: 0.7945 (mm-30) REVERT: A 122 MET cc_start: 0.8655 (mmm) cc_final: 0.8224 (tpt) REVERT: A 175 ARG cc_start: 0.8144 (tmm160) cc_final: 0.7618 (tmm-80) REVERT: A 307 ASP cc_start: 0.8580 (t0) cc_final: 0.8285 (t70) REVERT: A 386 ASP cc_start: 0.8572 (p0) cc_final: 0.8172 (t0) REVERT: A 542 GLU cc_start: 0.7965 (mt-10) cc_final: 0.7655 (pt0) REVERT: A 897 TYR cc_start: 0.8383 (m-80) cc_final: 0.7750 (m-80) REVERT: A 931 GLU cc_start: 0.8581 (tt0) cc_final: 0.8154 (tp30) REVERT: A 977 LYS cc_start: 0.9094 (tttp) cc_final: 0.8703 (ttpt) REVERT: A 1005 GLU cc_start: 0.8642 (mm-30) cc_final: 0.8191 (mt-10) REVERT: A 1012 ARG cc_start: 0.8387 (ttm110) cc_final: 0.7795 (mtt90) REVERT: A 1171 GLN cc_start: 0.8686 (pp30) cc_final: 0.8449 (pp30) REVERT: A 1173 HIS cc_start: 0.5742 (p90) cc_final: 0.5434 (t-90) REVERT: A 1225 PHE cc_start: 0.7571 (t80) cc_final: 0.7278 (t80) REVERT: A 1264 GLU cc_start: 0.8876 (tp30) cc_final: 0.8449 (tm-30) REVERT: A 1285 MET cc_start: 0.8075 (mmt) cc_final: 0.7540 (mmt) REVERT: A 1307 GLU cc_start: 0.8804 (mm-30) cc_final: 0.8549 (mp0) REVERT: A 1442 ASP cc_start: 0.8737 (m-30) cc_final: 0.8308 (m-30) REVERT: B 101 MET cc_start: 0.9052 (mtt) cc_final: 0.8759 (mpp) REVERT: B 241 ARG cc_start: 0.7671 (ttm-80) cc_final: 0.6422 (ttp-170) REVERT: B 272 THR cc_start: 0.8915 (m) cc_final: 0.8439 (p) REVERT: B 397 ASP cc_start: 0.9058 (p0) cc_final: 0.8830 (p0) REVERT: B 471 LYS cc_start: 0.7348 (mptt) cc_final: 0.6895 (tttt) REVERT: B 573 GLN cc_start: 0.8860 (tt0) cc_final: 0.8198 (mm-40) REVERT: B 595 ARG cc_start: 0.8304 (ttt180) cc_final: 0.8012 (tmt170) REVERT: B 621 GLU cc_start: 0.8287 (tp30) cc_final: 0.7597 (tp30) REVERT: B 775 LYS cc_start: 0.8809 (mtmt) cc_final: 0.8450 (mttm) REVERT: B 783 THR cc_start: 0.9239 (m) cc_final: 0.8809 (p) REVERT: B 864 LYS cc_start: 0.7490 (mtmt) cc_final: 0.6585 (pttp) REVERT: B 875 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7681 (pp20) REVERT: B 1049 ASP cc_start: 0.8328 (m-30) cc_final: 0.8018 (t0) REVERT: B 1152 MET cc_start: 0.8024 (mmm) cc_final: 0.7535 (mmm) REVERT: C 195 GLN cc_start: 0.8129 (mp10) cc_final: 0.7813 (mp10) REVERT: C 199 LYS cc_start: 0.8814 (ttmt) cc_final: 0.8485 (tptt) REVERT: C 209 TYR cc_start: 0.8820 (m-80) cc_final: 0.8374 (m-80) REVERT: C 220 ASP cc_start: 0.8410 (t0) cc_final: 0.7850 (p0) REVERT: C 253 LYS cc_start: 0.7965 (mmtt) cc_final: 0.7733 (mtpt) REVERT: C 265 MET cc_start: 0.7870 (tpt) cc_final: 0.7666 (ttp) REVERT: E 48 ASP cc_start: 0.6875 (t0) cc_final: 0.6542 (t0) REVERT: F 111 LEU cc_start: 0.8929 (mm) cc_final: 0.8698 (mt) REVERT: F 123 LYS cc_start: 0.8874 (tttm) cc_final: 0.8496 (tttp) REVERT: F 127 GLU cc_start: 0.8466 (mt-10) cc_final: 0.8153 (mt-10) REVERT: F 129 LYS cc_start: 0.8238 (mmtm) cc_final: 0.7966 (mmmm) REVERT: H 19 ARG cc_start: 0.7642 (mmt180) cc_final: 0.7381 (mtp85) REVERT: H 78 SER cc_start: 0.9100 (OUTLIER) cc_final: 0.8891 (m) REVERT: H 92 ASP cc_start: 0.8202 (m-30) cc_final: 0.7870 (t0) REVERT: H 129 TYR cc_start: 0.7185 (p90) cc_final: 0.6272 (p90) REVERT: H 131 ASN cc_start: 0.8326 (m110) cc_final: 0.7936 (m-40) REVERT: I 1 MET cc_start: 0.7056 (ppp) cc_final: 0.6376 (pmm) REVERT: I 13 MET cc_start: 0.7963 (ptt) cc_final: 0.7544 (ppp) REVERT: I 34 TYR cc_start: 0.7864 (t80) cc_final: 0.7222 (t80) REVERT: K 12 LEU cc_start: 0.8464 (mt) cc_final: 0.8180 (mm) REVERT: K 38 GLU cc_start: 0.8563 (mm-30) cc_final: 0.8094 (mm-30) REVERT: K 70 ARG cc_start: 0.8500 (mtm110) cc_final: 0.8162 (mtm110) REVERT: L 62 LYS cc_start: 0.8015 (mmmt) cc_final: 0.7808 (mptt) outliers start: 49 outliers final: 32 residues processed: 454 average time/residue: 0.2079 time to fit residues: 147.9500 Evaluate side-chains 420 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 386 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 286 HIS Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 708 MET Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 1238 ILE Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1424 VAL Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 398 ARG Chi-restraints excluded: chain B residue 529 GLU Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 550 ASP Chi-restraints excluded: chain B residue 597 MET Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 771 SER Chi-restraints excluded: chain B residue 805 THR Chi-restraints excluded: chain B residue 875 GLU Chi-restraints excluded: chain B residue 894 ASP Chi-restraints excluded: chain B residue 1104 HIS Chi-restraints excluded: chain B residue 1210 MET Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 133 ILE Chi-restraints excluded: chain E residue 4 GLU Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain I residue 59 VAL Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain K residue 11 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 286 optimal weight: 8.9990 chunk 81 optimal weight: 5.9990 chunk 141 optimal weight: 6.9990 chunk 293 optimal weight: 2.9990 chunk 343 optimal weight: 3.9990 chunk 298 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 285 optimal weight: 0.0770 chunk 265 optimal weight: 0.2980 chunk 213 optimal weight: 3.9990 chunk 17 optimal weight: 8.9990 overall best weight: 2.0744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 659 HIS ** A1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 224 GLN B 415 GLN B1074 ASN B1104 HIS ** B1187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 23 ASN K 2 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.124363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.091913 restraints weight = 42350.623| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 2.15 r_work: 0.2968 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 30339 Z= 0.201 Angle : 0.575 8.894 41238 Z= 0.299 Chirality : 0.044 0.174 4623 Planarity : 0.004 0.048 5103 Dihedral : 14.230 148.107 4592 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.54 % Favored : 95.40 % Rotamer: Outliers : 2.37 % Allowed : 10.63 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: 0.10 (0.14), residues: 3502 helix: 1.24 (0.15), residues: 1233 sheet: -0.37 (0.22), residues: 528 loop : -0.60 (0.15), residues: 1741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 135 TYR 0.024 0.002 TYR E 112 PHE 0.023 0.002 PHE A 219 TRP 0.010 0.001 TRP A1228 HIS 0.015 0.001 HIS A 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00480 / 0.20 (30307) covalent geometry : angle 0.56424 / 0.30 (41193) hydrogen bonds : bond 0.04088 / 2.75 ( 1243) hydrogen bonds : angle 4.85042 / 3.47 ( 3425) metal coordination : bond 0.00604 / 0.40 ( 32) metal coordination : angle 3.40635 / 2.22 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 387 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.7565 (ptt90) cc_final: 0.7111 (mtp180) REVERT: A 72 GLU cc_start: 0.8229 (mm-30) cc_final: 0.7999 (mm-30) REVERT: A 122 MET cc_start: 0.8579 (mmm) cc_final: 0.7957 (tpp) REVERT: A 175 ARG cc_start: 0.7953 (tmm160) cc_final: 0.7599 (tmm-80) REVERT: A 307 ASP cc_start: 0.8694 (t0) cc_final: 0.8248 (t0) REVERT: A 386 ASP cc_start: 0.8536 (p0) cc_final: 0.8177 (t0) REVERT: A 542 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7648 (pt0) REVERT: A 931 GLU cc_start: 0.8612 (tt0) cc_final: 0.8185 (tp30) REVERT: A 977 LYS cc_start: 0.9110 (tttp) cc_final: 0.8668 (ttpt) REVERT: A 1005 GLU cc_start: 0.8755 (mm-30) cc_final: 0.8284 (mt-10) REVERT: A 1171 GLN cc_start: 0.8744 (pp30) cc_final: 0.8518 (pp30) REVERT: A 1173 HIS cc_start: 0.5787 (p90) cc_final: 0.5469 (t-90) REVERT: A 1225 PHE cc_start: 0.7660 (t80) cc_final: 0.7363 (t80) REVERT: A 1234 GLU cc_start: 0.8309 (tm-30) cc_final: 0.7925 (mp0) REVERT: A 1259 MET cc_start: 0.8519 (mtp) cc_final: 0.8153 (mpp) REVERT: A 1264 GLU cc_start: 0.9070 (tp30) cc_final: 0.8812 (tp30) REVERT: A 1285 MET cc_start: 0.8052 (mmt) cc_final: 0.7545 (mmt) REVERT: A 1307 GLU cc_start: 0.8807 (mm-30) cc_final: 0.8512 (mp0) REVERT: A 1366 ARG cc_start: 0.8393 (OUTLIER) cc_final: 0.7077 (mtt-85) REVERT: A 1442 ASP cc_start: 0.8757 (m-30) cc_final: 0.8316 (m-30) REVERT: B 101 MET cc_start: 0.9059 (mtt) cc_final: 0.8737 (mpp) REVERT: B 241 ARG cc_start: 0.7824 (ttm-80) cc_final: 0.6580 (ttp-170) REVERT: B 272 THR cc_start: 0.8958 (m) cc_final: 0.8524 (p) REVERT: B 397 ASP cc_start: 0.9154 (p0) cc_final: 0.8937 (p0) REVERT: B 434 ARG cc_start: 0.7899 (mtm-85) cc_final: 0.6928 (mtm-85) REVERT: B 471 LYS cc_start: 0.7364 (mptt) cc_final: 0.6820 (tttt) REVERT: B 573 GLN cc_start: 0.8883 (tt0) cc_final: 0.8124 (mm-40) REVERT: B 595 ARG cc_start: 0.8334 (ttt180) cc_final: 0.8026 (tmt170) REVERT: B 621 GLU cc_start: 0.8368 (tp30) cc_final: 0.7619 (tp30) REVERT: B 775 LYS cc_start: 0.8902 (mtmt) cc_final: 0.8486 (mttm) REVERT: B 864 LYS cc_start: 0.7524 (mtmt) cc_final: 0.6553 (pttp) REVERT: B 945 GLU cc_start: 0.7790 (mm-30) cc_final: 0.7445 (mm-30) REVERT: B 1049 ASP cc_start: 0.8344 (m-30) cc_final: 0.8102 (t0) REVERT: B 1072 MET cc_start: 0.9235 (mtp) cc_final: 0.9025 (mtp) REVERT: B 1152 MET cc_start: 0.8051 (mmm) cc_final: 0.7610 (mmm) REVERT: C 199 LYS cc_start: 0.8817 (ttmt) cc_final: 0.8438 (tptt) REVERT: C 209 TYR cc_start: 0.8821 (m-80) cc_final: 0.8398 (m-80) REVERT: C 220 ASP cc_start: 0.8402 (t0) cc_final: 0.7917 (p0) REVERT: C 253 LYS cc_start: 0.7997 (mmtt) cc_final: 0.7741 (mtpt) REVERT: C 265 MET cc_start: 0.7958 (tpt) cc_final: 0.7729 (tpt) REVERT: E 50 MET cc_start: 0.8285 (ppp) cc_final: 0.8049 (ppp) REVERT: E 54 GLN cc_start: 0.8825 (mt0) cc_final: 0.8464 (mt0) REVERT: E 112 TYR cc_start: 0.7801 (p90) cc_final: 0.7594 (p90) REVERT: F 81 THR cc_start: 0.8815 (m) cc_final: 0.8534 (p) REVERT: F 89 GLU cc_start: 0.8604 (mt-10) cc_final: 0.8397 (mt-10) REVERT: F 110 ASP cc_start: 0.8240 (t0) cc_final: 0.8007 (t0) REVERT: F 129 LYS cc_start: 0.8253 (mmtm) cc_final: 0.8028 (mmmm) REVERT: H 19 ARG cc_start: 0.7705 (mmt180) cc_final: 0.7461 (mtp85) REVERT: H 92 ASP cc_start: 0.8254 (m-30) cc_final: 0.7940 (t0) REVERT: H 129 TYR cc_start: 0.7493 (p90) cc_final: 0.7128 (p90) REVERT: H 130 ARG cc_start: 0.8571 (mtt90) cc_final: 0.8314 (mtt90) REVERT: H 131 ASN cc_start: 0.8374 (m110) cc_final: 0.7939 (m-40) REVERT: I 1 MET cc_start: 0.7064 (ppp) cc_final: 0.6396 (pmm) REVERT: K 12 LEU cc_start: 0.8515 (mt) cc_final: 0.8210 (mm) REVERT: K 38 GLU cc_start: 0.8571 (mm-30) cc_final: 0.8055 (mm-30) REVERT: K 49 GLU cc_start: 0.8291 (mm-30) cc_final: 0.8025 (mm-30) REVERT: K 70 ARG cc_start: 0.8574 (mtm110) cc_final: 0.8217 (mtm110) outliers start: 74 outliers final: 46 residues processed: 436 average time/residue: 0.1992 time to fit residues: 136.9729 Evaluate side-chains 417 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 370 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 708 MET Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1101 LEU Chi-restraints excluded: chain A residue 1237 ILE Chi-restraints excluded: chain A residue 1238 ILE Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1299 VAL Chi-restraints excluded: chain A residue 1366 ARG Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 371 GLU Chi-restraints excluded: chain B residue 398 ARG Chi-restraints excluded: chain B residue 415 GLN Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 771 SER Chi-restraints excluded: chain B residue 805 THR Chi-restraints excluded: chain B residue 894 ASP Chi-restraints excluded: chain B residue 1104 HIS Chi-restraints excluded: chain B residue 1210 MET Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 133 ILE Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain E residue 4 GLU Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 128 ASN Chi-restraints excluded: chain I residue 59 VAL Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain K residue 11 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 209 optimal weight: 6.9990 chunk 7 optimal weight: 0.0670 chunk 335 optimal weight: 0.3980 chunk 327 optimal weight: 3.9990 chunk 272 optimal weight: 0.8980 chunk 158 optimal weight: 7.9990 chunk 124 optimal weight: 2.9990 chunk 334 optimal weight: 0.5980 chunk 257 optimal weight: 0.8980 chunk 164 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 659 HIS A1124 HIS B 415 GLN B1074 ASN ** B1187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 108 HIS K 2 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.126999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.094048 restraints weight = 42130.759| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 2.29 r_work: 0.2992 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 30339 Z= 0.108 Angle : 0.514 10.225 41238 Z= 0.269 Chirality : 0.042 0.179 4623 Planarity : 0.004 0.045 5103 Dihedral : 14.151 148.014 4592 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.40 % Favored : 96.54 % Rotamer: Outliers : 1.82 % Allowed : 11.43 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: 0.25 (0.14), residues: 3502 helix: 1.36 (0.15), residues: 1241 sheet: -0.28 (0.22), residues: 527 loop : -0.52 (0.15), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 135 TYR 0.015 0.001 TYR A 383 PHE 0.025 0.001 PHE B 166 TRP 0.008 0.001 TRP C 201 HIS 0.009 0.001 HIS A1173 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (30307) covalent geometry : angle 0.50583 / 0.27 (41193) hydrogen bonds : bond 0.03558 / 2.40 ( 1243) hydrogen bonds : angle 4.60942 / 3.30 ( 3425) metal coordination : bond 0.00385 / 0.24 ( 32) metal coordination : angle 2.85859 / 1.76 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 403 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.5170 (mmm) cc_final: 0.4636 (ttt) REVERT: A 63 ARG cc_start: 0.7555 (ptt90) cc_final: 0.7032 (mtp180) REVERT: A 72 GLU cc_start: 0.8196 (mm-30) cc_final: 0.7994 (mm-30) REVERT: A 122 MET cc_start: 0.8548 (mmm) cc_final: 0.7844 (tpt) REVERT: A 175 ARG cc_start: 0.7889 (tmm160) cc_final: 0.7534 (tmm-80) REVERT: A 307 