Starting phenix.real_space_refine on Tue Aug 26 01:50:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qq2_18573/08_2025/8qq2_18573.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qq2_18573/08_2025/8qq2_18573.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8qq2_18573/08_2025/8qq2_18573.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qq2_18573/08_2025/8qq2_18573.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8qq2_18573/08_2025/8qq2_18573.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qq2_18573/08_2025/8qq2_18573.map" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.026 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 75 5.49 5 Mg 1 5.21 5 S 194 5.16 5 C 20353 2.51 5 N 5713 2.21 5 O 6251 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 254 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 32595 Number of models: 1 Model: "" Number of chains: 23 Chain: "A" Number of atoms: 10926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1383, 10926 Classifications: {'peptide': 1383} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 2, 'PTRANS': 67, 'TRANS': 1313} Chain breaks: 8 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 57 Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 2, 'ARG:plan': 1, 'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "B" Number of atoms: 8848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1114, 8848 Classifications: {'peptide': 1114} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 52, 'TRANS': 1061} Chain breaks: 5 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'GLN:plan1': 2, 'ASN:plan1': 1, 'ASP:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "C" Number of atoms: 2039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 2039 Classifications: {'peptide': 255} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 15, 'TRANS': 239} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 9 Chain: "E" Number of atoms: 1687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1687 Classifications: {'peptide': 209} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 11, 'TRANS': 197} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "F" Number of atoms: 623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 623 Classifications: {'peptide': 78} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 72} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1172 Classifications: {'peptide': 148} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 143} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "I" Number of atoms: 921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 921 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 108} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "J" Number of atoms: 520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 520 Classifications: {'peptide': 66} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 63} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "K" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 920 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 8, 'TRANS': 106} Chain: "L" Number of atoms: 368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 368 Classifications: {'peptide': 44} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 1005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1005 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 3, 'TRANS': 124} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'GLU:plan': 5, 'GLN:plan1': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "G" Number of atoms: 1334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1334 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 10, 'TRANS': 160} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "R" Number of atoms: 679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 679 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 6, 'TRANS': 94} Chain breaks: 3 Unresolved non-hydrogen bonds: 156 Unresolved non-hydrogen angles: 187 Unresolved non-hydrogen dihedrals: 134 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 10, 'ASP:plan': 1, 'GLU:plan': 5, 'HIS:plan': 2, 'PHE:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 96 Chain: "P" Number of atoms: 293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 293 Classifications: {'RNA': 14} Modifications used: {'rna2p_pyr': 3, 'rna3p_pur': 5, 'rna3p_pyr': 6} Link IDs: {'rna2p': 2, 'rna3p': 11} Chain: "T" Number of atoms: 748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 748 Classifications: {'DNA': 36} Link IDs: {'rna3p': 35} Chain: "N" Number of atoms: 503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 503 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain breaks: 1 Chain: "A" 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: "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} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 464 SG CYS A 71 64.040 60.030 66.787 1.00 79.91 S ATOM 486 SG CYS A 74 63.985 63.380 66.579 1.00 80.38 S ATOM 533 SG CYS A 81 67.322 61.749 67.542 1.00 80.19 S ATOM 768 SG CYS A 111 68.119 75.915 114.410 1.00 98.79 S ATOM 790 SG CYS A 114 65.166 77.905 113.311 1.00101.88 S ATOM 19344 SG CYS B1119 61.312 77.220 75.583 1.00 76.41 S ATOM 19366 SG CYS B1122 62.907 74.984 78.258 1.00 79.45 S ATOM 19481 SG CYS B1137 60.071 73.748 75.950 1.00 86.69 S ATOM 19502 SG CYS B1140 59.623 76.298 78.920 1.00 87.21 S ATOM 20468 SG CYS C 88 109.049 51.848 14.512 1.00 53.40 S ATOM 20481 SG CYS C 90 107.082 49.502 16.854 1.00 64.39 S ATOM 20516 SG CYS C 94 109.541 48.230 14.218 1.00 47.78 S ATOM 20538 SG CYS C 97 110.662 49.920 17.496 1.00 41.58 S ATOM 25342 SG CYS I 17 125.135 51.357 139.959 1.00 86.09 S ATOM 25366 SG CYS I 20 121.980 50.793 137.972 1.00 88.12 S ATOM 25527 SG CYS I 39 122.384 53.988 140.152 1.00 88.51 S ATOM 25549 SG CYS I 42 122.311 51.149 142.140 1.00 91.58 S ATOM 25898 SG CYS I 86 159.218 60.208 110.785 1.00 73.63 S ATOM 25922 SG CYS I 89 161.184 56.953 110.171 1.00 78.19 S ATOM 26126 SG CYS I 114 158.156 57.700 108.081 1.00 58.40 S ATOM 26161 SG CYS I 119 157.768 56.893 111.758 1.00 70.43 S ATOM 26271 SG CYS J 7 132.985 54.821 39.767 1.00 30.55 S ATOM 26295 SG CYS J 10 134.000 56.654 36.575 1.00 26.37 S ATOM 26555 SG CYS J 44 135.636 57.658 39.842 1.00 27.85 S ATOM 26561 SG CYS J 45 136.429 54.434 37.995 1.00 30.50 S ATOM 27698 SG CYS L 19 107.006 20.804 53.152 1.00 66.82 S ATOM 27717 SG CYS L 22 108.318 17.802 51.123 1.00 72.19 S ATOM 27834 SG CYS L 36 104.722 18.023 52.189 1.00 81.62 S Time building chain proxies: 7.28, per 1000 atoms: 0.22 Number of scatterers: 32595 At special positions: 0 Unit cell: (172.555, 151.715, 162.552, 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 194 16.00 P 75 15.00 Mg 1 11.99 O 6251 8.00 N 5713 7.00 C 20353 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: 3.14 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 476.8 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2001 " pdb="ZN ZN A2001 " - pdb=" NE2 HIS A 84 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 71 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 74 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 81 " pdb=" ZN A2002 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 114 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 111 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1122 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1119 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1140 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1137 " pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 90 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 94 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 97 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 17 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 39 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 20 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 42 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 119 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 114 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 86 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 89 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 19 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 22 " Number of angles added : 33 7732 Ramachandran restraints generated. 3866 Oldfield, 0 Emsley, 3866 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7404 Finding SS restraints... Secondary structure from input PDB file: 138 helices and 44 sheets defined 39.5% alpha, 18.4% beta 36 base pairs and 53 stacking pairs defined. Time for finding SS restraints: 4.05 Creating SS restraints... Processing helix chain 'A' and resid 27 through 35 Processing helix chain 'A' and resid 99 through 110 Processing helix chain 'A' and resid 124 through 130 removed outlier: 3.798A pdb=" N LEU A 130 " --> pdb=" O ILE A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 149 Processing helix chain 'A' and resid 217 through 227 removed outlier: 3.893A pdb=" N ARG A 227 " --> pdb=" O GLU A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 237 Processing helix chain 'A' and resid 244 through 249 Processing helix chain 'A' and resid 274 through 297 Processing helix chain 'A' and resid 301 through 319 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 348 through 354 Processing helix chain 'A' and resid 382 through 388 Processing helix chain 'A' and resid 398 through 409 Processing helix chain 'A' and resid 465 through 467 No H-bonds generated for 'chain 'A' and resid 465 through 467' Processing helix chain 'A' and resid 488 through 493 removed outlier: 3.773A pdb=" N TYR A 492 " --> pdb=" O VAL A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 519 Processing helix chain 'A' and resid 520 through 525 removed outlier: 3.724A pdb=" N ILE A 525 " --> pdb=" O PRO A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 550 removed outlier: 4.097A pdb=" N ARG A 546 " --> pdb=" O LEU A 542 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N LYS A 547 " --> pdb=" O THR A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 566 Processing helix chain 'A' and resid 588 through 596 removed outlier: 4.142A pdb=" N LEU A 594 " --> pdb=" O GLN A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 646 Processing helix chain 'A' and resid 651 through 661 