Starting phenix.real_space_refine on Thu May 29 18:38:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qq2_18573/05_2025/8qq2_18573.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qq2_18573/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8qq2_18573/05_2025/8qq2_18573.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qq2_18573/05_2025/8qq2_18573.map" model { file = "/net/cci-nas-00/data/ceres_data/8qq2_18573/05_2025/8qq2_18573.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qq2_18573/05_2025/8qq2_18573.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.026 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): 1.26s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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, 'ASP:plan': 1, 'GLU:plan': 3} 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: {'GLN:plan1': 2, 'HIS:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} 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: {'GLN:plan1': 1, 'ARG:plan': 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: {'GLN:plan1': 3, 'GLU:plan': 5, '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: {'GLU:plan': 1, 'ASN:plan1': 2, '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: {'ASP:plan': 1, 'TYR:plan': 1, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 10} 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: 18.29, per 1000 atoms: 0.56 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: 7.57 Conformation dependent library (CDL) restraints added in 3.8 seconds 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: 11.73 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: 16.33 Time building geometry restraints manager: 8.90 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.260 Check model and map are aligned: 0.220 Set scattering table: 0.300 Process input model: 84.790 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 97.220 ------------------------------------------------------------------------------- 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 : 10.51 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (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 TRP 0.077 0.003 TRP R 504 HIS 0.009 0.001 HIS G 14 PHE 0.018 0.002 PHE A1284 TYR 0.061 0.002 TYR R 508 ARG 0.008 0.000 ARG G 16 Details of bonding type rmsd hydrogen bonds : bond 0.15953 ( 1412) hydrogen bonds : angle 6.83870 ( 3988) metal coordination : bond 0.04404 ( 29) metal coordination : angle 6.15092 ( 33) covalent geometry : bond 0.00572 (33351) covalent geometry : angle 0.69099 (45408) *********************** 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 : 3.407 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: 0.4638 time to fit residues: 371.2296 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 : 3.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 331 optimal weight: 0.1980 chunk 297 optimal weight: 9.9990 chunk 164 optimal weight: 0.0980 chunk 101 optimal weight: 0.9990 chunk 200 optimal weight: 0.9990 chunk 158 optimal weight: 6.9990 chunk 307 optimal weight: 8.9990 chunk 118 optimal weight: 0.9980 chunk 186 optimal weight: 2.9990 chunk 228 optimal weight: 2.9990 chunk 355 optimal weight: 0.0870 overall best weight: 0.4760 ------------------------------------------------------------------------------- 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 507 GLN ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 671 ASN A 673 GLN A1129 ASN A1190 GLN A1194 ASN B 90 GLN ** 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 D 38 HIS ** D 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 4 HIS R 509 GLN R 585 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.135155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.106056 restraints weight = 479464.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.106810 restraints weight = 343366.