ASP cc_start: 0.8609 (t0) cc_final: 0.8131 (t0) REVERT: A 386 ASP cc_start: 0.8546 (p0) cc_final: 0.8153 (t0) REVERT: A 487 MET cc_start: 0.9448 (mtp) cc_final: 0.9094 (mtp) REVERT: A 542 GLU cc_start: 0.7953 (mt-10) cc_final: 0.7575 (pt0) REVERT: A 931 GLU cc_start: 0.8604 (tt0) cc_final: 0.8156 (tp30) REVERT: A 977 LYS cc_start: 0.9266 (tttp) cc_final: 0.8772 (ttpt) REVERT: A 1005 GLU cc_start: 0.8804 (mm-30) cc_final: 0.8323 (mt-10) REVERT: A 1173 HIS cc_start: 0.6354 (p90) cc_final: 0.5901 (t-90) REVERT: A 1225 PHE cc_start: 0.7566 (t80) cc_final: 0.7227 (t80) REVERT: A 1264 GLU cc_start: 0.8999 (tp30) cc_final: 0.8439 (tp30) REVERT: A 1268 LEU cc_start: 0.8953 (mp) cc_final: 0.8726 (mp) REVERT: A 1285 MET cc_start: 0.7920 (mmt) cc_final: 0.7571 (mmm) REVERT: A 1307 GLU cc_start: 0.8774 (mm-30) cc_final: 0.8485 (mp0) REVERT: A 1442 ASP cc_start: 0.8649 (m-30) cc_final: 0.8181 (m-30) REVERT: B 101 MET cc_start: 0.9047 (mtt) cc_final: 0.8727 (mpp) REVERT: B 241 ARG cc_start: 0.7610 (ttm-80) cc_final: 0.6412 (ttp-170) REVERT: B 272 THR cc_start: 0.8928 (m) cc_final: 0.8489 (p) REVERT: B 434 ARG cc_start: 0.7831 (mtm-85) cc_final: 0.6946 (mtm-85) REVERT: B 471 LYS cc_start: 0.7293 (mptt) cc_final: 0.6818 (tttt) REVERT: B 595 ARG cc_start: 0.8310 (ttt180) cc_final: 0.7989 (tmt170) REVERT: B 621 GLU cc_start: 0.8390 (tp30) cc_final: 0.7628 (tp30) REVERT: B 775 LYS cc_start: 0.8808 (mtmt) cc_final: 0.8410 (mttm) REVERT: B 864 LYS cc_start: 0.7431 (mtmt) cc_final: 0.6475 (pttp) REVERT: B 875 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7758 (pp20) REVERT: B 935 ARG cc_start: 0.4598 (mmp-170) cc_final: 0.4261 (mmp-170) REVERT: B 945 GLU cc_start: 0.7771 (mm-30) cc_final: 0.7530 (mm-30) REVERT: B 1049 ASP cc_start: 0.8359 (m-30) cc_final: 0.8079 (t0) REVERT: B 1072 MET cc_start: 0.9186 (mtp) cc_final: 0.8953 (mtp) REVERT: B 1152 MET cc_start: 0.8007 (mmm) cc_final: 0.7612 (mmm) REVERT: C 199 LYS cc_start: 0.8798 (ttmt) cc_final: 0.8473 (tptt) REVERT: C 209 TYR cc_start: 0.8771 (m-80) cc_final: 0.8263 (m-80) REVERT: C 220 ASP cc_start: 0.8372 (t0) cc_final: 0.7810 (p0) REVERT: C 253 LYS cc_start: 0.8012 (mmtt) cc_final: 0.7672 (mtpt) REVERT: C 265 MET cc_start: 0.7873 (tpt) cc_final: 0.7637 (tpt) REVERT: E 54 GLN cc_start: 0.8812 (mt0) cc_final: 0.8054 (mp10) REVERT: E 186 LEU cc_start: 0.7914 (OUTLIER) cc_final: 0.7707 (mp) REVERT: F 81 THR cc_start: 0.8723 (m) cc_final: 0.8459 (p) REVERT: F 127 GLU cc_start: 0.8484 (mt-10) cc_final: 0.8238 (mt-10) REVERT: F 129 LYS cc_start: 0.8186 (mmtm) cc_final: 0.7958 (mmmm) REVERT: H 19 ARG cc_start: 0.7699 (mmt180) cc_final: 0.7404 (mtp85) REVERT: H 92 ASP cc_start: 0.8255 (m-30) cc_final: 0.7967 (t0) REVERT: H 129 TYR cc_start: 0.7452 (p90) cc_final: 0.7016 (p90) REVERT: H 130 ARG cc_start: 0.8555 (mtt90) cc_final: 0.8213 (mtt90) REVERT: H 131 ASN cc_start: 0.8326 (m110) cc_final: 0.7910 (m-40) REVERT: I 1 MET cc_start: 0.7057 (ppp) cc_final: 0.6335 (pmm) REVERT: I 13 MET cc_start: 0.8088 (ptt) cc_final: 0.7523 (ppp) REVERT: I 34 TYR cc_start: 0.7896 (t80) cc_final: 0.7206 (t80) REVERT: J 29 GLU cc_start: 0.8496 (mt-10) cc_final: 0.8089 (tm-30) REVERT: K 12 LEU cc_start: 0.8427 (mt) cc_final: 0.8226 (mt) REVERT: K 38 GLU cc_start: 0.8527 (mm-30) cc_final: 0.8071 (mm-30) REVERT: K 70 ARG cc_start: 0.8469 (mtm110) cc_final: 0.8105 (mtm110) outliers start: 57 outliers final: 40 residues processed: 433 average time/residue: 0.2046 time to fit residues: 139.6976 Evaluate side-chains 419 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 377 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 286 HIS Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 708 MET Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 1111 MET Chi-restraints excluded: chain A residue 1237 ILE Chi-restraints excluded: chain A residue 1238 ILE Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1366 ARG Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 371 GLU Chi-restraints excluded: chain B residue 398 ARG Chi-restraints excluded: chain B residue 415 GLN Chi-restraints excluded: chain B residue 425 THR Chi-restraints excluded: chain B residue 529 GLU Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 597 MET Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 771 SER Chi-restraints excluded: chain B residue 805 THR Chi-restraints excluded: chain B residue 875 GLU Chi-restraints excluded: chain B residue 894 ASP Chi-restraints excluded: chain B residue 1210 MET Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 133 ILE Chi-restraints excluded: chain E residue 4 GLU Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 128 ASN Chi-restraints excluded: chain I residue 59 VAL Chi-restraints excluded: chain I residue 60 GLN Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain K residue 79 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 291 optimal weight: 3.9990 chunk 292 optimal weight: 4.9990 chunk 351 optimal weight: 30.0000 chunk 119 optimal weight: 7.9990 chunk 183 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 28 optimal weight: 10.0000 chunk 212 optimal weight: 0.8980 chunk 186 optimal weight: 0.9980 chunk 236 optimal weight: 0.7980 chunk 285 optimal weight: 7.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 659 HIS B 415 GLN B1074 ASN ** B1187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 17 ASN ** I 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 108 HIS K 2 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.124920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.091876 restraints weight = 42291.935| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 2.30 r_work: 0.2954 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 30339 Z= 0.174 Angle : 0.542 10.943 41238 Z= 0.282 Chirality : 0.043 0.175 4623 Planarity : 0.004 0.044 5103 Dihedral : 14.162 147.134 4592 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.37 % Favored : 95.57 % Rotamer: Outliers : 2.08 % Allowed : 12.36 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: 0.23 (0.14), residues: 3502 helix: 1.38 (0.15), residues: 1233 sheet: -0.33 (0.22), residues: 530 loop : -0.54 (0.15), residues: 1739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 135 TYR 0.017 0.001 TYR A 383 PHE 0.022 0.001 PHE A 219 TRP 0.008 0.001 TRP C 192 HIS 0.009 0.001 HIS A1173 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.17 (30307) covalent geometry : angle 0.53237 / 0.28 (41193) hydrogen bonds : bond 0.03687 / 2.49 ( 1243) hydrogen bonds : angle 4.62125 / 3.31 ( 3425) metal coordination : bond 0.00534 / 0.35 ( 32) metal coordination : angle 3.10498 / 1.99 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 377 time to evaluate : 1.