Processing helix chain 'A' and resid 661 through 684 removed outlier: 4.124A pdb=" N LEU A 667 " --> pdb=" O ASP A 663 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ILE A 682 " --> pdb=" O ASN A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 693 Processing helix chain 'A' and resid 695 through 722 Processing helix chain 'A' and resid 732 through 759 Processing helix chain 'A' and resid 764 through 772 removed outlier: 3.553A pdb=" N SER A 772 " --> pdb=" O SER A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 777 through 786 Processing helix chain 'A' and resid 832 through 868 removed outlier: 3.835A pdb=" N GLU A 845 " --> pdb=" O MET A 841 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLY A 846 " --> pdb=" O GLY A 842 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N THR A 854 " --> pdb=" O THR A 850 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N ALA A 855 " --> pdb=" O ALA A 851 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N GLU A 856 " --> pdb=" O VAL A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 894 Processing helix chain 'A' and resid 897 through 901 removed outlier: 3.681A pdb=" N VAL A 901 " --> pdb=" O GLY A 898 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 921 Processing helix chain 'A' and resid 927 through 934 Processing helix chain 'A' and resid 935 through 945 removed outlier: 3.513A pdb=" N LYS A 940 " --> pdb=" O GLU A 936 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ASP A 941 " --> pdb=" O ASP A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 970 Processing helix chain 'A' and resid 971 through 974 removed outlier: 4.273A pdb=" N ASP A 974 " --> pdb=" O PRO A 971 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 971 through 974' Processing helix chain 'A' and resid 982 through 994 Processing helix chain 'A' and resid 1005 through 1018 removed outlier: 3.726A pdb=" N LYS A1018 " --> pdb=" O LYS A1014 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1049 removed outlier: 5.490A pdb=" N LEU A1040 " --> pdb=" O ASN A1036 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N PHE A1041 " --> pdb=" O ALA A1037 " (cutoff:3.500A) Processing helix chain 'A' and resid 1050 through 1057 Processing helix chain 'A' and resid 1061 through 1079 Processing helix chain 'A' and resid 1086 through 1097 Processing helix chain 'A' and resid 1098 through 1101 Processing helix chain 'A' and resid 1120 through 1129 Processing helix chain 'A' and resid 1145 through 1150 removed outlier: 3.827A pdb=" N ARG A1149 " --> pdb=" O GLY A1145 " (cutoff:3.500A) Processing helix chain 'A' and resid 1150 through 1161 Processing helix chain 'A' and resid 1189 through 1198 Processing helix chain 'A' and resid 1217 through 1224 removed outlier: 3.645A pdb=" N ARG A1224 " --> pdb=" O HIS A1220 " (cutoff:3.500A) Processing helix chain 'A' and resid 1227 through 1240 Processing helix chain 'A' and resid 1280 through 1295 Processing helix chain 'A' and resid 1342 through 1349 removed outlier: 3.531A pdb=" N VAL A1346 " --> pdb=" O SER A1342 " (cutoff:3.500A) Processing helix chain 'A' and resid 1361 through 1370 Processing helix chain 'A' and resid 1371 through 1388 Processing helix chain 'A' and resid 1394 through 1406 removed outlier: 3.720A pdb=" N LEU A1398 " --> pdb=" O ASN A1394 " (cutoff:3.500A) Processing helix chain 'A' and resid 1415 through 1422 removed outlier: 3.684A pdb=" N GLN A1422 " --> pdb=" O GLY A1418 " (cutoff:3.500A) Processing helix chain 'A' and resid 1425 through 1431 removed outlier: 3.665A pdb=" N LYS A1429 " --> pdb=" O GLY A1425 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N SER A1431 " --> pdb=" O LEU A1427 " (cutoff:3.500A) Processing helix chain 'A' and resid 1435 through 1446 Processing helix chain 'A' and resid 1453 through 1460 removed outlier: 3.849A pdb=" N LEU A1460 " --> pdb=" O GLU A1456 " (cutoff:3.500A) Processing helix chain 'A' and resid 1478 through 1482 removed outlier: 3.850A pdb=" N TYR A1482 " --> pdb=" O LYS A1479 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 37 removed outlier: 3.534A pdb=" N ALA B 25 " --> pdb=" O LEU B 21 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N TRP B 27 " --> pdb=" O GLN B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 62 removed outlier: 3.525A pdb=" N LEU B 44 " --> pdb=" O VAL B 40 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N VAL B 55 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N GLN B 56 " --> pdb=" O GLN B 52 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA B 62 " --> pdb=" O ILE B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 116 Processing helix chain 'B' and resid 167 through 174 Processing helix chain 'B' and resid 246 through 253 Processing helix chain 'B' and resid 269 through 276 Processing helix chain 'B' and resid 280 through 289 Processing helix chain 'B' and resid 294 through 306 Proline residue: B 303 - end of helix Processing helix chain 'B' and resid 307 through 309 No H-bonds generated for 'chain 'B' and resid 307 through 309' Processing helix chain 'B' and resid 313 through 323 Processing helix chain 'B' and resid 332 through 346 Processing helix chain 'B' and resid 357 through 377 removed outlier: 3.956A pdb=" N TYR B 363 " --> pdb=" O THR B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 389 No H-bonds generated for 'chain 'B' and resid 387 through 389' Processing helix chain 'B' and resid 395 through 425 removed outlier: 3.872A pdb=" N GLY B 406 " --> pdb=" O PHE B 402 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N MET B 407 " --> pdb=" O LEU B 403 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ARG B 425 " --> pdb=" O LYS B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 435 Processing helix chain 'B' and resid 436 through 451 removed outlier: 4.370A pdb=" N ILE B 440 " --> pdb=" O LYS B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 483 Processing helix chain 'B' and resid 502 through 506 removed outlier: 3.710A pdb=" N TRP B 506 " --> pdb=" O ASN B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 548 Processing helix chain 'B' and resid 554 through 556 No H-bonds generated for 'chain 'B' and resid 554 through 556' Processing helix chain 'B' and resid 579 through 594 Processing helix chain 'B' and resid 636 through 645 Processing helix chain 'B' and resid 652 through 658 Processing helix chain 'B' and resid 669 through 673 removed outlier: 3.683A pdb=" N VAL B 673 " --> pdb=" O GLU B 670 " (cutoff:3.500A) Processing helix chain 'B' and resid 678 through 683 Processing helix chain 'B' and resid 699 through 704 removed outlier: 3.707A pdb=" N ILE B 703 " --> pdb=" O PRO B 700 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU B 704 " --> pdb=" O SER B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 710 removed outlier: 3.937A pdb=" N ILE B 710 " --> pdb=" O CYS B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 717 Processing helix chain 'B' and resid 718 through 729 Processing helix chain 'B' and resid 739 through 743 removed outlier: 3.640A pdb=" N ARG B 743 " --> pdb=" O PHE B 740 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 765 removed outlier: 3.997A pdb=" N GLU B 765 " --> pdb=" O ARG B 762 " (cutoff:3.500A) Processing helix chain 'B' and resid 798 through 803 Processing helix chain 'B' and resid 970 through 976 removed outlier: 4.728A pdb=" N SER B 974 " --> pdb=" O HIS B 970 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ARG B 975 " --> pdb=" O ALA B 971 " (cutoff:3.500A) Processing helix chain 'B' and resid 977 through 994 removed outlier: 4.052A pdb=" N LEU B 981 " --> pdb=" O THR B 977 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASN B 992 " --> pdb=" O LYS B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1007 through 1017 removed outlier: 3.652A pdb=" N ASP B1017 " --> pdb=" O ASN B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1077 through 1081 Processing helix chain 'B' and resid 1087 through 1098 Processing helix chain 'B' and resid 1099 through 1108 Processing helix chain 'B' and resid 1152 through 1164 Processing helix chain 'C' and resid 27 through 40 removed outlier: 3.745A pdb=" N ILE C 39 " --> pdb=" O ARG C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 70 removed outlier: 3.659A pdb=" N LEU C 70 " --> pdb=" O HIS C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 88 removed outlier: 3.726A pdb=" N CYS C 88 " --> pdb=" O SER C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 120 No H-bonds generated for 'chain 'C' and resid 118 through 120' Processing helix chain 'C' and resid 173 through 177 removed outlier: 3.509A pdb=" N TRP C 176 " --> pdb=" O HIS C 173 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASN C 177 " --> pdb=" O ALA C 174 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 173 through 177' Processing helix chain 'C' and resid 199 through 203 removed outlier: 3.625A pdb=" N GLU C 202 " --> pdb=" O LYS C 199 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N TRP C 203 " --> pdb=" O PRO C 200 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 199 through 203' Processing helix chain 'C' and resid 242 through 268 Processing helix chain 'E' and resid 3 through 24 Processing helix chain 'E' and resid 29 through 34 Processing helix chain 'E' and resid 36 through 44 Processing helix chain 'E' and resid 83 through 98 Processing helix chain 'E' and resid 111 through 120 Processing helix chain 'E' and resid 133 through 136 removed outlier: 3.607A pdb=" N LEU E 136 " --> pdb=" O GLN E 133 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 133 through 136' Processing helix chain 'E' and resid 138 through 142 Processing helix chain 'E' and resid 152 through 164 Processing helix chain 'E' and resid 166 through 170 removed outlier: 3.596A pdb=" N LEU E 170 " --> pdb=" O GLU E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 184 Processing helix chain 'F' and resid 58 through 75 Processing helix chain 'F' and resid 88 through 100 Processing helix chain 'I' and resid 69 through 75 removed outlier: 3.727A pdb=" N VAL I 72 " --> pdb=" O ILE I 69 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER I 73 " --> pdb=" O ALA I 70 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 30 through 38 Processing helix chain 'J' and resid 42 through 51 removed outlier: 