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.106256 restraints weight = 320562.477| |-----------------------------------------------------------------------------| r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 33380 Z= 0.121 Angle : 0.567 10.966 45441 Z= 0.296 Chirality : 0.043 0.168 5130 Planarity : 0.004 0.069 5619 Dihedral : 13.511 165.639 5153 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.57 % Favored : 96.40 % Rotamer: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.14), residues: 3866 helix: 1.29 (0.14), residues: 1395 sheet: -0.26 (0.21), residues: 588 loop : -0.75 (0.14), residues: 1883 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1192 HIS 0.010 0.001 HIS R 585 PHE 0.027 0.002 PHE A 458 TYR 0.020 0.001 TYR L 41 ARG 0.010 0.000 ARG J 47 Details of bonding type rmsd hydrogen bonds : bond 0.03950 ( 1412) hydrogen bonds : angle 4.94137 ( 3988) metal coordination : bond 0.00795 ( 29) metal coordination : angle 3.91286 ( 33) covalent geometry : bond 0.00263 (33351) covalent geometry : angle 0.55758 (45408) *********************** 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 507 residues out of total 3479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 507 time to evaluate : 4.189 Fit side-chains REVERT: A 1026 ASP cc_start: 0.7555 (t0) cc_final: 0.7101 (t0) REVERT: A 1097 GLU cc_start: 0.7128 (tm-30) cc_final: 0.6927 (tm-30) REVERT: A 1183 SER cc_start: 0.7844 (t) cc_final: 0.7505 (m) REVERT: A 1215 GLU cc_start: 0.7907 (mm-30) cc_final: 0.7412 (mt-10) REVERT: A 1221 MET cc_start: 0.7293 (tpt) cc_final: 0.7036 (tpp) REVERT: A 1255 LEU cc_start: 0.8096 (tt) cc_final: 0.7719 (mt) REVERT: A 1261 ILE cc_start: 0.8299 (mm) cc_final: 0.7917 (tt) REVERT: A 1306 LYS cc_start: 0.7821 (tptt) cc_final: 0.7539 (tppt) REVERT: B 35 ASP cc_start: 0.7660 (m-30) cc_final: 0.7412 (m-30) REVERT: B 270 ILE cc_start: 0.8487 (mm) cc_final: 0.8115 (tp) REVERT: B 298 MET cc_start: 0.7149 (mmm) cc_final: 0.6888 (mmm) REVERT: B 334 LYS cc_start: 0.7860 (mmtt) cc_final: 0.7241 (pttm) REVERT: B 430 ASN cc_start: 0.5197 (t0) cc_final: 0.4535 (p0) REVERT: B 668 LEU cc_start: 0.7998 (pt) cc_final: 0.7583 (tp) REVERT: E 65 ASN cc_start: 0.7978 (m-40) cc_final: 0.7657 (t0) REVERT: E 134 GLU cc_start: 0.7450 (mt-10) cc_final: 0.7169 (mt-10) REVERT: H 18 GLU cc_start: 0.7891 (mt-10) cc_final: 0.7114 (pt0) REVERT: H 20 LYS cc_start: 0.6725 (tptm) cc_final: 0.6439 (tptm) REVERT: I 21 ASN cc_start: 0.9178 (m-40) cc_final: 0.8975 (m-40) REVERT: D 59 GLU cc_start: 0.6660 (tp30) cc_final: 0.6442 (mt-10) REVERT: G 70 VAL cc_start: 0.5863 (t) cc_final: 0.4909 (m) REVERT: R 511 GLN cc_start: 0.7853 (mm-40) cc_final: 0.7314 (mm-40) REVERT: R 512 MET cc_start: 0.6013 (mmm) cc_final: 0.5632 (mmp) REVERT: R 514 LEU cc_start: 0.5601 (mt) cc_final: 0.4876 (tp) REVERT: R 583 LEU cc_start: 0.7643 (mt) cc_final: 0.7213 (mt) outliers start: 0 outliers final: 0 residues processed: 507 average time/residue: 0.4537 time to fit residues: 366.1194 Evaluate side-chains 374 residues out of total 3479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 374 time to evaluate : 3.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 197 optimal weight: 0.9980 chunk 110 optimal weight: 9.9990 chunk 296 optimal weight: 0.0870 chunk 242 optimal weight: 0.8980 chunk 98 optimal weight: 5.9990 chunk 356 optimal weight: 20.0000 chunk 385 optimal weight: 20.0000 chunk 317 optimal weight: 6.9990 chunk 353 optimal weight: 3.9990 chunk 121 optimal weight: 4.9990 chunk 286 optimal weight: 0.9980 overall best weight: 1.3960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 673 GLN A1129 ASN A1190 GLN A1194 ASN A1457 ASN B 56 GLN B1040 GLN E 129 GLN I 18 GLN ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 34 ASN D 48 ASN G 14 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.132579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.102994 restraints weight = 477513.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.103440 restraints weight = 339914.