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.7534 (ptt90) cc_final: 0.7007 (mtp180) REVERT: A 72 GLU cc_start: 0.8194 (mm-30) cc_final: 0.7977 (mm-30) REVERT: A 74 MET cc_start: 0.7079 (tpp) cc_final: 0.6758 (tpp) REVERT: A 122 MET cc_start: 0.8574 (mmm) cc_final: 0.7937 (tpp) REVERT: A 175 ARG cc_start: 0.7887 (tmm160) cc_final: 0.7536 (tmm-80) REVERT: A 307 ASP cc_start: 0.8669 (t0) cc_final: 0.8224 (t0) REVERT: A 386 ASP cc_start: 0.8573 (p0) cc_final: 0.8172 (t0) REVERT: A 417 TYR cc_start: 0.6455 (m-80) cc_final: 0.6167 (m-80) REVERT: A 542 GLU cc_start: 0.8000 (mt-10) cc_final: 0.7610 (pt0) REVERT: A 931 GLU cc_start: 0.8614 (tt0) cc_final: 0.8161 (tp30) REVERT: A 977 LYS cc_start: 0.9212 (tttp) cc_final: 0.8701 (ttpt) REVERT: A 1005 GLU cc_start: 0.8863 (mm-30) cc_final: 0.8370 (mt-10) REVERT: A 1151 GLU cc_start: 0.8077 (pm20) cc_final: 0.7718 (pm20) REVERT: A 1167 GLU cc_start: 0.7978 (tp30) cc_final: 0.7722 (tp30) REVERT: A 1173 HIS cc_start: 0.6240 (p90) cc_final: 0.5893 (t-90) REVERT: A 1225 PHE cc_start: 0.7549 (t80) cc_final: 0.7262 (t80) REVERT: A 1259 MET cc_start: 0.8513 (mtp) cc_final: 0.8127 (mpp) REVERT: A 1285 MET cc_start: 0.7949 (mmt) cc_final: 0.7569 (mmm) REVERT: A 1307 GLU cc_start: 0.8779 (mm-30) cc_final: 0.8431 (mp0) REVERT: A 1442 ASP cc_start: 0.8644 (m-30) cc_final: 0.8158 (m-30) REVERT: B 101 MET cc_start: 0.9070 (mtt) cc_final: 0.8650 (mpp) REVERT: B 241 ARG cc_start: 0.7737 (ttm-80) cc_final: 0.6533 (ttp-170) REVERT: B 272 THR cc_start: 0.8952 (m) cc_final: 0.8534 (p) REVERT: B 310 MET cc_start: 0.7864 (ttm) cc_final: 0.7454 (ttp) REVERT: B 443 ASN cc_start: 0.7846 (t0) cc_final: 0.6998 (p0) REVERT: B 471 LYS cc_start: 0.7297 (mptt) cc_final: 0.6800 (tttt) REVERT: B 595 ARG cc_start: 0.8354 (ttt180) cc_final: 0.8011 (tmt170) REVERT: B 621 GLU cc_start: 0.8430 (tp30) cc_final: 0.7660 (tp30) REVERT: B 775 LYS cc_start: 0.8851 (mtmt) cc_final: 0.8422 (mttm) REVERT: B 864 LYS cc_start: 0.7439 (mtmt) cc_final: 0.6445 (pttp) REVERT: B 875 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7802 (pp20) REVERT: B 935 ARG cc_start: 0.4575 (mmp-170) cc_final: 0.4217 (mmp-170) REVERT: B 1049 ASP cc_start: 0.8362 (m-30) cc_final: 0.8096 (t0) REVERT: B 1152 MET cc_start: 0.8051 (mmm) cc_final: 0.7619 (mmm) REVERT: C 199 LYS cc_start: 0.8811 (ttmt) cc_final: 0.8426 (tptt) REVERT: C 209 TYR cc_start: 0.8785 (m-80) cc_final: 0.8297 (m-80) REVERT: C 220 ASP cc_start: 0.8421 (t0) cc_final: 0.7882 (p0) REVERT: C 253 LYS cc_start: 0.7938 (mmtt) cc_final: 0.7692 (mtpt) REVERT: C 265 MET cc_start: 0.7934 (tpt) cc_final: 0.7680 (tpt) REVERT: E 54 GLN cc_start: 0.8828 (mt0) cc_final: 0.8058 (mp10) REVERT: F 127 GLU cc_start: 0.8500 (mt-10) cc_final: 0.8226 (mt-10) REVERT: F 129 LYS cc_start: 0.8215 (mmtm) cc_final: 0.7980 (mmmm) REVERT: H 19 ARG cc_start: 0.7727 (mmt180) cc_final: 0.7423 (mtp85) REVERT: H 92 ASP cc_start: 0.8302 (m-30) cc_final: 0.8025 (t0) REVERT: H 129 TYR cc_start: 0.7485 (p90) cc_final: 0.7202 (p90) REVERT: H 130 ARG cc_start: 0.8612 (mtt90) cc_final: 0.8394 (mtt90) REVERT: H 131 ASN cc_start: 0.8355 (m110) cc_final: 0.7950 (m-40) REVERT: I 1 MET cc_start: 0.7166 (ppp) cc_final: 0.6426 (pmm) REVERT: J 29 GLU cc_start: 0.8574 (mt-10) cc_final: 0.8161 (tm-30) REVERT: K 12 LEU cc_start: 0.8454 (mt) cc_final: 0.8220 (mt) REVERT: K 38 GLU cc_start: 0.8537 (mm-30) cc_final: 0.8111 (mm-30) REVERT: K 49 GLU cc_start: 0.8218 (mm-30) cc_final: 0.7984 (mm-30) outliers start: 65 outliers final: 55 residues processed: 419 average time/residue: 0.1902 time to fit residues: 126.0486 Evaluate side-chains 424 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 368 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 708 MET Chi-restraints excluded: chain A residue 764 CYS Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1111 MET Chi-restraints excluded: chain A residue 1237 ILE Chi-restraints excluded: chain A residue 1238 ILE Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1299 VAL Chi-restraints excluded: chain A residue 1366 ARG Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1377 THR Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 371 GLU Chi-restraints excluded: chain B residue 398 ARG Chi-restraints excluded: chain B residue 415 GLN Chi-restraints excluded: chain B residue 425 THR Chi-restraints excluded: chain B residue 529 GLU Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 550 ASP Chi-restraints excluded: chain B residue 597 MET Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 771 SER Chi-restraints excluded: chain B residue 805 THR Chi-restraints excluded: chain B residue 875 GLU Chi-restraints excluded: chain B residue 894 ASP Chi-restraints excluded: chain B residue 1103 ILE Chi-restraints excluded: chain B residue 1169 MET Chi-restraints excluded: chain B residue 1210 MET Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 133 ILE Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain E residue 4 GLU Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 128 ASN Chi-restraints excluded: chain I residue 59 VAL Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain K residue 11 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 222 optimal weight: 3.9990 chunk 315 optimal weight: 5.9990 chunk 246 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 317 optimal weight: 2.9990 chunk 306 optimal weight: 5.9990 chunk 49 optimal weight: 0.6980 chunk 163 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 215 optimal weight: 1.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 415 GLN B1104 HIS ** B1187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 2 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.124648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.091381 restraints weight = 42410.182| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 2.32 r_work: 0.2954 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 30339 Z= 0.172 Angle : 0.543 11.473 41238 Z= 0.282 Chirality : 0.043 0.175 4623 Planarity : 0.004 0.044 5103 Dihedral : 14.165 146.929 4592 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.05 % Favored : 95.89 % Rotamer: Outliers : 2.24 % Allowed : 13.00 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: 0.22 (0.14), residues: 3502 helix: 1.38 (0.15), residues: 1234 sheet: -0.32 (0.22), residues: 535 loop : -0.55 (0.15), residues: 1733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 434 TYR 0.019 0.001 TYR A 383 PHE 0.022 0.001 PHE A 219 TRP 0.007 0.001 TRP C 192 HIS 0.009 0.001 HIS A1173 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.17 (30307) covalent geometry : angle 0.53288 / 0.28 (41193) hydrogen bonds : bond 0.03638 / 2.46 ( 1243) hydrogen bonds : angle 4.58278 / 3.28 ( 3425) metal coordination : bond 0.00540 / 0.36 ( 32) metal coordination : angle 3.12614 / 1.98 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 368 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.5192 (mmm) cc_final: 0.4699 (ttt) REVERT: A 63 ARG cc_start: 0.7544 (ptt90) cc_final: 0.6995 (mtp180) REVERT: A 72 GLU cc_start: 0.8218 (mm-30) cc_final: 0.7996 (mm-30) REVERT: A 74 MET cc_start: 0.7268 (tpp) cc_final: 0.6980 (tpp) REVERT: A 122 MET cc_start: 0.8594 (mmm) cc_final: 0.7969 (tpp) REVERT: A 175 ARG cc_start: 0.7903 (tmm160) cc_final: 0.7553 (tmm-80) REVERT: A 307 ASP cc_start: 0.8653 (t0) cc_final: 0.8261 (t0) REVERT: A 386 ASP cc_start: 0.8558 (p0) cc_final: 0.8166 (t0) REVERT: A 417 TYR cc_start: 0.6480 (m-80) cc_final: 0.6199 (m-80) REVERT: A 542 GLU cc_start: 0.8012 (mt-10) cc_final: 0.7600 (pt0) REVERT: A 931 GLU cc_start: 0.8617 (tt0) cc_final: 0.8164 (tp30) REVERT: A 977 LYS cc_start: 0.9253 (tttp) cc_final: 0.8722 (ttpt) REVERT: A 1005 GLU cc_start: 0.8887 (mm-30) cc_final: 0.8388 (mt-10) REVERT: A 1151 GLU cc_start: 0.8008 (pm20) cc_final: 0.7652 (pm20) REVERT: A 1167 GLU cc_start: 0.7923 (tp30) cc_final: 0.7660 (tp30) REVERT: A 1173 HIS cc_start: 0.6213 (p90) cc_final: 0.5906 (t-90) REVERT: A 1225 PHE cc_start: 0.7588 (t80) cc_final: 0.7305 (t80) REVERT: A 1234 GLU cc_start: 0.8464 (tm-30) cc_final: 0.8217 (tm-30) REVERT: A 1285 MET cc_start: 0.7919 (mmt) cc_final: 0.7542 (mmm) REVERT: A 1287 TYR cc_start: 0.8186 (m-10) cc_final: 0.7789 (m-10) REVERT: A 1307 GLU cc_start: 0.8786 (mm-30) cc_final: 0.8319 (mt-10) REVERT: A 1442 ASP cc_start: 0.8646 (m-30) cc_final: 0.8156 (m-30) REVERT: B 101 MET cc_start: 0.9020 (mtt) cc_final: 0.8633 (mpp) REVERT: B 241 ARG cc_start: 0.7763 (ttm-80) cc_final: 0.6570 (ttp-170) REVERT: B 272 THR cc_start: 0.8967 (m) cc_final: 0.8555 (p) REVERT: B 348 ARG cc_start: 0.8066 (mtm110) cc_final: 0.7314 (ptp-170) REVERT: B 443 ASN cc_start: 0.7856 (t0) cc_final: 0.7020 (p0) REVERT: B 471 LYS cc_start: 0.7273 (mptt) cc_final: 0.6761 (tttt) REVERT: B 595 ARG cc_start: 0.8336 (ttt180) cc_final: 0.7998 (tmt170) REVERT: B 621 GLU cc_start: 0.8430 (tp30) cc_final: 0.7659 (tp30) REVERT: B 775 LYS cc_start: 0.8930 (mtmt) cc_final: 0.8475 (mttm) REVERT: B 864 LYS cc_start: 0.7465 (mtmt) cc_final: 0.6464 (pttp) REVERT: B 875 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7802 (pp20) REVERT: B 1152 MET cc_start: 0.7973 (mmm) cc_final: 0.7579 (mmm) REVERT: C 199 LYS cc_start: 0.8824 (ttmt) cc_final: 0.8445 (tptt) REVERT: C 209 TYR cc_start: 0.8772 (m-80) cc_final: 0.8306 (m-80) REVERT: C 220 ASP cc_start: 0.8437 (t0) cc_final: 0.7840 (p0) REVERT: C 253 LYS cc_start: 0.7990 (mmtt) cc_final: 0.7727 (mtpt) REVERT: C 265 MET cc_start: 0.7946 (tpt) cc_final: 0.7693 (tpt) REVERT: E 54 GLN cc_start: 0.8825 (mt0) cc_final: 0.8069 (mp10) REVERT: F 127 GLU cc_start: 0.8548 (mt-10) cc_final: 0.8242 (mt-10) REVERT: F 129 LYS cc_start: 0.8205 (mmtm) cc_final: 0.7965 (mmmm) REVERT: H 19 ARG cc_start: 0.7706 (mmt180) cc_final: 0.7403 (mtp85) REVERT: H 92 ASP cc_start: 0.8304 (m-30) cc_final: 0.8035 (t0) REVERT: H 129 TYR cc_start: 0.7463 (p90) cc_final: 0.7163 (p90) REVERT: H 130 ARG cc_start: 0.8611 (mtt90) cc_final: 0.8365 (mtt90) REVERT: H 131 ASN cc_start: 0.8368 (m110) cc_final: 0.7954 (m-40) REVERT: I 1 MET cc_start: 0.7199 (ppp) cc_final: 0.6460 (pmm) REVERT: J 29 GLU cc_start: 0.8624 (mt-10) cc_final: 0.8236 (tm-30) REVERT: K 12 LEU cc_start: 0.8447 (mt) cc_final: 0.8218 (mt) REVERT: K 38 GLU cc_start: 0.8533 (mm-30) cc_final: 0.8102 (mm-30) REVERT: K 49 GLU cc_start: 0.8237 (mm-30) cc_final: 0.7973 (mm-30) REVERT: K 70 ARG cc_start: 0.8579 (mtm110) cc_final: 0.8311 (mtm110) REVERT: L 65 VAL cc_start: 0.8263 (OUTLIER) cc_final: 0.7944 (p) outliers start: 70 outliers final: 58 residues processed: 412 average time/residue: 0.1997 time to fit residues: 129.5174 Evaluate side-chains 418 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 358 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 708 MET Chi-restraints excluded: chain A residue 764 CYS Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1111 MET Chi-restraints excluded: chain A residue 1237 ILE Chi-restraints excluded: chain A residue 1238 ILE Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1299 VAL Chi-restraints excluded: chain A residue 1358 SER Chi-restraints excluded: chain A residue 1366 ARG Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1377 THR Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 371 GLU Chi-restraints excluded: chain B residue 398 ARG Chi-restraints excluded: chain B residue 415 GLN Chi-restraints excluded: chain B residue 425 THR Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 529 GLU Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 597 MET Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 771 SER Chi-restraints excluded: chain B residue 805 THR Chi-restraints excluded: chain B residue 875 GLU Chi-restraints excluded: chain B residue 894 ASP Chi-restraints excluded: chain B residue 1103 ILE Chi-restraints excluded: chain B residue 1169 MET Chi-restraints excluded: chain B residue 1210 MET Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 133 ILE Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain E residue 4 GLU Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 128 ASN Chi-restraints excluded: chain I residue 59 VAL Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain L residue 65 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 267 optimal weight: 0.9980 chunk 146 optimal weight: 0.9990 chunk 184 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 chunk 306 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 352 optimal weight: 40.0000 chunk 278 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 188 optimal weight: 0.9980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1270 ASN ** B1187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.125794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.092532 restraints weight = 42364.343| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 2.32 r_work: 0.2964 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 30339 Z= 0.126 Angle : 0.518 11.713 41238 Z= 0.270 Chirality : 0.042 0.185 4623 Planarity : 0.004 0.043 5103 Dihedral : 14.135 147.607 4592 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.74 % Favored : 96.20 % Rotamer: Outliers : 2.02 % Allowed : 13.28 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: 0.32 (0.14), residues: 3502 helix: 1.47 (0.15), residues: 1236 sheet: -0.26 (0.22), residues: 522 loop : -0.51 (0.15), residues: 1744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 135 TYR 0.020 0.001 TYR A 383 PHE 0.022 0.001 PHE A 219 TRP 0.007 0.001 TRP C 201 HIS 0.008 0.001 HIS A1173 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (30307) covalent geometry : angle 0.50918 / 0.27 (41193) hydrogen bonds : bond 0.03446 / 2.32 ( 1243) hydrogen bonds : angle 4.47585 / 3.21 ( 3425) metal coordination : bond 0.00397 / 0.26 ( 32) metal coordination : angle 2.94543 / 1.84 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 380 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.5138 (mmm) cc_final: 0.4587 (ttt) REVERT: A 60 SER cc_start: 0.7953 (p) cc_final: 0.7552 (t) REVERT: A 63 ARG cc_start: 0.7522 (ptt90) cc_final: 0.6974 (mtp180) REVERT: A 72 GLU cc_start: 0.8222 (mm-30) cc_final: 