3.902A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 60 Processing helix chain 'K' and resid 5 through 10 removed outlier: 3.530A pdb=" N SER K 9 " --> pdb=" O ALA K 6 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 53 removed outlier: 4.578A pdb=" N ILE K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS K 52 " --> pdb=" O SER K 48 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ASP K 53 " --> pdb=" O GLN K 49 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 113 Processing helix chain 'D' and resid 33 through 50 Processing helix chain 'D' and resid 58 through 71 Processing helix chain 'D' and resid 76 through 90 Processing helix chain 'D' and resid 93 through 104 Processing helix chain 'D' and resid 107 through 115 Processing helix chain 'D' and resid 116 through 119 Processing helix chain 'D' and resid 123 through 138 Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 21 through 35 Processing helix chain 'R' and resid 502 through 514 removed outlier: 3.788A pdb=" N LEU R 506 " --> pdb=" O ARG R 502 " (cutoff:3.500A) Processing helix chain 'R' and resid 546 through 565 Processing helix chain 'R' and resid 577 through 591 Processing helix chain 'R' and resid 593 through 614 Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 16 removed outlier: 4.598A pdb=" N ARG B1150 " --> pdb=" O ARG A 16 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1448 through 1449 removed outlier: 3.516A pdb=" N ARG A 20 " --> pdb=" O MET B1172 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 86 through 94 removed outlier: 6.519A pdb=" N THR A 251 " --> pdb=" O LEU A 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 190 through 192 removed outlier: 3.564A pdb=" N GLU A 201 " --> pdb=" O ARG A 190 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 357 through 359 removed outlier: 3.860A pdb=" N LEU B1084 " --> pdb=" O VAL A 359 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1060 through 1062 removed outlier: 3.779A pdb=" N THR A 365 " --> pdb=" O MET A 501 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N MET A 501 " --> pdb=" O THR A 365 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N PHE A 482 " --> pdb=" O ARG A 364 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N VAL A 366 " --> pdb=" O PHE A 482 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N LEU A 484 " --> pdb=" O VAL A 366 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N THR A 368 " --> pdb=" O LEU A 484 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 389 through 393 removed outlier: 3.907A pdb=" N TYR A 418 " --> pdb=" O GLU A 447 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N HIS A 449 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ALA A 416 " --> pdb=" O HIS A 449 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 554 through 555 Processing sheet with id=AA9, first strand: chain 'A' and resid 579 through 581 removed outlier: 6.165A pdb=" N VAL H 91 " --> pdb=" O LEU A 580 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N HIS H 29 " --> pdb=" O LYS H 13 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU H 121 " --> pdb=" O TYR H 118 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ARG H 98 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N SER H 117 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N VAL H 96 " --> pdb=" O SER H 117 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 602 through 603 removed outlier: 3.598A pdb=" N MET A 637 " --> pdb=" O VAL A 629 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N GLU A 631 " --> pdb=" O LEU A 635 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N LEU A 635 " --> pdb=" O GLU A 631 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 789 through 790 Processing sheet with id=AB3, first strand: chain 'A' and resid 792 through 793 Processing sheet with id=AB4, first strand: chain 'A' and resid 872 through 873 removed outlier: 6.702A pdb=" N VAL A 879 " --> pdb=" O VAL A 887 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 902 through 905 Processing sheet with id=AB6, first strand: chain 'A' and resid 1307 through 1310 removed outlier: 3.676A pdb=" N ILE A1335 " --> pdb=" O HIS A1310 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LEU A1139 " --> pdb=" O THR A1338 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1243 through 1247 Processing sheet with id=AB8, first strand: chain 'A' and resid 1319 through 1322 removed outlier: 3.634A pdb=" N LYS A1319 " --> pdb=" O LEU A1331 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 115 through 119 removed outlier: 5.419A pdb=" N LEU A1473 " --> pdb=" O ILE G 59 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N GLY G 57 " --> pdb=" O LEU A1475 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL G 66 " --> pdb=" O LEU G 13 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU D 30 " --> pdb=" O HIS G 4 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 115 through 119 removed outlier: 5.419A pdb=" N LEU A1473 " --> pdb=" O ILE G 59 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N GLY G 57 " --> pdb=" O LEU A1475 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N ILE G 54 " --> pdb=" O PRO G 69 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N LYS G 71 " --> pdb=" O ASP G 52 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ILE G 75 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N VAL G 48 " --> pdb=" O ILE G 75 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N PHE G 77 " --> pdb=" O ILE G 46 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N ILE G 46 " --> pdb=" O PHE G 77 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 83 through 93 removed outlier: 6.422A pdb=" N ASP B 127 " --> pdb=" O GLU B 89 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ILE B 91 " --> pdb=" O TYR B 125 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N TYR B 125 " --> pdb=" O ILE B 91 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N LEU B 93 " --> pdb=" O PRO B 123 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLY B 150 " --> pdb=" O LEU B 124 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N VAL B 126 " --> pdb=" O PHE B 148 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N PHE B 148 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N ILE B 128 " --> pdb=" O LYS B 146 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N LYS B 146 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N LYS B 130 " --> pdb=" O HIS B 144 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N HIS B 144 " --> pdb=" O LYS B 130 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N VAL B 132 " --> pdb=" O THR B 142 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N THR B 142 " --> pdb=" O VAL B 132 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 185 through 187 Processing sheet with id=AC4, first strand: chain 'B' and resid 197 through 200 Processing sheet with id=AC5, first strand: chain 'B' and resid 205 through 209 removed outlier: 6.634A pdb=" N MET B 239 " --> pdb=" O ALA B 216 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N THR B 218 " --> pdb=" O VAL B 237 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N VAL B 237 " --> pdb=" O THR B 218 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N GLU B 220 " --> pdb=" O ILE B 235 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE B 235 " --> pdb=" O GLU B 220 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N ARG B 222 " --> pdb=" O SER B 233 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N SER B 233 " --> pdb=" O ARG B 222 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TRP B 236 " --> pdb=" O THR B 259 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 531 through 532 Processing sheet with id=AC7, first strand: chain 'B' and resid 531 through 532 Processing sheet with id=AC8, first strand: chain 'B' and resid 551 through 552 removed outlier: 5.403A pdb=" N TRP B 573 " --> pdb=" O VAL B 569 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N VAL B 569 " --> pdb=" O TRP B 573 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY B 575 " --> pdb=" O ILE B 567 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 747 through 751 removed outlier: 3.576A pdb=" N GLN B 906 " --> pdb=" O ARG B 922 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N ARG B 924 " --> pdb=" O VAL B 904 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N VAL B 904 " --> pdb=" O ARG B 924 " (cutoff:3.500A) removed outlier: 8.561A pdb=" N VAL B 926 " --> pdb=" O GLY B 902 " (cutoff:3.500A) removed outlier: 8.485A pdb=" N GLY B 902 " --> pdb=" O VAL B 926 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 747 through 751 removed outlier: 3.576A pdb=" N GLN B 906 " --> pdb=" O ARG B 922 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N ARG B 924 " --> pdb=" O VAL B 904 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N VAL B 904 " --> pdb=" O ARG B 924 " (cutoff:3.500A) removed outlier: 8.561A pdb=" N VAL B 926 " --> pdb=" O GLY B 902 " (cutoff:3.500A) removed outlier: 8.485A pdb=" N GLY B 902 " --> pdb=" O VAL B 926 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N VAL B 907 " --> pdb=" O LYS L 46 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 759 through 760 Processing sheet with id=AD3, first strand: chain 'B' and resid 1025 through 1026 removed outlier: 7.124A pdb=" N VAL B 794 " --> pdb=" O GLY B 946 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N GLN B 948 " --> pdb=" O VAL B 794 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N MET B 796 " --> pdb=" O GLN B 948 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N PHE B1042 " --> pdb=" O ILE B 782 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 827 through 829 Processing sheet with id=AD5, first strand: chain 'B' and resid 865 through 867 removed outlier: 3.952A pdb=" N ILE B 867 " --> pdb=" O THR B 894 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 8 through 14 removed outlier: 5.832A pdb=" N VAL C 9 " --> pdb=" O GLU C 24 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N GLU C 24 " --> pdb=" O VAL C 9 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N ILE C 11 " --> pdb=" O ILE C 22 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N ILE C 22 " --> pdb=" O ILE C 11 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE C 21 " --> pdb=" O TYR C 231 