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.103008 restraints weight = 320314.259| |-----------------------------------------------------------------------------| r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 33380 Z= 0.152 Angle : 0.552 10.871 45441 Z= 0.288 Chirality : 0.043 0.164 5130 Planarity : 0.004 0.076 5619 Dihedral : 13.511 167.305 5153 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.27 % Favored : 95.71 % Rotamer: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.14), residues: 3866 helix: 1.39 (0.14), residues: 1397 sheet: -0.31 (0.21), residues: 587 loop : -0.77 (0.14), residues: 1882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1192 HIS 0.009 0.001 HIS C 60 PHE 0.021 0.002 PHE A 458 TYR 0.021 0.001 TYR B 752 ARG 0.010 0.000 ARG B 721 Details of bonding type rmsd hydrogen bonds : bond 0.03960 ( 1412) hydrogen bonds : angle 4.69603 ( 3988) metal coordination : bond 0.00611 ( 29) metal coordination : angle 3.57966 ( 33) covalent geometry : bond 0.00366 (33351) covalent geometry : angle 0.54410 (45408) *********************** 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 454 residues out of total 3479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 454 time to evaluate : 3.587 Fit side-chains REVERT: A 1097 GLU cc_start: 0.7261 (tm-30) cc_final: 0.6862 (tm-30) REVERT: A 1221 MET cc_start: 0.7297 (tpt) cc_final: 0.7007 (tpp) REVERT: A 1255 LEU cc_start: 0.8059 (tt) cc_final: 0.7590 (mt) REVERT: A 1306 LYS cc_start: 0.7886 (tptt) cc_final: 0.7609 (tppt) REVERT: B 35 ASP cc_start: 0.7619 (m-30) cc_final: 0.7371 (m-30) REVERT: B 169 ARG cc_start: 0.5470 (mmm-85) cc_final: 0.5229 (mmm-85) REVERT: B 270 ILE cc_start: 0.8563 (mm) cc_final: 0.8127 (tp) REVERT: B 294 ASP cc_start: 0.7392 (m-30) cc_final: 0.6961 (m-30) REVERT: B 298 MET cc_start: 0.7281 (mmm) cc_final: 0.7062 (mmm) REVERT: B 334 LYS cc_start: 0.7747 (mmtt) cc_final: 0.7206 (pttm) REVERT: B 405 ARG cc_start: 0.7432 (mtm180) cc_final: 0.7114 (mtm-85) REVERT: B 430 ASN cc_start: 0.5307 (t0) cc_final: 0.4570 (p0) REVERT: C 17 GLU cc_start: 0.7660 (pm20) cc_final: 0.7168 (tp30) REVERT: E 65 ASN cc_start: 0.8013 (m-40) cc_final: 0.7672 (t0) REVERT: E 91 CYS cc_start: 0.7281 (p) cc_final: 0.7068 (p) REVERT: H 18 GLU cc_start: 0.8038 (mt-10) cc_final: 0.7273 (pt0) REVERT: H 20 LYS cc_start: 0.7021 (tptm) cc_final: 0.6803 (tptm) REVERT: I 21 ASN cc_start: 0.9240 (m-40) cc_final: 0.8976 (m-40) REVERT: D 59 GLU cc_start: 0.6820 (tp30) cc_final: 0.6545 (mt-10) REVERT: G 48 VAL cc_start: 0.6468 (t) cc_final: 0.6044 (t) REVERT: R 511 GLN cc_start: 0.7716 (mm-40) cc_final: 0.7479 (mm-40) REVERT: R 514 LEU cc_start: 0.5929 (mt) cc_final: 0.5196 (tp) REVERT: R 583 LEU cc_start: 0.7704 (mt) cc_final: 0.7179 (mt) outliers start: 0 outliers final: 0 residues processed: 454 average time/residue: 0.4717 time to fit residues: 342.3837 Evaluate side-chains 365 residues out of total 3479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 365 time to evaluate : 3.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 352 optimal weight: 20.0000 chunk 268 optimal weight: 0.6980 chunk 185 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 170 optimal weight: 5.9990 chunk 239 optimal weight: 0.5980 chunk 357 optimal weight: 6.9990 chunk 378 optimal weight: 5.9990 chunk 186 optimal weight: 3.9990 chunk 339 optimal weight: 2.9990 chunk 102 optimal weight: 0.8980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 GLN B 452 ASN 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** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.132649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.103187 restraints weight = 476406.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.103638 restraints weight = 342746.