0.7977 (mm-30) REVERT: A 74 MET cc_start: 0.7130 (tpp) cc_final: 0.6820 (tpp) REVERT: A 122 MET cc_start: 0.8596 (mmm) cc_final: 0.7889 (tpt) REVERT: A 175 ARG cc_start: 0.7874 (tmm160) cc_final: 0.7522 (tmm-80) REVERT: A 307 ASP cc_start: 0.8710 (t0) cc_final: 0.8257 (t0) REVERT: A 386 ASP cc_start: 0.8568 (p0) cc_final: 0.8144 (t0) REVERT: A 542 GLU cc_start: 0.7994 (mt-10) cc_final: 0.7575 (pt0) REVERT: A 931 GLU cc_start: 0.8616 (tt0) cc_final: 0.8148 (tp30) REVERT: A 977 LYS cc_start: 0.9248 (tttp) cc_final: 0.8709 (ttpt) REVERT: A 1005 GLU cc_start: 0.8900 (mm-30) cc_final: 0.8414 (mt-10) REVERT: A 1151 GLU cc_start: 0.7932 (pm20) cc_final: 0.7568 (pm20) REVERT: A 1167 GLU cc_start: 0.7832 (tp30) cc_final: 0.7556 (tp30) REVERT: A 1173 HIS cc_start: 0.6148 (p90) cc_final: 0.5925 (t-90) REVERT: A 1225 PHE cc_start: 0.7598 (t80) cc_final: 0.7325 (t80) REVERT: A 1259 MET cc_start: 0.8526 (mtp) cc_final: 0.8147 (mpp) REVERT: A 1285 MET cc_start: 0.7772 (mmt) cc_final: 0.7368 (mmm) REVERT: A 1287 TYR cc_start: 0.8221 (m-10) cc_final: 0.7800 (m-10) REVERT: A 1307 GLU cc_start: 0.8764 (mm-30) cc_final: 0.8325 (mt-10) REVERT: A 1442 ASP cc_start: 0.8630 (m-30) cc_final: 0.8135 (m-30) REVERT: B 101 MET cc_start: 0.9007 (mtt) cc_final: 0.8622 (mpp) REVERT: B 241 ARG cc_start: 0.7682 (ttm-80) cc_final: 0.6481 (ttp-170) REVERT: B 272 THR cc_start: 0.8958 (m) cc_final: 0.8587 (p) REVERT: B 348 ARG cc_start: 0.8062 (mtm110) cc_final: 0.7324 (ptp-170) REVERT: B 443 ASN cc_start: 0.7858 (t0) cc_final: 0.7040 (p0) REVERT: B 471 LYS cc_start: 0.7250 (mptt) cc_final: 0.6761 (tttt) REVERT: B 595 ARG cc_start: 0.8379 (ttt180) cc_final: 0.8070 (tmt170) REVERT: B 621 GLU cc_start: 0.8436 (tp30) cc_final: 0.7645 (tp30) REVERT: B 775 LYS cc_start: 0.8872 (mtmt) cc_final: 0.8417 (mttm) REVERT: B 864 LYS cc_start: 0.7444 (mtmt) cc_final: 0.6446 (pttp) REVERT: B 875 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7792 (pp20) REVERT: B 1152 MET cc_start: 0.7968 (mmm) cc_final: 0.7564 (mmm) REVERT: C 199 LYS cc_start: 0.8815 (ttmt) cc_final: 0.8440 (tptt) REVERT: C 209 TYR cc_start: 0.8761 (m-80) cc_final: 0.8287 (m-80) REVERT: C 220 ASP cc_start: 0.8411 (t0) cc_final: 0.7836 (p0) REVERT: C 253 LYS cc_start: 0.8063 (mmtt) cc_final: 0.7701 (mtpt) REVERT: C 265 MET cc_start: 0.7935 (tpt) cc_final: 0.7679 (tpt) REVERT: E 54 GLN cc_start: 0.8853 (mt0) cc_final: 0.8115 (mp10) REVERT: F 127 GLU cc_start: 0.8542 (mt-10) cc_final: 0.8277 (mt-10) REVERT: F 129 LYS cc_start: 0.8178 (mmtm) cc_final: 0.7841 (mmmm) REVERT: H 19 ARG cc_start: 0.7669 (mmt180) cc_final: 0.7400 (mtp85) REVERT: H 92 ASP cc_start: 0.8310 (m-30) cc_final: 0.8070 (t0) REVERT: H 129 TYR cc_start: 0.7463 (p90) cc_final: 0.7141 (p90) REVERT: H 130 ARG cc_start: 0.8590 (mtt90) cc_final: 0.8328 (mtt90) REVERT: H 131 ASN cc_start: 0.8352 (m110) cc_final: 0.7977 (m-40) REVERT: I 1 MET cc_start: 0.7094 (ppp) cc_final: 0.6441 (pmm) REVERT: I 30 ARG cc_start: 0.6943 (mpt180) cc_final: 0.6537 (mpt180) REVERT: J 29 GLU cc_start: 0.8616 (mt-10) cc_final: 0.8217 (tm-30) REVERT: K 38 GLU cc_start: 0.8506 (mm-30) cc_final: 0.8059 (mm-30) REVERT: K 49 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7972 (mm-30) REVERT: K 70 ARG cc_start: 0.8478 (mtm110) cc_final: 0.8203 (mtm110) REVERT: L 65 VAL cc_start: 0.8302 (OUTLIER) cc_final: 0.7957 (p) outliers start: 63 outliers final: 56 residues processed: 420 average time/residue: 0.1921 time to fit residues: 128.2287 Evaluate side-chains 418 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 360 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 708 MET Chi-restraints excluded: chain A residue 764 CYS Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1111 MET Chi-restraints excluded: chain A residue 1237 ILE Chi-restraints excluded: chain A residue 1238 ILE Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1358 SER Chi-restraints excluded: chain A residue 1366 ARG Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1377 THR Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 371 GLU Chi-restraints excluded: chain B residue 398 ARG Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 529 GLU Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 550 ASP Chi-restraints excluded: chain B residue 597 MET Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 771 SER Chi-restraints excluded: chain B residue 805 THR Chi-restraints excluded: chain B residue 875 GLU Chi-restraints excluded: chain B residue 894 ASP Chi-restraints excluded: chain B residue 1103 ILE Chi-restraints excluded: chain B residue 1210 MET Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 133 ILE Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain E residue 4 GLU Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 128 ASN Chi-restraints excluded: chain I residue 59 VAL Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain L residue 65 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 327 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 209 optimal weight: 6.9990 chunk 275 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 352 optimal weight: 40.0000 chunk 249 optimal weight: 0.8980 chunk 182 optimal weight: 3.9990 chunk 291 optimal weight: 0.2980 chunk 323 optimal weight: 4.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 75 ASN ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 2 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.125035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.091810 restraints weight = 42280.270| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 2.32 r_work: 0.2953 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 30339 Z= 0.153 Angle : 0.536 11.595 41238 Z= 0.278 Chirality : 0.043 0.187 4623 Planarity : 0.004 0.043 5103 Dihedral : 14.147 148.362 4592 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.05 % Favored : 95.89 % Rotamer: Outliers : 2.21 % Allowed : 13.48 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: 0.28 (0.14), residues: 3502 helix: 1.45 (0.15), residues: 1236 sheet: -0.30 (0.22), residues: 537 loop : -0.53 (0.15), residues: 1729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 135 TYR 0.019 0.001 TYR E 112 PHE 0.022 0.001 PHE A 219 TRP 0.007 0.001 TRP C 192 HIS 0.008 0.001 HIS A1173 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.15 (30307) covalent geometry : angle 0.52711 / 0.28 (41193) hydrogen bonds : bond 0.03515 / 2.36 ( 1243) hydrogen bonds : angle 4.46604 / 3.20 ( 3425) metal coordination : bond 0.00477 / 0.31 ( 32) metal coordination : angle 3.05362 / 1.94 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 370 time to evaluate : 1.127 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 SER cc_start: 0.7982 (p) cc_final: 0.7592 (t) REVERT: A 63 ARG cc_start: 0.7532 (ptt90) cc_final: 0.6972 (mtp180) REVERT: A 72 GLU cc_start: 0.8223 (mm-30) cc_final: 0.8003 (mm-30) REVERT: A 74 MET cc_start: 0.7198 (tpp) cc_final: 0.6912 (tpp) REVERT: A 122 MET cc_start: 0.8595 (mmm) cc_final: 0.7986 (tpp) REVERT: A 175 ARG cc_start: 0.7846 (tmm160) cc_final: 0.7500 (tmm-80) REVERT: A 307 ASP cc_start: 0.8721 (t0) cc_final: 0.8299 (t0) REVERT: A 386 ASP cc_start: 0.8564 (p0) cc_final: 0.8163 (t0) REVERT: A 542 GLU cc_start: 0.8003 (mt-10) cc_final: 0.7588 (pt0) REVERT: A 791 ASP cc_start: 0.8073 (t0) cc_final: 0.7727 (t0) REVERT: A 931 GLU cc_start: 0.8613 (tt0) cc_final: 0.8148 (tp30) REVERT: A 977 LYS cc_start: 0.9254 (tttp) cc_final: 0.8708 (ttpt) REVERT: A 1005 GLU cc_start: 0.8911 (mm-30) cc_final: 0.8427 (mt-10) REVERT: A 1151 GLU cc_start: 0.7943 (pm20) cc_final: 0.7579 (pm20) REVERT: A 1167 GLU cc_start: 0.7832 (tp30) cc_final: 0.7569 (tp30) REVERT: A 1285 MET cc_start: 0.7782 (mmt) cc_final: 0.7398 (mmt) REVERT: A 1287 TYR cc_start: 0.8230 (m-10) cc_final: 0.7807 (m-10) REVERT: A 1307 GLU cc_start: 0.8771 (mm-30) cc_final: 0.8364 (mt-10) REVERT: A 1366 ARG cc_start: 0.8363 (OUTLIER) cc_final: 0.7024 (mtt-85) REVERT: A 1442 ASP cc_start: 0.8628 (m-30) cc_final: 0.8132 (m-30) REVERT: B 101 MET cc_start: 0.9019 (mtt) cc_final: 0.8631 (mpp) REVERT: B 135 ARG cc_start: 0.7136 (ttm110) cc_final: 0.6429 (mtm110) REVERT: B 241 ARG cc_start: 0.7716 (ttm-80) cc_final: 0.6507 (ttp-170) REVERT: B 272 THR cc_start: 0.8966 (m) cc_final: 0.8601 (p) REVERT: B 310 MET cc_start: 0.7856 (ttm) cc_final: 0.7449 (ttp) REVERT: B 348 ARG cc_start: 0.8072 (mtm110) cc_final: 0.7331 (ptp-170) REVERT: B 353 LYS cc_start: 0.7566 (mtmt) cc_final: 0.7358 (mtmt) REVERT: B 443 ASN cc_start: 0.7752 (t0) cc_final: 0.7031 (p0) REVERT: B 471 LYS cc_start: 0.7192 (mptt) cc_final: 0.6696 (tttt) REVERT: B 595 ARG cc_start: 0.8381 (ttt180) cc_final: 0.8080 (tmt170) REVERT: B 621 GLU cc_start: 0.8455 (tp30) cc_final: 0.7662 (tp30) REVERT: B 775 LYS cc_start: 0.8931 (mtmt) cc_final: 0.8470 (mttm) REVERT: B 864 LYS cc_start: 0.7468 (mtmt) cc_final: 0.6556 (pttp) REVERT: B 875 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7774 (pp20) REVERT: B 945 GLU cc_start: 0.7784 (mm-30) cc_final: 0.7417 (mm-30) REVERT: B 1152 MET cc_start: 0.7952 (mmm) cc_final: 0.7609 (mmm) REVERT: C 199 LYS cc_start: 0.8821 (ttmt) cc_final: 0.8443 (tptt) REVERT: C 209 TYR cc_start: 0.8758 (m-80) cc_final: 0.8258 (m-80) REVERT: C 220 ASP cc_start: 0.8415 (t0) cc_final: 0.7845 (p0) REVERT: C 253 LYS cc_start: 0.8068 (mmtt) cc_final: 0.7700 (mtpt) REVERT: C 265 MET cc_start: 0.7960 (tpt) cc_final: 0.7706 (tpt) REVERT: E 54 GLN cc_start: 0.8849 (mt0) cc_final: 0.8207 (mp10) REVERT: F 123 LYS cc_start: 0.8674 (tttt) cc_final: 0.8411 (tttt) REVERT: F 127 GLU cc_start: 0.8554 (mt-10) cc_final: 0.8209 (mt-10) REVERT: F 129 LYS cc_start: 0.8176 (mmtm) cc_final: 0.7847 (mmmm) REVERT: H 19 ARG cc_start: 0.7732 (mmt180) cc_final: 0.7441 (mtp85) REVERT: H 92 ASP cc_start: 0.8307 (m-30) cc_final: 0.8081 (t0) REVERT: H 131 ASN cc_start: 0.8354 (m110) cc_final: 0.7966 (m-40) REVERT: I 1 MET cc_start: 0.7132 (ppp) cc_final: 0.6471 (pmm) REVERT: I 30 ARG cc_start: 0.7002 (mpt180) cc_final: 0.6670 (mpt180) REVERT: I 34 TYR cc_start: 0.7944 (t80) cc_final: 0.7267 (t80) REVERT: J 29 GLU cc_start: 0.8610 (mt-10) cc_final: 0.8181 (tm-30) REVERT: K 38 GLU cc_start: 0.8507 (mm-30) cc_final: 0.8067 (mm-30) REVERT: K 49 GLU cc_start: 0.8199 (mm-30) cc_final: 0.7921 (mm-30) REVERT: K 70 ARG cc_start: 0.8500 (mtm110) cc_final: 0.8215 (mtm110) REVERT: L 65 VAL cc_start: 0.8299 (OUTLIER) cc_final: 0.7965 (p) outliers start: 69 outliers final: 54 residues processed: 417 average time/residue: 0.2033 time to fit residues: 134.1814 Evaluate side-chains 420 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 363 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 708 MET Chi-restraints excluded: chain A residue 748 MET Chi-restraints excluded: chain A residue 764 CYS Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1111 MET Chi-restraints excluded: chain A residue 1237 ILE Chi-restraints excluded: chain A residue 1238 ILE Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1299 VAL Chi-restraints excluded: chain A residue 1358 SER Chi-restraints excluded: chain A residue 1366 ARG Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1377 THR Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 371 GLU Chi-restraints excluded: chain B residue 398 ARG Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 529 GLU Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 550 ASP Chi-restraints excluded: chain B residue 597 MET Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 771 SER Chi-restraints excluded: chain B residue 805 THR Chi-restraints excluded: chain B residue 875 GLU Chi-restraints excluded: chain B residue 1103 ILE Chi-restraints excluded: chain B residue 1210 MET Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 133 ILE Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain E residue 4 GLU Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 128 ASN Chi-restraints excluded: chain I residue 59 VAL Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain L residue 65 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 355 optimal weight: 30.0000 chunk 3 optimal weight: 9.9990 chunk 167 optimal weight: 10.0000 chunk 113 optimal weight: 0.0270 chunk 275 optimal weight: 0.6980 chunk 168 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 351 optimal weight: 30.0000 chunk 110 optimal weight: 0.6980 chunk 266 optimal weight: 3.9990 chunk 155 optimal weight: 0.9990 overall best weight: 1.2842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 75 ASN ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1270 ASN ** B1187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 54 GLN K 2 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.125490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.092215 restraints weight = 42337.549| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 2.31 r_work: 0.2960 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 30339 Z= 0.141 Angle : 0.527 11.088 41238 Z= 0.274 Chirality : 0.042 0.200 4623 Planarity : 0.004 0.043 5103 Dihedral : 14.142 149.867 4592 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.83 % Favored : 96.12 % Rotamer: Outliers : 1.98 % Allowed : 13.80 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: 0.31 (0.14), residues: 3502 helix: 1.47 (0.15), residues: 1237 sheet: -0.31 (0.22), residues: 517 loop : -0.51 (0.15), residues: 1748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 130 TYR 0.017 0.001 TYR A 383 PHE 0.023 0.001 PHE A 219 TRP 0.007 0.001 TRP C 192 HIS 0.006 0.001 HIS A1258 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 (30307) covalent geometry : angle 0.51828 / 0.27 (41193) hydrogen bonds : bond 0.03423 / 2.31 ( 1243) hydrogen bonds : angle 4.43328 / 3.17 ( 3425) metal coordination : bond 0.00436 / 0.28 ( 32) metal coordination : angle 2.98131 / 1.88 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 365 time