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU C 234 " --> pdb=" O GLY C 181 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLY C 181 " --> pdb=" O GLU C 234 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 44 through 47 Processing sheet with id=AD8, first strand: chain 'C' and resid 44 through 47 removed outlier: 6.792A pdb=" N GLU C 158 " --> pdb=" O ASN C 55 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ASN C 55 " --> pdb=" O GLU C 158 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ARG C 160 " --> pdb=" O ASP C 53 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 113 through 116 removed outlier: 6.481A pdb=" N ARG C 113 " --> pdb=" O LYS C 152 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N LYS C 152 " --> pdb=" O ARG C 113 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N VAL C 115 " --> pdb=" O ILE C 150 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 60 through 64 removed outlier: 6.274A pdb=" N ASP E 70 " --> pdb=" O HIS E 64 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N ARG E 101 " --> pdb=" O THR E 69 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N GLN E 71 " --> pdb=" O ARG E 101 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N LEU E 103 " --> pdb=" O GLN E 71 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N PHE E 73 " --> pdb=" O LEU E 103 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N VAL E 105 " --> pdb=" O PHE E 73 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N PHE E 75 " --> pdb=" O VAL E 105 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 81 through 82 Processing sheet with id=AE3, first strand: chain 'E' and resid 147 through 150 Processing sheet with id=AE4, first strand: chain 'I' and resid 25 through 29 removed outlier: 3.675A pdb=" N ILE I 34 " --> pdb=" O ASP I 29 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 80 through 81 Processing sheet with id=AE6, first strand: chain 'K' and resid 19 through 23 removed outlier: 6.777A pdb=" N ILE K 72 " --> pdb=" O TYR K 61 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N TYR K 61 " --> pdb=" O ILE K 72 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ARG K 74 " --> pdb=" O ALA K 59 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ALA K 59 " --> pdb=" O ARG K 74 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N GLN K 76 " --> pdb=" O LEU K 57 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 169 through 170 removed outlier: 5.817A pdb=" N ILE G 147 " --> pdb=" O SER G 162 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N SER G 162 " --> pdb=" O ILE G 147 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N SER G 105 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N SER G 109 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N GLU G 100 " --> pdb=" O VAL G 89 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N VAL G 89 " --> pdb=" O GLU G 100 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 118 through 120 1360 hydrogen bonds defined for protein. 3810 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 89 hydrogen bonds 178 hydrogen bond angles 0 basepair planarities 36 basepair parallelities 53 stacking parallelities Total time for adding SS restraints: 9.09 Time building geometry restraints manager: 4.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9392 1.33 - 1.45: 5723 1.45 - 1.58: 17784 1.58 - 1.70: 146 1.70 - 1.82: 306 Bond restraints: 33351 Sorted by residual: bond pdb=" CA PRO R 527 " pdb=" C PRO R 527 " ideal model delta sigma weight residual 1.517 1.546 -0.029 9.30e-03 1.16e+04 9.46e+00 bond pdb=" N ILE A1128 " pdb=" CA ILE A1128 " ideal model delta sigma weight residual 1.459 1.495 -0.035 1.21e-02 6.83e+03 8.44e+00 bond pdb=" N CYS A 114 " pdb=" CA CYS A 114 " ideal model delta sigma weight residual 1.458 1.496 -0.039 1.33e-02 5.65e+03 8.43e+00 bond pdb=" N CYS A 71 " pdb=" CA CYS A 71 " ideal model delta sigma weight residual 1.455 1.490 -0.035 1.25e-02 6.40e+03 7.93e+00 bond pdb=" N LYS A1481 " pdb=" CA LYS A1481 " ideal model delta sigma weight residual 1.456 1.493 -0.037 1.31e-02 5.83e+03 7.85e+00 ... (remaining 33346 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 44401 2.09 - 4.18: 924 4.18 - 6.28: 70 6.28 - 8.37: 10 8.37 - 10.46: 3 Bond angle restraints: 45408 Sorted by residual: angle pdb=" N ARG C 228 " pdb=" CA ARG C 228 " pdb=" C ARG C 228 " ideal model delta sigma weight residual 111.74 120.41 -8.67 1.35e+00 5.49e-01 4.13e+01 angle pdb=" N GLY A 973 " pdb=" CA GLY A 973 " pdb=" C GLY A 973 " ideal model delta sigma weight residual 113.76 124.22 -10.46 1.80e+00 3.09e-01 3.38e+01 angle pdb=" N PHE C 229 " pdb=" CA PHE C 229 " pdb=" C PHE C 229 " ideal model delta sigma weight residual 110.24 117.39 -7.15 1.47e+00 4.63e-01 2.37e+01 angle pdb=" N ALA L 57 " pdb=" CA ALA L 57 " pdb=" C ALA L 57 " ideal model delta sigma weight residual 112.72 107.32 5.40 1.14e+00 7.69e-01 2.24e+01 angle pdb=" CA PHE E 44 " pdb=" C PHE E 44 " pdb=" O PHE E 44 " ideal model delta sigma weight residual 121.89 115.83 6.06 1.29e+00 6.01e-01 2.21e+01 ... (remaining 45403 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.06: 19723 34.06 - 68.12: 492 68.12 - 102.19: 49 102.19 - 136.25: 0 136.25 - 170.31: 4 Dihedral angle restraints: 20268 sinusoidal: 8842 harmonic: 11426 Sorted by residual: dihedral pdb=" CA VAL A 538 " pdb=" C VAL A 538 " pdb=" N GLN A 539 " pdb=" CA GLN A 539 " ideal model delta harmonic sigma weight residual 180.00 152.08 27.92 0 5.00e+00 4.00e-02 3.12e+01 dihedral pdb=" CA ASN G 124 " pdb=" C ASN G 124 " pdb=" N PRO G 125 " pdb=" CA PRO G 125 " ideal model delta harmonic sigma weight residual 180.00 152.21 27.79 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" CA ASP A 540 " pdb=" C ASP A 540 " pdb=" N THR A 541 " pdb=" CA THR A 541 " ideal model delta harmonic sigma weight residual 180.00 154.61 25.39 0 5.00e+00 4.00e-02 2.58e+01 ... (remaining 20265 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 4656 0.083 - 0.166: 452 0.166 - 0.249: 16 0.249 - 0.332: 4 0.332 - 0.415: 2 Chirality restraints: 5130 Sorted by residual: chirality pdb=" CA ARG C 228 " pdb=" N ARG C 228 " pdb=" C ARG C 228 " pdb=" CB ARG C 228 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.30e+00 chirality pdb=" P DG T 25 " pdb=" OP1 DG T 25 " pdb=" OP2 DG T 25 " pdb=" O5' DG T 25 " both_signs ideal model delta sigma weight residual True 2.35 -2.75 -0.40 2.00e-01 2.50e+01 4.03e+00 chirality pdb=" P DG T 28 " pdb=" OP1 DG T 28 " pdb=" OP2 DG T 28 " pdb=" O5' DG T 28 " both_signs ideal model delta sigma weight residual True 2.35 -2.63 -0.28 2.00e-01 2.50e+01 1.98e+00 ... (remaining 5127 not shown) Planarity restraints: 5619 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP R 504 " -0.077 2.00e-02 2.50e+03 3.77e-02 3.56e+01 pdb=" CG TRP R 504 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 TRP R 504 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 TRP R 504 " 0.050 2.00e-02 2.50e+03 pdb=" NE1 TRP R 504 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP R 504 " 0.013 2.00e-02 2.50e+03 pdb=" CE3 TRP R 504 " 0.043 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 504 " -0.027 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 504 " -0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP R 504 " -0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR R 508 " 0.061 2.00e-02 2.50e+03 3.19e-02 2.03e+01 pdb=" CG TYR R 508 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 TYR R 508 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 TYR R 508 " -0.028 2.00e-02 2.50e+03 pdb=" CE1 TYR R 508 " -0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR R 508 " -0.013 2.00e-02 2.50e+03 pdb=" CZ TYR R 508 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR R 508 " 0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 539 " 0.017 2.00e-02 2.50e+03 3.33e-02 1.11e+01 pdb=" C GLN A 539 " -0.058 2.00e-02 2.50e+03 pdb=" O GLN A 539 " 0.021 2.00e-02 2.50e+03 pdb=" N ASP A 540 " 0.020 2.00e-02 2.50e+03 ... (remaining 5616 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.36: 71 2.36 - 2.99: 16708 2.99 - 3.63: 46489 3.63 - 4.26: 72873 4.26 - 4.90: 125299 Nonbonded interactions: 261440 Sorted by model distance: nonbonded pdb=" OP1 C P 17 " pdb="MG MG P 101 " model vdw 1.719 2.170 nonbonded pdb=" OD1 ASP A 495 " pdb="MG MG P 101 " model vdw 1.978 2.170 nonbonded pdb=" O ASN D 34 " pdb=" OG1 THR D 68 " model vdw 2.114 3.040 nonbonded pdb=" O CYS A1480 " pdb=" C GLY G 19 " model vdw 2.140 3.270 nonbonded pdb=" OD2 ASP D 16 " pdb=" OG SER D 18 " model vdw 2.172 3.040 ... (remaining 261435 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 group one per residue 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: 7.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.600 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 38.580 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 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 : 0.006 0.211 33380 Z= 0.274 Angle : 0.710 18.207 45441 Z= 0.426 Chirality : 0.048 0.415 5130 Planarity : 0.004 0.101 5619 Dihedral : 14.386 170.312 12864 Min Nonbonded Distance : 1.719 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.20 % Favored : 94.75 % Rotamer: Outliers : 0.56 % Allowed : 6.35 % Favored : 93.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.05 % 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 aren not related in a simple way. whole: -0.40 (0.13), residues: 3866 helix: 0.72 (0.14), residues: 1383 sheet: -0.39 (0.23), residues: 533 loop : -0.92 (0.14), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 16 TYR 0.061 0.002 TYR R 508 PHE 0.018 0.002 PHE A1284 TRP 0.077 0.003 TRP R 504 HIS 0.009 0.001 HIS G 14 Details of bonding type rmsd covalent geometry : bond 0.00572 (33351) covalent geometry : angle 0.69099 (45408) hydrogen bonds : bond 0.15953 ( 1412) hydrogen bonds : angle 6.83870 ( 3988) metal coordination : bond 0.04404 ( 29) metal coordination : angle 6.15092 ( 33) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7732 Ramachandran restraints generated. 3866 Oldfield, 0 Emsley, 3866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7732 Ramachandran restraints generated. 