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.103266 restraints weight = 325407.386| |-----------------------------------------------------------------------------| r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 33380 Z= 0.137 Angle : 0.539 12.359 45441 Z= 0.279 Chirality : 0.043 0.215 5130 Planarity : 0.004 0.062 5619 Dihedral : 13.495 168.061 5153 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.14), residues: 3866 helix: 1.43 (0.14), residues: 1402 sheet: -0.27 (0.21), residues: 585 loop : -0.73 (0.14), residues: 1879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1192 HIS 0.006 0.001 HIS A 465 PHE 0.024 0.002 PHE E 73 TYR 0.030 0.001 TYR B1048 ARG 0.006 0.000 ARG H 24 Details of bonding type rmsd hydrogen bonds : bond 0.03655 ( 1412) hydrogen bonds : angle 4.56932 ( 3988) metal coordination : bond 0.00466 ( 29) metal coordination : angle 3.40970 ( 33) covalent geometry : bond 0.00328 (33351) covalent geometry : angle 0.53122 (45408) *********************** 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 438 residues out of total 3479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 438 time to evaluate : 3.859 Fit side-chains REVERT: A 57 LEU cc_start: 0.8154 (mm) cc_final: 0.7951 (mm) REVERT: A 1097 GLU cc_start: 0.7319 (tm-30) cc_final: 0.6898 (tm-30) REVERT: A 1221 MET cc_start: 0.7171 (tpt) cc_final: 0.6856 (tpp) REVERT: A 1261 ILE cc_start: 0.8192 (mm) cc_final: 0.7979 (mm) REVERT: A 1292 MET cc_start: 0.7375 (ttm) cc_final: 0.7128 (ttm) REVERT: A 1306 LYS cc_start: 0.7994 (tptt) cc_final: 0.7658 (tppt) REVERT: B 35 ASP cc_start: 0.7605 (m-30) cc_final: 0.7327 (m-30) REVERT: B 61 ASP cc_start: 0.7068 (t70) cc_final: 0.6862 (t0) REVERT: B 200 MET cc_start: 0.8333 (tpp) cc_final: 0.7801 (tpt) REVERT: B 270 ILE cc_start: 0.8573 (mm) cc_final: 0.8336 (mm) REVERT: B 294 ASP cc_start: 0.7621 (m-30) cc_final: 0.6877 (m-30) REVERT: B 334 LYS cc_start: 0.7751 (mmtt) cc_final: 0.7219 (pttm) REVERT: B 430 ASN cc_start: 0.5114 (t0) cc_final: 0.4479 (p0) REVERT: B 668 LEU cc_start: 0.7989 (pt) cc_final: 0.7689 (tp) REVERT: C 17 GLU cc_start: 0.7534 (pm20) cc_final: 0.7146 (tp30) REVERT: H 18 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7222 (pt0) REVERT: H 20 LYS cc_start: 0.7115 (tptm) cc_final: 0.6832 (tptm) REVERT: I 15 ARG cc_start: 0.5951 (ptp90) cc_final: 0.5751 (mtm-85) REVERT: I 21 ASN cc_start: 0.9217 (m-40) cc_final: 0.8938 (m-40) REVERT: D 59 GLU cc_start: 0.6795 (tp30) cc_final: 0.6527 (mt-10) REVERT: R 511 GLN cc_start: 0.7969 (mm-40) cc_final: 0.7659 (mm-40) REVERT: R 514 LEU cc_start: 0.6012 (mt) cc_final: 0.5162 (tp) REVERT: R 583 LEU cc_start: 0.7766 (mt) cc_final: 0.7272 (mt) outliers start: 0 outliers final: 0 residues processed: 438 average time/residue: 0.4469 time to fit residues: 313.1593 Evaluate side-chains 367 residues out of total 3479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 367 time to evaluate : 3.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 315 optimal weight: 5.9990 chunk 215 optimal weight: 8.9990 chunk 5 optimal weight: 0.7980 chunk 282 optimal weight: 2.9990 chunk 156 optimal weight: 8.9990 chunk 323 optimal weight: 7.9990 chunk 261 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 193 optimal weight: 0.9980 chunk 340 optimal weight: 0.9980 chunk 95 optimal weight: 0.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 740 GLN ** B 968 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 18 GLN ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.132825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.104077 restraints weight = 474369.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.104579 restraints weight = 338737.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.104152 restraints weight = 320447.823| |-----------------------------------------------------------------------------| r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 33380 Z= 0.145 Angle : 0.540 12.782 45441 Z= 0.280 Chirality : 0.043 0.189 5130 Planarity : 0.004 0.078 5619 Dihedral : 13.505 169.064 5153 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.14), residues: 3866 helix: 1.46 (0.14), residues: 1394 sheet: -0.15 (0.21), residues: 580 loop : -0.71 (0.14), residues: 1892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1192 HIS 0.007 0.001 HIS A 465 PHE 0.024 0.001 PHE A 668 TYR 0.023 0.001 TYR B 752 ARG 0.008 0.000 ARG B1062 Details of bonding type rmsd hydrogen bonds : bond 0.03657 ( 1412) hydrogen bonds : angle 4.47788 ( 3988) metal coordination : bond 0.00905 ( 29) metal coordination : angle 3.26805 ( 33) covalent geometry : bond 0.00349 (33351) covalent geometry : angle 0.53306 (45408) *********************** 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 431 residues out of total 3479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 431 time to evaluate : 3.407 Fit side-chains revert: symmetry clash REVERT: A 33 ARG cc_start: 0.7440 (mtp85) cc_final: 0.7202 (mtm110) REVERT: A 361 PHE cc_start: 0.7550 (m-80) cc_final: 0.7291 (m-80) REVERT: A 1097 GLU cc_start: 0.7446 (tm-30) cc_final: 0.6953 (tm-30) REVERT: A 1221 MET cc_start: 0.7310 (tpt) cc_final: 0.6968 (tpp) REVERT: A 1306 LYS cc_start: 0.7912 (tptt) cc_final: 0.7641 (tppt) REVERT: B 35 ASP cc_start: 0.7547 (m-30) cc_final: 0.7325 (m-30) REVERT: B 61 ASP cc_start: 0.6980 (t70) cc_final: 0.6775 (t0) REVERT: B 200 MET cc_start: 0.8304 (tpp) cc_final: 0.7786 (tpt) REVERT: B 294 ASP cc_start: 0.8007 (m-30) cc_final: 0.7060 (m-30) REVERT: B 334 LYS cc_start: 0.7759 (mmtt) cc_final: 0.7249 (pttm) REVERT: B 381 GLU cc_start: 0.7245 (mp0) cc_final: 0.6974 (mp0) REVERT: B 407 MET cc_start: 0.7902 (mtt) cc_final: 0.7634 (mtt) REVERT: B 430 ASN cc_start: 0.5374 (t0) cc_final: 0.4667 (p0) REVERT: B 668 LEU cc_start: 0.7946 (pt) cc_final: 0.7666 (tp) REVERT: C 17 GLU cc_start: 0.7581 (pm20) cc_final: 0.7248 (tp30) REVERT: E 91 CYS cc_start: 0.7506 (p) cc_final: 0.7288 (p) REVERT: E 97 GLU cc_start: 0.7732 (tp30) cc_final: 0.7424 (mm-30) REVERT: H 18 GLU cc_start: 0.7973 (mt-10) cc_final: 0.7196 (pt0) REVERT: H 20 LYS cc_start: 0.7086 (tptm) cc_final: 0.6832 (tptm) REVERT: I 21 ASN cc_start: 0.9158 (m-40) cc_final: 0.8930 (m-40) REVERT: D 59 GLU cc_start: 0.6837 (tp30) cc_final: 0.6553 (mt-10) REVERT: G 66 VAL cc_start: 0.8632 (p) cc_final: 0.8338 (t) REVERT: R 511 GLN cc_start: 0.7954 (mm-40) cc_final: 0.7535 (mm-40) REVERT: R 514 LEU cc_start: 0.6052 (mt) cc_final: 0.5292 (tp) REVERT: R 525 PHE cc_start: 0.4795 (t80) cc_final: 0.4422 (t80) REVERT: R 583 LEU cc_start: 0.7736 (mt) cc_final: 0.7197 (mt) outliers start: 0 outliers final: 0 residues processed: 431 average time/residue: 0.4470 time to fit residues: 307.8967 Evaluate side-chains 367 residues out of total 3479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 367 time to evaluate : 3.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 127 optimal weight: 5.9990 chunk 341 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 chunk 222 optimal weight: 0.8980 chunk 93 optimal weight: 5.9990 chunk 379 optimal weight: 9.9990 chunk 314 optimal weight: 0.9980 chunk 175 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 125 optimal weight: 3.9990 chunk 199 optimal weight: 0.0980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 341 GLN ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1093 GLN A1299 GLN B 143 GLN B 552 ASN E 92 GLN I 18 GLN ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.133124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.103925 restraints weight = 471640.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.104414 restraints weight = 336001.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.103980 restraints weight = 317694.467| |-----------------------------------------------------------------------------| r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 33380 Z= 0.113 Angle : 0.519 12.158 45441 Z= 0.269 Chirality : 0.042 0.164 5130 Planarity : 0.004 0.049 5619 Dihedral : 13.478 169.303 5153 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.14), residues: 3866 helix: 1.56 (0.14), residues: 1400 sheet: -0.06 (0.21), residues: 579 loop : -0.66 (0.15), residues: 1887 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A1192 HIS 0.005 0.001 HIS K 69 PHE 0.019 0.001 PHE A 668 TYR 0.018 0.001 TYR B 752 ARG 0.006 0.000 ARG B 438 Details of bonding type rmsd hydrogen bonds : bond 0.03358 ( 1412) hydrogen bonds : angle 4.35904 ( 3988) metal coordination : bond 0.00581 ( 29) metal coordination : angle 2.94305 ( 33) covalent geometry : bond 0.00262 (33351) covalent geometry : angle 0.51269 (45408) *********************** 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 439 residues out of total 