to evaluate : 1.261 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.5288 (mmm) cc_final: 0.4604 (ttt) REVERT: A 60 SER cc_start: 0.7960 (p) cc_final: 0.7577 (t) REVERT: A 63 ARG cc_start: 0.7533 (ptt90) cc_final: 0.6972 (mtp180) REVERT: A 72 GLU cc_start: 0.8215 (mm-30) cc_final: 0.7996 (mm-30) REVERT: A 74 MET cc_start: 0.7184 (tpp) cc_final: 0.6943 (tpp) REVERT: A 122 MET cc_start: 0.8584 (mmm) cc_final: 0.7882 (tpt) REVERT: A 175 ARG cc_start: 0.7830 (tmm160) cc_final: 0.7491 (tmm-80) REVERT: A 307 ASP cc_start: 0.8725 (t0) cc_final: 0.8321 (t0) REVERT: A 386 ASP cc_start: 0.8575 (p0) cc_final: 0.8142 (t0) REVERT: A 542 GLU cc_start: 0.8005 (mt-10) cc_final: 0.7583 (pt0) REVERT: A 791 ASP cc_start: 0.8042 (t0) cc_final: 0.7677 (t0) REVERT: A 931 GLU cc_start: 0.8613 (tt0) cc_final: 0.8144 (tp30) REVERT: A 977 LYS cc_start: 0.9249 (tttp) cc_final: 0.8699 (ttpt) REVERT: A 1005 GLU cc_start: 0.8906 (mm-30) cc_final: 0.8421 (mt-10) REVERT: A 1151 GLU cc_start: 0.7889 (pm20) cc_final: 0.7538 (pm20) REVERT: A 1167 GLU cc_start: 0.7841 (tp30) cc_final: 0.7585 (tp30) REVERT: A 1259 MET cc_start: 0.8564 (mtp) cc_final: 0.8178 (mpp) REVERT: A 1285 MET cc_start: 0.7768 (mmt) cc_final: 0.7391 (mmt) REVERT: A 1287 TYR cc_start: 0.8189 (m-10) cc_final: 0.7804 (m-10) REVERT: A 1307 GLU cc_start: 0.8753 (mm-30) cc_final: 0.8322 (mt-10) REVERT: A 1366 ARG cc_start: 0.8348 (OUTLIER) cc_final: 0.6992 (mtt-85) REVERT: A 1442 ASP cc_start: 0.8680 (m-30) cc_final: 0.8182 (m-30) REVERT: B 101 MET cc_start: 0.9022 (mtt) cc_final: 0.8630 (mpp) REVERT: B 135 ARG cc_start: 0.7143 (ttm110) cc_final: 0.6474 (mtm110) REVERT: B 241 ARG cc_start: 0.7737 (ttm-80) cc_final: 0.6533 (ttp-170) REVERT: B 272 THR cc_start: 0.8951 (m) cc_final: 0.8584 (p) REVERT: B 443 ASN cc_start: 0.7749 (t0) cc_final: 0.7045 (p0) REVERT: B 471 LYS cc_start: 0.7189 (mptt) cc_final: 0.6689 (tttt) REVERT: B 595 ARG cc_start: 0.8399 (ttt180) cc_final: 0.8079 (tmt170) REVERT: B 621 GLU cc_start: 0.8489 (tp30) cc_final: 0.7704 (tp30) REVERT: B 775 LYS cc_start: 0.8931 (mtmt) cc_final: 0.8459 (mttm) REVERT: B 864 LYS cc_start: 0.7454 (mtmt) cc_final: 0.6547 (pttp) REVERT: B 875 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7797 (pp20) REVERT: B 945 GLU cc_start: 0.7770 (mm-30) cc_final: 0.7453 (mm-30) REVERT: B 1111 MET cc_start: 0.8563 (mmt) cc_final: 0.7841 (mmt) REVERT: B 1152 MET cc_start: 0.8027 (mmm) cc_final: 0.7675 (mmm) REVERT: C 199 LYS cc_start: 0.8820 (ttmt) cc_final: 0.8438 (tptt) REVERT: C 209 TYR cc_start: 0.8743 (m-80) cc_final: 0.8238 (m-80) REVERT: C 220 ASP cc_start: 0.8411 (t0) cc_final: 0.7832 (p0) REVERT: C 253 LYS cc_start: 0.8053 (mmtt) cc_final: 0.7696 (mtpt) REVERT: C 265 MET cc_start: 0.7946 (tpt) cc_final: 0.7692 (tpt) REVERT: E 54 GLN cc_start: 0.8895 (mt0) cc_final: 0.8578 (mt0) REVERT: E 58 MET cc_start: 0.8775 (ptp) cc_final: 0.8526 (ptp) REVERT: F 129 LYS cc_start: 0.8152 (mmtm) cc_final: 0.7831 (mmmm) REVERT: H 19 ARG cc_start: 0.7770 (mmt180) cc_final: 0.7439 (mtp85) REVERT: H 126 GLU cc_start: 0.7500 (tt0) cc_final: 0.7221 (tt0) REVERT: H 131 ASN cc_start: 0.8395 (m110) cc_final: 0.8028 (m-40) REVERT: I 1 MET cc_start: 0.7113 (ppp) cc_final: 0.6501 (pmm) REVERT: I 30 ARG cc_start: 0.6989 (mpt180) cc_final: 0.6537 (mpt180) REVERT: J 29 GLU cc_start: 0.8633 (mt-10) cc_final: 0.8212 (tm-30) REVERT: K 38 GLU cc_start: 0.8521 (mm-30) cc_final: 0.8092 (mm-30) REVERT: K 49 GLU cc_start: 0.8214 (mm-30) cc_final: 0.7947 (mm-30) REVERT: K 70 ARG cc_start: 0.8508 (mtm110) cc_final: 0.8217 (mtm110) REVERT: K 78 THR cc_start: 0.9141 (t) cc_final: 0.8930 (p) REVERT: L 65 VAL cc_start: 0.8277 (OUTLIER) cc_final: 0.7930 (p) outliers start: 62 outliers final: 51 residues processed: 405 average time/residue: 0.1943 time to fit residues: 125.2811 Evaluate side-chains 409 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 355 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 708 MET Chi-restraints excluded: chain A residue 748 MET Chi-restraints excluded: chain A residue 764 CYS Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1111 MET Chi-restraints excluded: chain A residue 1237 ILE Chi-restraints excluded: chain A residue 1238 ILE Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1299 VAL Chi-restraints excluded: chain A residue 1358 SER Chi-restraints excluded: chain A residue 1366 ARG Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 371 GLU Chi-restraints excluded: chain B residue 398 ARG Chi-restraints excluded: chain B residue 425 THR Chi-restraints excluded: chain B residue 529 GLU Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 550 ASP Chi-restraints excluded: chain B residue 597 MET Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 771 SER Chi-restraints excluded: chain B residue 805 THR Chi-restraints excluded: chain B residue 875 GLU Chi-restraints excluded: chain B residue 1103 ILE Chi-restraints excluded: chain B residue 1210 MET Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 133 ILE Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 128 ASN Chi-restraints excluded: chain I residue 13 MET Chi-restraints excluded: chain I residue 59 VAL Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain L residue 65 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 352 optimal weight: 40.0000 chunk 314 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 293 optimal weight: 2.9990 chunk 238 optimal weight: 0.6980 chunk 83 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 249 optimal weight: 1.9990 chunk 250 optimal weight: 0.6980 chunk 98 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 2 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.126310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.093281 restraints weight = 42297.878| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 2.31 r_work: 0.2980 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 30339 Z= 0.114 Angle : 0.514 10.820 41238 Z= 0.268 Chirality : 0.042 0.196 4623 Planarity : 0.004 0.042 5103 Dihedral : 14.126 152.073 4592 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.66 % Favored : 96.29 % Rotamer: Outliers : 1.73 % Allowed : 14.05 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: 0.37 (0.14), residues: 3502 helix: 1.51 (0.15), residues: 1244 sheet: -0.24 (0.22), residues: 514 loop : -0.49 (0.15), residues: 1744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 38 TYR 0.019 0.001 TYR E 112 PHE 0.023 0.001 PHE A 219 TRP 0.008 0.001 TRP C 201 HIS 0.006 0.001 HIS A1258 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 (30307) covalent geometry : angle 0.50570 / 0.27 (41193) hydrogen bonds : bond 0.03278 / 2.21 ( 1243) hydrogen bonds : angle 4.37500 / 3.13 ( 3425) metal coordination : bond 0.00364 / 0.23 ( 32) metal coordination : angle 2.83819 / 1.78 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7494.50 seconds wall clock time: 129 minutes 7.73 seconds (7747.73 seconds total)