3866 Oldfield, 0 Emsley, 3866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 3479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 496 time to evaluate : 1.113 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 361 PHE cc_start: 0.7671 (m-80) cc_final: 0.7377 (m-80) REVERT: A 1180 ASN cc_start: 0.7801 (t0) cc_final: 0.7564 (t0) REVERT: A 1183 SER cc_start: 0.8063 (t) cc_final: 0.7590 (m) REVERT: A 1221 MET cc_start: 0.7552 (tpt) cc_final: 0.7265 (tpp) REVERT: A 1255 LEU cc_start: 0.8363 (tt) cc_final: 0.7786 (mt) REVERT: A 1261 ILE cc_start: 0.8202 (mm) cc_final: 0.7934 (tt) REVERT: A 1292 MET cc_start: 0.7557 (ttm) cc_final: 0.7319 (ttm) REVERT: A 1306 LYS cc_start: 0.7363 (tmtm) cc_final: 0.6961 (tppt) REVERT: A 1309 MET cc_start: 0.7798 (ttt) cc_final: 0.7582 (ttt) REVERT: A 1396 ARG cc_start: 0.6689 (OUTLIER) cc_final: 0.6152 (mtp85) REVERT: B 200 MET cc_start: 0.8376 (tpp) cc_final: 0.8085 (tpt) REVERT: B 298 MET cc_start: 0.7821 (mmm) cc_final: 0.7493 (mmm) REVERT: B 334 LYS cc_start: 0.7765 (mmtt) cc_final: 0.7142 (pttm) REVERT: B 381 GLU cc_start: 0.7191 (mp0) cc_final: 0.6922 (mp0) REVERT: B 388 TYR cc_start: 0.7290 (OUTLIER) cc_final: 0.6400 (t80) REVERT: B 405 ARG cc_start: 0.7327 (mtm180) cc_final: 0.7099 (mtm180) REVERT: E 91 CYS cc_start: 0.7301 (p) cc_final: 0.7083 (p) REVERT: F 94 MET cc_start: 0.8383 (tpp) cc_final: 0.8052 (tpp) REVERT: F 105 ILE cc_start: 0.8430 (pt) cc_final: 0.8186 (pt) REVERT: H 18 GLU cc_start: 0.8061 (mt-10) cc_final: 0.7088 (pt0) REVERT: H 20 LYS cc_start: 0.7012 (tptm) cc_final: 0.6703 (tptm) REVERT: H 65 TYR cc_start: 0.5905 (OUTLIER) cc_final: 0.5234 (m-10) REVERT: H 136 GLU cc_start: 0.6949 (mp0) cc_final: 0.6568 (mp0) REVERT: H 138 ASP cc_start: 0.7812 (m-30) cc_final: 0.7562 (m-30) REVERT: I 71 ASP cc_start: 0.7934 (m-30) cc_final: 0.7685 (m-30) REVERT: D 62 MET cc_start: 0.6345 (mmt) cc_final: 0.6006 (tpp) REVERT: G 14 HIS cc_start: 0.6825 (t70) cc_final: 0.6582 (t-90) REVERT: G 70 VAL cc_start: 0.3976 (t) cc_final: 0.3435 (m) REVERT: G 104 MET cc_start: 0.2531 (ttp) cc_final: 0.2062 (ppp) REVERT: R 514 LEU cc_start: 0.5553 (mt) cc_final: 0.4836 (tp) REVERT: R 583 LEU cc_start: 0.7670 (mt) cc_final: 0.7138 (mt) outliers start: 19 outliers final: 11 residues processed: 511 average time/residue: 0.2175 time to fit residues: 174.0813 Evaluate side-chains 378 residues out of total 3479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 364 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 197 optimal weight: 0.9980 chunk 388 optimal weight: 10.0000 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 0.1980 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 4.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 507 GLN ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 671 ASN A1129 ASN A1190 GLN A1194 ASN ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1115 GLN C 217 GLN E 65 ASN E 108 GLN E 116 GLN ** E 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 18 GLN ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 HIS ** D 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 4 HIS G 14 HIS R 509 GLN R 585 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.131543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.101795 restraints weight = 478953.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.102343 restraints weight = 344969.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.101963 restraints weight = 324880.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.101975 restraints weight = 325142.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.101822 restraints weight = 320857.548| |-----------------------------------------------------------------------------| r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.1268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 33380 Z= 0.163 Angle : 0.591 10.943 45441 Z= 0.308 Chirality : 0.044 0.168 5130 Planarity : 0.004 0.068 5619 Dihedral : 13.566 165.937 5153 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.06 % Favored : 95.91 % Rotamer: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.05 % 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 aren not related in a simple way. whole: -0.04 (0.14), residues: 3866 helix: 1.17 (0.14), residues: 1391 sheet: -0.30 (0.21), residues: 586 loop : -0.82 (0.14), residues: 1889 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.000 ARG J 47 TYR 0.024 0.002 TYR B1048 PHE 0.025 0.002 PHE A 458 TRP 0.018 0.002 TRP A1192 HIS 0.011 0.001 HIS R 585 Details of bonding type rmsd covalent geometry : bond 0.00384 (33351) covalent geometry : angle 0.58030 (45408) hydrogen bonds : bond 0.04488 ( 1412) hydrogen bonds : angle 5.04582 ( 3988) metal coordination : bond 0.00704 ( 29) metal coordination : angle 4.23587 ( 33) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7732 Ramachandran restraints generated. 3866 Oldfield, 0 Emsley, 3866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7732 Ramachandran restraints generated. 3866 Oldfield, 0 Emsley, 3866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 3479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 482 time to evaluate : 0.808 Fit side-chains REVERT: A 1097 GLU cc_start: 0.7099 (tm-30) cc_final: 0.6879 (tm-30) REVERT: A 1183 SER cc_start: 0.7939 (t) cc_final: 0.7513 (m) REVERT: A 1215 GLU cc_start: 0.7711 (mm-30) cc_final: 0.7181 (mt-10) REVERT: A 1221 MET cc_start: 0.7315 (tpt) cc_final: 0.7018 (tpp) REVERT: A 1255 LEU cc_start: 0.8105 (tt) cc_final: 0.7733 (mt) REVERT: A 1261 ILE cc_start: 0.8292 (mm) cc_final: 0.7990 (tt) REVERT: A 1306 LYS cc_start: 0.7821 (tptt) cc_final: 0.7503 (tppt) REVERT: B 35 ASP cc_start: 0.7736 (m-30) cc_final: 0.7430 (m-30) REVERT: B 200 MET cc_start: 0.8447 (tpp) cc_final: 0.8047 (tpt) REVERT: B 270 ILE cc_start: 0.8487 (mm) cc_final: 0.8072 (tp) REVERT: B 298 MET cc_start: 0.7259 (mmm) cc_final: 0.7010 (mmm) REVERT: B 334 LYS cc_start: 0.7839 (mmtt) cc_final: 0.7202 (pttm) REVERT: B 430 ASN cc_start: 0.5216 (t0) cc_final: 0.4579 (p0) REVERT: E 65 ASN cc_start: 0.7975 (m-40) cc_final: 0.7709 (t0) REVERT: E 110 MET cc_start: 0.7351 (mtp) cc_final: 0.6988 (mtt) REVERT: E 134 GLU cc_start: 0.7480 (mt-10) cc_final: 0.7277 (mt-10) REVERT: H 18 GLU cc_start: 0.7860 (mt-10) cc_final: 0.7091 (pt0) REVERT: H 20 LYS cc_start: 0.6746 (tptm) cc_final: 0.6457 (tptm) REVERT: J 41 LYS cc_start: 0.8144 (ttpt) cc_final: 0.7904 (ttpp) REVERT: D 59 GLU cc_start: 0.6644 (tp30) cc_final: 0.6392 (mt-10) REVERT: G 70 VAL cc_start: 0.5797 (t) cc_final: 0.4836 (m) REVERT: R 511 GLN cc_start: 0.7862 (mm-40) cc_final: 0.7438 (mm-40) REVERT: R 514 LEU cc_start: 0.5789 (mt) cc_final: 0.4978 (tp) REVERT: R 583 LEU cc_start: 0.7663 (mt) cc_final: 0.7234 (mt) outliers start: 0 outliers final: 0 residues processed: 482 average time/residue: 0.2050 time to fit residues: 155.4451 Evaluate side-chains 372 residues out of total 3479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 372 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 298 optimal weight: 0.9980 chunk 111 optimal weight: 2.9990 chunk 258 optimal weight: 2.9990 chunk 71 optimal weight: 0.4980 chunk 144 optimal weight: 0.6980 chunk 386 optimal weight: 9.9990 chunk 48 optimal weight: 0.7980 chunk 316 optimal weight: 6.9990 chunk 128 optimal weight: 5.9990 chunk 272 optimal weight: 1.9990 chunk 361 optimal weight: 8.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 GLN ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 485 ASN A 673 GLN A1190 GLN A1194 ASN A1457 ASN B 90 GLN B 552 ASN B1040 GLN C 217 GLN E 129 GLN ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 48 ASN G 14 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.132526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.102952 restraints weight = 478031.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.103447 restraints weight = 336648.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.102969 restraints weight = 319920.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.103018 restraints weight = 320706.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.102842 restraints weight = 314735.746| |-----------------------------------------------------------------------------| r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 33380 Z= 0.128 Angle : 0.539 10.756 45441 Z= 0.281 Chirality : 0.043 0.165 5130 Planarity : 0.004 0.073 5619 Dihedral : 13.522 167.029 5153 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.96 % Favored : 96.02 % Rotamer: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 aren not related in a simple way. whole: 0.14 (0.14), residues: 3866 helix: 1.39 (0.14), residues: 1396 sheet: -0.23 (0.21), residues: 574 loop : -0.76 (0.14), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 721 TYR 0.016 0.001 TYR A 669 PHE 0.023 0.001 PHE A 458 TRP 0.019 0.001 TRP A1192 HIS 0.006 0.001 HIS A 465 Details of bonding type rmsd covalent geometry : bond 0.00298 (33351) covalent geometry : angle 0.53016 (45408) hydrogen bonds : bond 0.03799 ( 1412) hydrogen bonds : angle 4.68855 ( 3988) metal coordination : bond 0.00567 ( 29) metal coordination : angle 3.64180 ( 33) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7732 Ramachandran restraints generated. 3866 Oldfield, 0 Emsley, 3866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7732 Ramachandran restraints generated. 3866 Oldfield, 0 Emsley, 3866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 3479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 453 time to evaluate : 1.267 Fit side-chains REVERT: A 1097 GLU cc_start: 0.7258 (tm-30) cc_final: 0.6890 (tm-30) REVERT: A 1221 MET cc_start: 0.7279 (tpt) cc_final: 0.6985 (tpp) REVERT: A 1255 LEU cc_start: 0.8061 (tt) cc_final: 0.7593 (mt) REVERT: A 1306 LYS cc_start: 0.7840 (tptt) cc_final: 0.7559 (tppt) REVERT: B 35 ASP cc_start: 0.7603 (m-30) cc_final: 0.7370 (m-30) REVERT: B 169 ARG cc_start: 0.5505 (mmm-85) cc_final: 0.5242 (mmm-85) REVERT: B 200 MET cc_start: 0.8486 (tpp) cc_final: 0.8197 (tpt) REVERT: B 270 ILE cc_start: 0.8547 (mm) cc_final: 0.8089 (tp) REVERT: B 334 LYS cc_start: 0.7771 (mmtt) cc_final: 0.7209 (pttm) REVERT: B 405 ARG cc_start: 0.7421 (mtm180) cc_final: 0.7182 (mtm-85) REVERT: B 430 ASN cc_start: 0.5228 (t0) cc_final: 0.4511 (p0) REVERT: E 65 ASN cc_start: 0.8029 (m-40) cc_final: 0.7686 (t0) REVERT: E 91 CYS cc_start: 0.7298 (p) cc_final: 0.7081 (p) REVERT: E 110 MET cc_start: 0.7212 (mtp) cc_final: 0.6896 (mtt) REVERT: H 18 GLU cc_start: 0.7984 (mt-10) cc_final: 0.7194 (pt0) REVERT: H 20 LYS cc_start: 0.7011 (tptm) cc_final: 0.6759 (tptm) REVERT: I 21 ASN cc_start: 0.9230 (m-40) cc_final: 0.8910 (m-40) REVERT: D 59 GLU cc_start: 0.6808 (tp30) cc_final: 0.6566 (mt-10) REVERT: R 511 GLN cc_start: 0.7742 (mm-40) cc_final: 0.7416 (mm-40) REVERT: R 514 LEU cc_start: 0.5918 (mt) cc_final: 0.5127 (tp) REVERT: R 583 LEU cc_start: 0.7743 (mt) cc_final: 0.7228 (mt) outliers start: 0 outliers final: 0 residues processed: 453 average time/residue: 0.2057 time to fit residues: 148.6069 Evaluate side-chains 371 residues out of total 3479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 371 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 308 optimal weight: 3.9990 chunk 75 optimal weight: 6.9990 chunk 158 optimal weight: 30.0000 chunk 50 optimal weight: 0.6980 chunk 373 optimal weight: 7.9990 chunk 37 optimal weight: 7.9990 chunk 350 optimal weight: 6.9990 chunk 169 optimal weight: 5.9990 chunk 241 optimal weight: 0.9980 chunk 286 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 673 GLN B 56 GLN C 217 GLN E 92 GLN I 18 GLN ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.129738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.100241 restraints weight = 480175.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.100633 restraints weight = 348067.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.100289 restraints weight = 330546.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.100302 restraints weight = 336606.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.100169 restraints weight = 325075.269| |-----------------------------------------------------------------------------| r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 33380 Z= 0.200 Angle : 0.593 13.016 45441 Z= 0.307 Chirality : 0.045 0.165 5130 Planarity : 0.004 0.064 5619 Dihedral : 13.587 168.444 5153 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 aren not related in a simple way. whole: 0.01 (0.14), residues: 3866 helix: 1.28 (0.14), residues: 1389 sheet: -0.32 (0.21), residues: 592 loop : -0.82 (0.14), residues: 1885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 47 TYR 0.033 0.002 TYR B1048 PHE 0.030 0.002 PHE R 507 TRP 0.020 0.002 TRP A1192 HIS 0.010 0.001 HIS A 465 Details of bonding type rmsd covalent geometry : bond 0.00495 (33351) covalent geometry : angle 0.58511 (45408) hydrogen bonds : bond 0.04239 ( 1412) hydrogen bonds : angle 4.70148 ( 3988) metal coordination : bond 0.00902 ( 29) metal coordination : angle 3.71660 ( 33) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7732 Ramachandran restraints generated. 3866 Oldfield, 0 Emsley, 3866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7732 Ramachandran restraints generated. 3866 Oldfield, 0 Emsley, 3866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 3479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 427 time to evaluate : 1.245 Fit side-chains revert: symmetry clash REVERT: A 29 ASP cc_start: 0.8248 (p0) cc_final: 0.8045 (p0) REVERT: A 57 LEU cc_start: 0.8248 (mm) cc_final: 0.8000 (mm) REVERT: A 361 PHE cc_start: 0.7611 (m-80) cc_final: 0.7347 (m-80) REVERT: A 1097 GLU cc_start: 0.7359 (tm-30) cc_final: 0.7063 (tm-30) REVERT: A 1221 MET cc_start: 0.7197 (tpt) cc_final: 0.6871 (tpp) REVERT: A 1306 LYS cc_start: 0.8014 (tptt) cc_final: 0.7698 (tppt) REVERT: B 169 ARG cc_start: 0.5270 (mmm-85) cc_final: 0.5062 (mmm-85) REVERT: B 200 MET cc_start: 0.8376 (tpp) cc_final: 0.7724 (tpt) REVERT: B 334 LYS cc_start: 0.7765 (mmtt) cc_final: 0.7226 (pttm) REVERT: B 407 MET cc_start: 0.7921 (mtt) cc_final: 0.7656 (mtt) REVERT: B 430 ASN cc_start: 0.5259 (t0) cc_final: 0.4710 (p0) REVERT: E 110 MET cc_start: 0.7369 (mtp) cc_final: 0.7065 (mtt) REVERT: H 18 GLU cc_start: 0.7989 (mt-10) cc_final: 0.7215 (pt0) REVERT: H 20 LYS cc_start: 0.7037 (tptm) cc_final: 0.6816 (tptm) REVERT: D 59 GLU cc_start: 0.6824 (tp30) cc_final: 0.6518 (mt-10) REVERT: G 46 ILE cc_start: 0.6885 (mm) cc_final: 0.6457 (mm) REVERT: G 48 VAL cc_start: 0.6441 (t) cc_final: 0.6020 (t) REVERT: R 511 GLN cc_start: 0.7960 (mm-40) cc_final: 0.7726 (mm-40) REVERT: R 514 LEU cc_start: 0.6233 (mt) cc_final: 0.5495 (tp) REVERT: R 583 LEU cc_start: 0.7785 (mt) cc_final: 0.7290 (mt) outliers start: 0 outliers final: 0 residues processed: 427 average time/residue: 0.2060 time to fit residues: 140.6575 Evaluate side-chains 359 residues out of total 3479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 359 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 181 optimal weight: 0.8980 chunk 222 optimal weight: 0.5980 chunk 161 optimal weight: 7.9990 chunk 312 optimal weight: 0.9980 chunk 327 optimal weight: 0.7980 chunk 104 optimal weight: 2.9990 chunk 282 optimal weight: 6.9990 chunk 244 optimal weight: 10.0000 chunk 226 optimal weight: 3.9990 chunk 266 optimal weight: 1.9990 chunk 133 optimal weight: 7.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 341 GLN A 740 GLN B 56 GLN I 18 GLN ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 60 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.133599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.104602 restraints weight = 476064.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.105211 restraints weight = 339655.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.104745 restraints weight = 317804.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.104829 restraints weight = 324193.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.104651 restraints weight = 311984.806| |-----------------------------------------------------------------------------| r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 33380 Z= 0.128 Angle : 0.544 13.594 45441 Z= 0.280 Chirality : 0.043 0.195 5130 Planarity : 0.004 0.053 5619 Dihedral : 13.538 168.907 5153 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.05 % 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 aren not related in a simple way. whole: 0.17 (0.14), residues: 3866 helix: 1.43 (0.14), residues: 1395 sheet: -0.24 (0.21), residues: 591 loop : -0.75 (0.14), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 33 TYR 0.013 0.001 TYR A 669 PHE 0.019 0.001 PHE E 73 TRP 0.022 0.001 TRP A1192 HIS 0.005 0.001 HIS A 465 Details of bonding type rmsd covalent geometry : bond 0.00302 (33351) covalent geometry : angle 0.53645 (45408) hydrogen bonds : bond 0.03640 ( 1412) hydrogen bonds : angle 4.50567 ( 3988) metal coordination : bond 0.00571 ( 29) metal coordination : angle 3.49122 ( 33) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7732 Ramachandran restraints generated. 3866 Oldfield, 0 Emsley, 3866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7732 Ramachandran restraints generated. 3866 Oldfield, 0 Emsley, 3866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 3479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 424 time to evaluate : 1.205 Fit side-chains revert: symmetry clash REVERT: A 1097 GLU cc_start: 0.7477 (tm-30) cc_final: 0.7119 (tm-30) REVERT: A 1221 MET cc_start: 0.7295 (tpt) cc_final: 0.6963 (tpp) REVERT: A 1306 LYS cc_start: 0.7909 (tptt) cc_final: 0.7628 (tppt) REVERT: B 35 ASP cc_start: 0.7482 (m-30) cc_final: 0.7266 (m-30) REVERT: B 169 ARG cc_start: 0.5170 (mmm-85) cc_final: 0.4963 (mmm-85) REVERT: B 200 MET cc_start: 0.8392 (tpp) cc_final: 0.8128 (tpt) REVERT: B 294 ASP cc_start: 0.7990 (t0) cc_final: 0.7447 (m-30) REVERT: B 334 LYS cc_start: 0.7718 (mmtt) cc_final: 0.7229 (pttm) REVERT: B 381 GLU cc_start: 0.7244 (mp0) cc_final: 0.6913 (mp0) REVERT: B 430 ASN cc_start: 0.5389 (t0) cc_final: 0.4686 (p0) REVERT: B 668 LEU cc_start: 0.7983 (pt) cc_final: 0.7664 (tp) REVERT: E 91 CYS cc_start: 0.7426 (p) cc_final: 0.7171 (p) REVERT: E 110 MET cc_start: 0.7365 (mtp) cc_final: 0.6939 (mtt) REVERT: H 18 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7176 (pt0) REVERT: H 20 LYS cc_start: 0.6977 (tptm) cc_final: 0.6736 (tptm) REVERT: D 59 GLU cc_start: 0.6826 (tp30) cc_final: 0.6554 (mt-10) REVERT: D 86 LEU cc_start: 0.5903 (mm) cc_final: 0.4984 (tp) REVERT: R 511 GLN cc_start: 0.7993 (mm-40) cc_final: 0.7549 (mm-40) REVERT: R 514 LEU cc_start: 0.6258 (mt) cc_final: 0.5508 (tp) REVERT: R 525 PHE cc_start: 0.4805 (t80) cc_final: 0.4404 (t80) REVERT: R 583 LEU cc_start: 0.7772 (mt) cc_final: 0.7236 (mt) outliers start: 0 outliers final: 0 residues processed: 424 average time/residue: 0.1939 time to fit residues: 131.9872 Evaluate side-chains 359 residues out of total 3479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 359 time to evaluate : 1.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 31 optimal weight: 0.5980 chunk 280 optimal weight: 10.0000 chunk 7 optimal weight: 40.0000 chunk 47 optimal weight: 2.9990 chunk 368 optimal weight: 6.9990 chunk 204 optimal weight: 3.9990 chunk 363 optimal weight: 0.0970 chunk 342 optimal weight: 0.8980 chunk 320 optimal weight: 0.0370 chunk 0 optimal weight: 8.9990 chunk 313 optimal weight: 4.9990 overall best weight: 0.9258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN A 377 GLN B 552 ASN E 92 GLN I 18 GLN ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 34 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.130042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.102049 restraints weight = 475391.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.102410 restraints weight = 340349.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.102068 restraints weight = 321647.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.102141 restraints weight = 328002.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.102005 restraints weight = 315420.565| |-----------------------------------------------------------------------------| r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 33380 Z= 0.122 Angle : 0.531 14.324 45441 Z= 0.275 Chirality : 0.042 0.163 5130 Planarity : 0.004 0.050 5619 Dihedral : 13.517 169.516 5153 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.05 % 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 aren not related in a simple way. whole: 0.29 (0.14), residues: 3866 helix: 1.51 (0.14), residues: 1399 sheet: -0.19 (0.21), residues: 597 loop : -0.66 (0.15), residues: 1870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 438 TYR 0.020 0.001 TYR B 752 PHE 0.017 0.001 PHE E 73 TRP 0.021 0.001 TRP A1192 HIS 0.005 0.001 HIS A 465 Details of bonding type rmsd covalent geometry : bond 0.00285 (33351) covalent geometry : angle 0.52506 (45408) hydrogen bonds : bond 0.03479 ( 1412) hydrogen bonds : angle 4.39878 ( 3988) metal coordination : bond 0.00555 ( 29) metal coordination : angle 3.09222 ( 33) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7732 Ramachandran restraints generated. 3866 Oldfield, 0 Emsley, 3866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7732 Ramachandran restraints generated. 3866 Oldfield, 0 Emsley, 3866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 3479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 430 time to evaluate : 0.892 Fit side-chains revert: symmetry clash REVERT: A 1097 GLU cc_start: 0.7408 (tm-30) cc_final: 0.7066 (tm-30) REVERT: A 1221 MET cc_start: 0.7220 (tpt) cc_final: 0.6885 (tpp) REVERT: A 1247 PHE cc_start: 0.8510 (p90) cc_final: 0.8300 (p90) REVERT: A 1306 LYS cc_start: 0.7943 (tptt) cc_final: 0.7688 (tppt) REVERT: B 35 ASP cc_start: 0.7630 (m-30) cc_final: 0.7370 (m-30) REVERT: B 200 MET cc_start: 0.8482 (tpp) cc_final: 0.8163 (tpt) REVERT: B 270 ILE cc_start: 0.8567 (mm) cc_final: 0.8184 (tp) REVERT: B 334 LYS cc_start: 0.7606 (mmtt) cc_final: 0.7177 (pttm) REVERT: B 430 ASN cc_start: 0.5499 (t0) cc_final: 0.4744 (p0) REVERT: B 668 LEU cc_start: 0.7925 (pt) cc_final: 0.7657 (tp) REVERT: H 18 GLU cc_start: 0.7967 (mt-10) cc_final: 0.7147 (pt0) REVERT: H 20 LYS cc_start: 0.6989 (tptm) cc_final: 0.6764 (tptm) REVERT: I 21 ASN cc_start: 0.9135 (m-40) cc_final: 0.8930 (m-40) REVERT: D 59 GLU cc_start: 0.6669 (tp30) cc_final: 0.6431 (mt-10) REVERT: R 514 LEU cc_start: 0.6289 (mt) cc_final: 0.5492 (tp) REVERT: R 525 PHE cc_start: 0.5019 (t80) cc_final: 0.4588 (t80) REVERT: R 583 LEU cc_start: 0.7806 (mt) cc_final: 0.7293 (mt) outliers start: 0 outliers final: 0 residues processed: 430 average time/residue: 0.1984 time to fit residues: 136.6614 Evaluate side-chains 364 residues out of total 3479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 364 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 252 optimal weight: 0.9990 chunk 170 optimal weight: 3.9990 chunk 124 optimal weight: 9.9990 chunk 373 optimal weight: 10.0000 chunk 166 optimal weight: 0.9980 chunk 360 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 290 optimal weight: 1.9990 chunk 113 optimal weight: 10.0000 chunk 122 optimal weight: 8.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 341 GLN B 143 GLN E 98 ASN E 129 GLN I 18 GLN D 66 ASN G 21 ASN G 60 GLN R 511 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.131320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.101755 restraints weight = 475240.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.102165 restraints weight = 342921.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.101843 restraints weight = 327107.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.101846 restraints weight = 326606.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.101738 restraints weight = 322305.268| |-----------------------------------------------------------------------------| r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 33380 Z= 0.175 Angle : 0.578 11.744 45441 Z= 0.298 Chirality : 0.044 0.220 5130 Planarity : 0.004 0.051 5619 Dihedral : 13.568 169.514 5153 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.03 % Allowed : 1.30 % Favored : 98.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.05 % 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 aren not related in a simple way. whole: 0.23 (0.14), residues: 3866 helix: 1.50 (0.14), residues: 1383 sheet: -0.21 (0.21), residues: 590 loop : -0.71 (0.14), residues: 1893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 483 TYR 0.033 0.001 TYR B1048 PHE 0.034 0.002 PHE A 458 TRP 0.024 0.001 TRP A1192 HIS 0.007 0.001 HIS A 465 Details of bonding type rmsd covalent geometry : bond 0.00433 (33351) covalent geometry : angle 0.57118 (45408) hydrogen bonds : bond 0.03889 ( 1412) hydrogen bonds : angle 4.47206 ( 3988) metal coordination : bond 0.00560 ( 29) metal coordination : angle 3.43126 ( 33) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7732 Ramachandran restraints generated. 3866 Oldfield, 0 Emsley, 3866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7732 Ramachandran restraints generated. 3866 Oldfield, 0 Emsley, 3866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 3479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 414 time to evaluate : 1.520 Fit side-chains revert: symmetry clash REVERT: A 976 LYS cc_start: 0.7434 (tttt) cc_final: 0.7016 (tppt) REVERT: A 1097 GLU cc_start: 0.7358 (tm-30) cc_final: 0.7011 (tm-30) REVERT: A 1221 MET cc_start: 0.7283 (tpt) cc_final: 0.6898 (tpp) REVERT: A 1306 LYS cc_start: 0.7971 (tptt) cc_final: 0.7649 (tppt) REVERT: B 200 MET cc_start: 0.8501 (tpp) cc_final: 0.8252 (tpt) REVERT: B 270 ILE cc_start: 0.8540 (mm) cc_final: 0.8105 (tp) REVERT: B 334 LYS cc_start: 0.7698 (mmtt) cc_final: 0.7245 (pttm) REVERT: B 345 LYS cc_start: 0.8910 (mmtp) cc_final: 0.8367 (mmmt) REVERT: B 430 ASN cc_start: 0.5433 (t0) cc_final: 0.4686 (p0) REVERT: B 668 LEU cc_start: 0.7937 (pt) cc_final: 0.7638 (tp) REVERT: C 17 GLU cc_start: 0.6948 (tp30) cc_final: 0.6732 (tp30) REVERT: E 91 CYS cc_start: 0.7438 (p) cc_final: 0.7190 (p) REVERT: H 18 GLU cc_start: 0.7987 (mt-10) cc_final: 0.7198 (pt0) REVERT: H 20 LYS cc_start: 0.6965 (tptm) cc_final: 0.6742 (tptm) REVERT: D 59 GLU cc_start: 0.6705 (tp30) cc_final: 0.6473 (mt-10) REVERT: R 510 LYS cc_start: 0.7254 (pttm) cc_final: 0.6809 (ptmt) REVERT: R 514 LEU cc_start: 0.6389 (mt) cc_final: 0.5614 (tp) REVERT: R 525 PHE cc_start: 0.5070 (t80) cc_final: 0.4641 (t80) REVERT: R 583 LEU cc_start: 0.7793 (mt) cc_final: 0.7287 (mt) outliers start: 1 outliers final: 0 residues processed: 414 average time/residue: 0.2169 time to fit residues: 144.2020 Evaluate side-chains 354 residues out of total 3479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 354 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 72 optimal weight: 0.3980 chunk 278 optimal weight: 9.9990 chunk 229 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 41 optimal weight: 0.6980 chunk 163 optimal weight: 1.9990 chunk 260 optimal weight: 0.0770 chunk 250 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 154 optimal weight: 0.6980 chunk 282 optimal weight: 2.9990 overall best weight: 0.5740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1190 GLN A1194 ASN B 143 GLN B 552 ASN C 51 GLN E 92 GLN H 76 ASN I 18 GLN R 511 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.134300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.105592 restraints weight = 471173.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.106116 restraints weight = 334562.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.105668 restraints weight = 319785.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.105706 restraints weight = 321222.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.105559 restraints weight = 313276.811| |-----------------------------------------------------------------------------| r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 33380 Z= 0.106 Angle : 0.526 11.917 45441 Z= 0.273 Chirality : 0.042 0.170 5130 Planarity : 0.004 0.053 5619 Dihedral : 13.516 169.184 5153 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 0.03 % Allowed : 0.56 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.05 % 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 aren not related in a simple way. whole: 0.39 (0.14), residues: 3866 helix: 1.60 (0.14), residues: 1401 sheet: -0.13 (0.21), residues: 582 loop : -0.61 (0.15), residues: 1883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 483 TYR 0.016 0.001 TYR B 752 PHE 0.024 0.001 PHE A 458 TRP 0.025 0.001 TRP A1192 HIS 0.005 0.001 HIS K 69 Details of bonding type rmsd covalent geometry : bond 0.00238 (33351) covalent geometry : angle 0.51954 (45408) hydrogen bonds : bond 0.03289 ( 1412) hydrogen bonds : angle 4.29086 ( 3988) metal coordination : bond 0.00517 ( 29) metal coordination : angle 3.03125 ( 33) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7732 Ramachandran restraints generated. 3866 Oldfield, 0 Emsley, 3866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7732 Ramachandran restraints generated. 3866 Oldfield, 0 Emsley, 3866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 3479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 438 time to evaluate : 1.602 Fit side-chains revert: symmetry clash REVERT: A 29 ASP cc_start: 0.8247 (p0) cc_final: 0.7955 (p0) REVERT: A 976 LYS cc_start: 0.7394 (tttt) cc_final: 0.7035 (tppt) REVERT: A 1026 ASP cc_start: 0.7573 (t0) cc_final: 0.7021 (t0) REVERT: A 1097 GLU cc_start: 0.7379 (tm-30) cc_final: 0.7080 (tm-30) REVERT: A 1221 MET cc_start: 0.7275 (tpt) cc_final: 0.6900 (tpp) REVERT: A 1247 PHE cc_start: 0.8621 (p90) cc_final: 0.8397 (p90) REVERT: A 1306 LYS cc_start: 0.7967 (tptt) cc_final: 0.7679 (tppt) REVERT: B 35 ASP cc_start: 0.7634 (m-30) cc_final: 0.7407 (m-30) REVERT: B 200 MET cc_start: 0.8588 (tpp) cc_final: 0.8296 (tpt) REVERT: B 334 LYS cc_start: 0.7656 (mmtt) cc_final: 0.7245 (pttm) REVERT: B 345 LYS cc_start: 0.8802 (mmtp) cc_final: 0.8301 (mmmt) REVERT: B 430 ASN cc_start: 0.5356 (t0) cc_final: 0.4803 (p0) REVERT: B 668 LEU cc_start: 0.8014 (pt) cc_final: 0.7754 (tp) REVERT: E 91 CYS cc_start: 0.7451 (p) cc_final: 0.7222 (p) REVERT: H 18 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7226 (pt0) REVERT: H 20 LYS cc_start: 0.6977 (tptm) cc_final: 0.6660 (tptm) REVERT: K 17 LYS cc_start: 0.8321 (mtpp) cc_final: 0.7719 (mttt) REVERT: R 510 LYS cc_start: 0.7081 (pttm) cc_final: 0.6763 (ptmt) REVERT: R 514 LEU cc_start: 0.6295 (mt) cc_final: 0.5540 (tp) REVERT: R 525 PHE cc_start: 0.5026 (t80) cc_final: 0.4634 (t80) REVERT: R 583 LEU cc_start: 0.7840 (mt) cc_final: 0.7306 (mt) outliers start: 1 outliers final: 1 residues processed: 438 average time/residue: 0.2014 time to fit residues: 140.5036 Evaluate side-chains 367 residues out of total 3479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 366 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 149 optimal weight: 0.9980 chunk 361 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 chunk 280 optimal weight: 10.0000 chunk 170 optimal weight: 1.9990 chunk 276 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 308 optimal weight: 6.9990 chunk 300 optimal weight: 0.9990 chunk 147 optimal weight: 7.9990 chunk 227 optimal weight: 3.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 143 GLN I 18 GLN ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 GLN R 511 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.129470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.101566 restraints weight = 478009.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.102083 restraints weight = 345659.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.101619 restraints weight = 328071.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.101680 restraints weight = 332890.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.101519 restraints weight = 321560.779| |-----------------------------------------------------------------------------| r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 33380 Z= 0.143 Angle : 0.548 10.688 45441 Z= 0.283 Chirality : 0.043 0.171 5130 Planarity : 0.004 0.047 5619 Dihedral : 13.529 169.251 5153 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.05 % 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 aren not related in a simple way. whole: 0.38 (0.14), residues: 3866 helix: 1.58 (0.14), residues: 1403 sheet: -0.09 (0.21), residues: 591 loop : -0.63 (0.15), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 483 TYR 0.020 0.001 TYR B 752 PHE 0.023 0.001 PHE A 458 TRP 0.025 0.001 TRP A1192 HIS 0.006 0.001 HIS A 465 Details of bonding type rmsd covalent geometry : bond 0.00344 (33351) covalent geometry : angle 0.54083 (45408) hydrogen bonds : bond 0.03608 ( 1412) hydrogen bonds : angle 4.32341 ( 3988) metal coordination : bond 0.00505 ( 29) metal coordination : angle 3.25663 ( 33) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7732 Ramachandran restraints generated. 3866 Oldfield, 0 Emsley, 3866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7732 Ramachandran restraints generated. 3866 Oldfield, 0 Emsley, 3866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 3479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 423 time to evaluate : 0.996 Fit side-chains revert: symmetry clash REVERT: A 29 ASP cc_start: 0.8296 (p0) cc_final: 0.8016 (p0) REVERT: A 824 GLU cc_start: 0.6880 (pt0) cc_final: 0.6671 (pt0) REVERT: A 868 MET cc_start: 0.6748 (mtm) cc_final: 0.6529 (mtt) REVERT: A 976 LYS cc_start: 0.7499 (tttt) cc_final: 0.7089 (tppt) REVERT: A 1026 ASP cc_start: 0.7661 (t0) cc_final: 0.7082 (t0) REVERT: A 1097 GLU cc_start: 0.7384 (tm-30) cc_final: 0.7038 (tm-30) REVERT: A 1221 MET cc_start: 0.7200 (tpt) cc_final: 0.6845 (tpp) REVERT: A 1306 LYS cc_start: 0.8073 (tptt) cc_final: 0.7744 (tppt) REVERT: B 200 MET cc_start: 0.8507 (tpp) cc_final: 0.8241 (tpt) REVERT: B 334 LYS cc_start: 0.7556 (mmtt) cc_final: 0.7180 (pttm) REVERT: B 345 LYS cc_start: 0.8784 (mmtp) cc_final: 0.8353 (mmmt) REVERT: B 430 ASN cc_start: 0.5485 (t0) cc_final: 0.4810 (p0) REVERT: B 668 LEU cc_start: 0.8013 (pt) cc_final: 0.7744 (tp) REVERT: E 91 CYS cc_start: 0.7362 (p) cc_final: 0.7073 (p) REVERT: H 18 GLU cc_start: 0.7973 (mt-10) cc_final: 0.7162 (pt0) REVERT: H 20 LYS cc_start: 0.6888 (tptm) cc_final: 0.6654 (tptm) REVERT: K 13 PHE cc_start: 0.5925 (p90) cc_final: 0.5445 (m-10) REVERT: K 17 LYS cc_start: 0.8261 (mtpp) cc_final: 0.7825 (mttt) REVERT: R 505 ASN cc_start: 0.6606 (m110) cc_final: 0.5883 (m110) REVERT: R 510 LYS cc_start: 0.7225 (pttm) cc_final: 0.6794 (ptmt) REVERT: R 514 LEU cc_start: 0.6351 (mt) cc_final: 0.5606 (tp) REVERT: R 525 PHE cc_start: 0.4991 (t80) cc_final: 0.4548 (t80) REVERT: R 583 LEU cc_start: 0.7911 (mt) cc_final: 0.7389 (mt) outliers start: 0 outliers final: 0 residues processed: 423 average time/residue: 0.2032 time to fit residues: 136.3652 Evaluate side-chains 366 residues out of total 3479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 366 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 46 optimal weight: 6.9990 chunk 305 optimal weight: 0.0370 chunk 197 optimal weight: 1.9990 chunk 162 optimal weight: 0.8980 chunk 294 optimal weight: 5.9990 chunk 123 optimal weight: 1.9990 chunk 148 optimal weight: 9.9990 chunk 94 optimal weight: 0.7980 chunk 96 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 chunk 16 optimal weight: 5.9990 overall best weight: 0.9060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 143 GLN B 552 ASN ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 92 GLN I 18 GLN ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 511 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.128701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.100249 restraints weight = 470982.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.100761 restraints weight = 339977.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.100368 restraints weight = 321249.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.100406 restraints weight = 324545.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.100273 restraints weight = 315091.911| |-----------------------------------------------------------------------------| r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 33380 Z= 0.120 Angle : 0.540 12.775 45441 Z= 0.278 Chirality : 0.043 0.165 5130 Planarity : 0.004 0.046 5619 Dihedral : 13.517 168.792 5153 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.05 % 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 aren not related in a simple way. whole: 0.43 (0.14), residues: 3866 helix: 1.60 (0.14), residues: 1410 sheet: -0.02 (0.21), residues: 589 loop : -0.61 (0.15), residues: 1867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 438 TYR 0.020 0.001 TYR B 766 PHE 0.023 0.001 PHE A 458 TRP 0.023 0.001 TRP A1192 HIS 0.005 0.001 HIS A 465 Details of bonding type rmsd covalent geometry : bond 0.00282 (33351) covalent geometry : angle 0.53375 (45408) hydrogen bonds : bond 0.03395 ( 1412) hydrogen bonds : angle 4.28482 ( 3988) metal coordination : bond 0.00469 ( 29) metal coordination : angle 3.07196 ( 33) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7732 Ramachandran restraints generated. 3866 Oldfield, 0 Emsley, 3866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7732 Ramachandran restraints generated. 3866 Oldfield, 0 Emsley, 3866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 3479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 416 time to evaluate : 1.386 Fit side-chains revert: symmetry clash REVERT: A 29 ASP cc_start: 0.8210 (p0) cc_final: 0.7859 (p0) REVERT: A 824 GLU cc_start: 0.7034 (pt0) cc_final: 0.6812 (pt0) REVERT: A 976 LYS cc_start: 0.7458 (tttt) cc_final: 0.7093 (tppt) REVERT: A 1026 ASP cc_start: 0.7490 (t0) cc_final: 0.6932 (t0) REVERT: A 1097 GLU cc_start: 0.7309 (tm-30) cc_final: 0.7021 (tm-30) REVERT: A 1221 MET cc_start: 0.7099 (tpt) cc_final: 0.6702 (tpp) REVERT: A 1306 LYS cc_start: 0.8236 (tptt) cc_final: 0.7913 (tppt) REVERT: A 1428 MET cc_start: 0.7611 (mtp) cc_final: 0.7272 (mtp) REVERT: B 200 MET cc_start: 0.8541 (tpp) cc_final: 0.8251 (tpt) REVERT: B 334 LYS cc_start: 0.7566 (mmtt) cc_final: 0.7176 (pttm) REVERT: B 345 LYS cc_start: 0.8745 (mmtp) cc_final: 0.8330 (mmmt) REVERT: B 430 ASN cc_start: 0.5663 (t0) cc_final: 0.4959 (p0) REVERT: B 668 LEU cc_start: 0.7991 (pt) cc_final: 0.7769 (tp) REVERT: E 91 CYS cc_start: 0.7463 (p) cc_final: 0.7255 (p) REVERT: H 18 GLU cc_start: 0.7978 (mt-10) cc_final: 0.7172 (pt0) REVERT: H 20 LYS cc_start: 0.6901 (tptm) cc_final: 0.6665 (tptm) REVERT: K 13 PHE cc_start: 0.5920 (p90) cc_final: 0.5395 (m-10) REVERT: K 17 LYS cc_start: 0.8198 (mtpp) cc_final: 0.7732 (mttt) REVERT: R 510 LYS cc_start: 0.7211 (pttm) cc_final: 0.6784 (ptmt) REVERT: R 514 LEU cc_start: 0.6393 (mt) cc_final: 0.5584 (tp) REVERT: R 525 PHE cc_start: 0.5026 (t80) cc_final: 0.4590 (t80) REVERT: R 583 LEU cc_start: 0.7840 (mt) cc_final: 0.7334 (mt) outliers start: 0 outliers final: 0 residues processed: 416 average time/residue: 0.2120 time to fit residues: 140.7409 Evaluate side-chains 366 residues out of total 3479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 366 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 313 optimal weight: 4.9990 chunk 336 optimal weight: 1.9990 chunk 133 optimal weight: 0.6980 chunk 243 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 45 optimal weight: 0.4980 chunk 347 optimal weight: 10.0000 chunk 387 optimal weight: 10.0000 chunk 66 optimal weight: 5.9990 chunk 76 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 757 GLN B 143 GLN C 51 GLN I 18 GLN ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 511 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.130480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.101113 restraints weight = 467301.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.101604 restraints weight = 342964.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.101184 restraints weight = 323240.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.101215 restraints weight = 323194.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.101106 restraints weight = 321677.816| |-----------------------------------------------------------------------------| r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 33380 Z= 0.177 Angle : 0.582 14.616 45441 Z= 0.300 Chirality : 0.044 0.166 5130 Planarity : 0.004 0.048 5619 Dihedral : 13.568 168.470 5153 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.05 % 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 aren not related in a simple way. whole: 0.33 (0.14), residues: 3866 helix: 1.55 (0.14), residues: 1402 sheet: -0.12 (0.21), residues: 594 loop : -0.67 (0.15), residues: 1870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 438 TYR 0.022 0.001 TYR B 752 PHE 0.023 0.002 PHE A 668 TRP 0.024 0.001 TRP A1192 HIS 0.007 0.001 HIS A 465 Details of bonding type rmsd covalent geometry : bond 0.00436 (33351) covalent geometry : angle 0.57448 (45408) hydrogen bonds : bond 0.03908 ( 1412) hydrogen bonds : angle 4.39900 ( 3988) metal coordination : bond 0.00535 ( 29) metal coordination : angle 3.46077 ( 33) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4258.88 seconds wall clock time: 75 minutes 1.79 seconds (4501.79 seconds total)