3479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 439 time to evaluate : 3.958 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1026 ASP cc_start: 0.7526 (t0) cc_final: 0.6991 (t0) REVERT: A 1097 GLU cc_start: 0.7386 (tm-30) cc_final: 0.6948 (tm-30) REVERT: A 1221 MET cc_start: 0.7338 (tpt) cc_final: 0.6991 (tpp) REVERT: A 1306 LYS cc_start: 0.7906 (tptt) cc_final: 0.7670 (tppt) REVERT: B 35 ASP cc_start: 0.7592 (m-30) cc_final: 0.7316 (m-30) REVERT: B 61 ASP cc_start: 0.7058 (t70) cc_final: 0.6805 (t0) REVERT: B 200 MET cc_start: 0.8470 (tpp) cc_final: 0.7773 (tpt) REVERT: B 294 ASP cc_start: 0.8104 (m-30) cc_final: 0.7206 (m-30) REVERT: B 334 LYS cc_start: 0.7686 (mmtt) cc_final: 0.7224 (pttm) REVERT: B 407 MET cc_start: 0.7937 (mtt) cc_final: 0.7680 (mtt) REVERT: B 430 ASN cc_start: 0.5361 (t0) cc_final: 0.4631 (p0) REVERT: B 668 LEU cc_start: 0.7948 (pt) cc_final: 0.7723 (tp) REVERT: C 17 GLU cc_start: 0.7572 (pm20) cc_final: 0.7176 (tp30) REVERT: E 91 CYS cc_start: 0.7419 (p) cc_final: 0.7163 (p) REVERT: E 97 GLU cc_start: 0.7667 (tp30) cc_final: 0.7408 (mm-30) REVERT: H 18 GLU cc_start: 0.7967 (mt-10) cc_final: 0.7227 (pt0) REVERT: H 20 LYS cc_start: 0.7052 (tptm) cc_final: 0.6837 (tptm) REVERT: I 21 ASN cc_start: 0.9133 (m-40) cc_final: 0.8914 (m-40) REVERT: D 59 GLU cc_start: 0.6732 (tp30) cc_final: 0.6495 (mt-10) REVERT: R 514 LEU cc_start: 0.6142 (mt) cc_final: 0.5309 (tp) REVERT: R 525 PHE cc_start: 0.5000 (t80) cc_final: 0.4685 (t80) REVERT: R 583 LEU cc_start: 0.7755 (mt) cc_final: 0.7232 (mt) outliers start: 0 outliers final: 0 residues processed: 439 average time/residue: 0.4449 time to fit residues: 312.6369 Evaluate side-chains 361 residues out of total 3479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 361 time to evaluate : 3.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 365 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 216 optimal weight: 7.9990 chunk 276 optimal weight: 0.9980 chunk 214 optimal weight: 3.9990 chunk 319 optimal weight: 9.9990 chunk 211 optimal weight: 2.9990 chunk 377 optimal weight: 9.9990 chunk 236 optimal weight: 0.7980 chunk 230 optimal weight: 1.9990 chunk 174 optimal weight: 4.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 GLN A1093 GLN B 143 GLN E 95 GLN I 18 GLN ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 21 ASN R 511 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.128798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.100465 restraints weight = 477062.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.100928 restraints weight = 346364.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.100491 restraints weight = 328450.681| |-----------------------------------------------------------------------------| r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 33380 Z= 0.170 Angle : 0.563 11.785 45441 Z= 0.291 Chirality : 0.044 0.191 5130 Planarity : 0.004 0.051 5619 Dihedral : 13.541 169.574 5153 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 0.03 % Allowed : 1.09 % Favored : 98.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.14), residues: 3866 helix: 1.47 (0.14), residues: 1400 sheet: -0.13 (0.21), residues: 582 loop : -0.68 (0.14), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A1192 HIS 0.007 0.001 HIS A 465 PHE 0.027 0.002 PHE A 668 TYR 0.040 0.001 TYR B1048 ARG 0.006 0.000 ARG B 438 Details of bonding type rmsd hydrogen bonds : bond 0.03833 ( 1412) hydrogen bonds : angle 4.45015 ( 3988) metal coordination : bond 0.00583 ( 29) metal coordination : angle 3.32499 ( 33) covalent geometry : bond 0.00421 (33351) covalent geometry : angle 0.55573 (45408) *********************** 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 428 residues out of total 3479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 427 time to evaluate : 3.652 Fit side-chains revert: symmetry clash REVERT: A 361 PHE cc_start: 0.7773 (m-80) cc_final: 0.7502 (m-80) REVERT: A 1026 ASP cc_start: 0.7531 (t0) cc_final: 0.6983 (t0) REVERT: A 1097 GLU cc_start: 0.7362 (tm-30) cc_final: 0.7017 (tm-30) REVERT: A 1221 MET cc_start: 0.7204 (tpt) cc_final: 0.6811 (tpp) REVERT: A 1306 LYS cc_start: 0.7996 (tptt) cc_final: 0.7701 (tppt) REVERT: B 35 ASP cc_start: 0.7716 (m-30) cc_final: 0.7475 (m-30) REVERT: B 200 MET cc_start: 0.8383 (tpp) cc_final: 0.7702 (tpt) REVERT: B 294 ASP cc_start: 0.7971 (m-30) cc_final: 0.7061 (m-30) REVERT: B 298 MET cc_start: 0.7157 (mmm) cc_final: 0.6921 (mmm) REVERT: B 334 LYS cc_start: 0.7655 (mmtt) cc_final: 0.7206 (pttm) REVERT: B 430 ASN cc_start: 0.5119 (t0) cc_final: 0.4739 (p0) REVERT: B 668 LEU cc_start: 0.7969 (pt) cc_final: 0.7718 (tp) REVERT: C 17 GLU cc_start: 0.7394 (pm20) cc_final: 0.7116 (tp30) REVERT: E 91 CYS cc_start: 0.7366 (p) cc_final: 0.7142 (p) REVERT: E 97 GLU cc_start: 0.7684 (tp30) cc_final: 0.7381 (mm-30) REVERT: H 18 GLU cc_start: 0.7999 (mt-10) cc_final: 0.7195 (pt0) REVERT: H 20 LYS cc_start: 0.6962 (tptm) cc_final: 0.6739 (tptm) REVERT: H 136 GLU cc_start: 0.6831 (mp0) cc_final: 0.6569 (mp0) REVERT: R 514 LEU cc_start: 0.6274 (mt) cc_final: 0.5533 (tp) REVERT: R 525 PHE cc_start: 0.5096 (t80) cc_final: 0.4722 (t80) REVERT: R 583 LEU cc_start: 0.7782 (mt) cc_final: 0.7252 (mt) outliers start: 1 outliers final: 0 residues processed: 428 average time/residue: 0.4453 time to fit residues: 307.1552 Evaluate side-chains 360 residues out of total 3479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 360 time to evaluate : 3.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 233 optimal weight: 3.9990 chunk 150 optimal weight: 0.8980 chunk 225 optimal weight: 2.9990 chunk 113 optimal weight: 9.9990 chunk 74 optimal weight: 0.3980 chunk 73 optimal weight: 0.9990 chunk 240 optimal weight: 4.9990 chunk 257 optimal weight: 2.9990 chunk 186 optimal weight: 1.9990 chunk 35 optimal weight: 7.9990 chunk 296 optimal weight: 0.8980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1093 GLN A1190 GLN A1194 ASN B 143 GLN B 552 ASN ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 92 GLN E 95 GLN I 18 GLN ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 511 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.130927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.101816 restraints weight = 470725.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.102376 restraints weight = 336010.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.101902 restraints weight = 318739.558| |-----------------------------------------------------------------------------| r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 33380 Z= 0.126 Angle : 0.535 13.044 45441 Z= 0.277 Chirality : 0.043 0.166 5130 Planarity : 0.004 0.047 5619 Dihedral : 13.520 169.282 5153 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.14), residues: 3866 helix: 1.53 (0.14), residues: 1400 sheet: -0.08 (0.21), residues: 583 loop : -0.64 (0.15), residues: 1883 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A1192 HIS 0.005 0.001 HIS A 465 PHE 0.028 0.001 PHE A 458 TYR 0.016 0.001 TYR B 752 ARG 0.006 0.000 ARG B 438 Details of bonding type rmsd hydrogen bonds : bond 0.03476 ( 1412) hydrogen bonds : angle 4.35173 ( 3988) metal coordination : bond 0.00523 ( 29) metal coordination : angle 3.00209 ( 33) covalent geometry : bond 0.00299 (33351) covalent geometry : angle 0.52866 (45408) *********************** 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 428 residues out of total 3479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 428 time to evaluate : 3.392 Fit side-chains revert: symmetry clash REVERT: A 361 PHE cc_start: 0.7515 (m-80) cc_final: 0.7283 (m-80) REVERT: A 976 LYS cc_start: 0.7390 (tttt) cc_final: 0.6993 (tppt) REVERT: A 1026 ASP cc_start: 0.7547 (t0) cc_final: 0.6998 (t0) REVERT: A 1097 GLU cc_start: 0.7438 (tm-30) cc_final: 0.7083 (tm-30) REVERT: A 1221 MET cc_start: 0.7234 (tpt) cc_final: 0.6838 (tpp) REVERT: A 1306 LYS cc_start: 0.8035 (tptt) cc_final: 0.7706 (tppt) REVERT: B 200 MET cc_start: 0.8449 (tpp) cc_final: 0.7725 (tpt) REVERT: B 270 ILE cc_start: 0.8493 (mm) cc_final: 0.8062 (tp) REVERT: B 294 ASP cc_start: 0.7950 (m-30) cc_final: 0.7039 (m-30) REVERT: B 298 MET cc_start: 0.7172 (mmm) cc_final: 0.6927 (mmm) REVERT: B 334 LYS cc_start: 0.7653 (mmtt) cc_final: 0.7224 (pttm) REVERT: B 345 LYS cc_start: 0.8852 (mmtp) cc_final: 0.8323 (mmmt) REVERT: B 430 ASN cc_start: 0.5440 (t0) cc_final: 0.4812 (p0) REVERT: B 668 LEU cc_start: 0.8075 (pt) cc_final: 0.7785 (tp) REVERT: C 17 GLU cc_start: 0.7317 (pm20) cc_final: 0.7099 (tp30) REVERT: E 91 CYS cc_start: 0.7502 (p) cc_final: 0.7218 (p) REVERT: E 97 GLU cc_start: 0.7658 (tp30) cc_final: 0.7405 (mm-30) REVERT: H 18 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7262 (pt0) REVERT: H 20 LYS cc_start: 0.7017 (tptm) cc_final: 0.6744 (tptm) REVERT: K 17 LYS cc_start: 0.8199 (mtpp) cc_final: 0.7745 (mttt) REVERT: R 514 LEU cc_start: 0.6307 (mt) cc_final: 0.5543 (tp) REVERT: R 525 PHE cc_start: 0.4976 (t80) cc_final: 0.4554 (t80) REVERT: R 583 LEU cc_start: 0.7878 (mt) cc_final: 0.7339 (mt) outliers start: 0 outliers final: 0 residues processed: 428 average time/residue: 0.4890 time to fit residues: 333.5515 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 : 3.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 343 optimal weight: 2.9990 chunk 361 optimal weight: 3.9990 chunk 330 optimal weight: 0.6980 chunk 352 optimal weight: 7.9990 chunk 211 optimal weight: 0.6980 chunk 153 optimal weight: 3.9990 chunk 276 optimal weight: 1.9990 chunk 108 optimal weight: 9.9990 chunk 318 optimal weight: 0.9980 chunk 332 optimal weight: 0.0670 chunk 350 optimal weight: 2.9990 overall best weight: 0.8920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 757 GLN A1093 GLN A1299 GLN B 143 GLN C 51 GLN E 95 GLN H 76 ASN I 18 GLN ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 21 ASN R 511 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.131156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.102196 restraints weight = 474615.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.102575 restraints weight = 338365.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.102287 restraints weight = 327198.509| |-----------------------------------------------------------------------------| r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 33380 Z= 0.119 Angle : 0.530 11.441 45441 Z= 0.274 Chirality : 0.043 0.172 5130 Planarity : 0.004 0.047 5619 Dihedral : 13.503 169.419 5153 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 0.03 % Allowed : 0.30 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.14), residues: 3866 helix: 1.59 (0.14), residues: 1405 sheet: -0.06 (0.21), residues: 590 loop : -0.61 (0.15), residues: 1871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A1192 HIS 0.005 0.001 HIS A 465 PHE 0.028 0.001 PHE A 458 TYR 0.015 0.001 TYR B 752 ARG 0.006 0.000 ARG B 438 Details of bonding type rmsd hydrogen bonds : bond 0.03398 ( 1412) hydrogen bonds : angle 4.29408 ( 3988) metal coordination : bond 0.00505 ( 29) metal coordination : angle 2.99073 ( 33) covalent geometry : bond 0.00280 (33351) covalent geometry : angle 0.52421 (45408) *********************** 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 425 residues out of total 3479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 424 time to evaluate : 3.492 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 361 PHE cc_start: 0.7547 (m-80) cc_final: 0.7346 (m-80) REVERT: A 824 GLU cc_start: 0.7099 (pt0) cc_final: 0.6894 (pt0) REVERT: A 976 LYS cc_start: 0.7472 (tttt) cc_final: 0.7081 (tppt) REVERT: A 1026 ASP cc_start: 0.7635 (t0) cc_final: 0.7079 (t0) REVERT: A 1097 GLU cc_start: 0.7349 (tm-30) cc_final: 0.7139 (tm-30) REVERT: A 1221 MET cc_start: 0.7227 (tpt) cc_final: 0.6860 (tpp) REVERT: A 1306 LYS cc_start: 0.8086 (tptt) cc_final: 0.7775 (tppt) REVERT: A 1428 MET cc_start: 0.7045 (mtm) cc_final: 0.6714 (mtp) REVERT: B 200 MET cc_start: 0.8442 (tpp) cc_final: 0.8215 (tpt) REVERT: B 239 MET cc_start: 0.7914 (ttt) cc_final: 0.7713 (ttt) REVERT: B 270 ILE cc_start: 0.8485 (mm) cc_final: 0.8076 (tp) REVERT: B 294 ASP cc_start: 0.7885 (m-30) cc_final: 0.7031 (m-30) REVERT: B 298 MET cc_start: 0.7393 (mmm) cc_final: 0.7121 (mmm) REVERT: B 334 LYS cc_start: 0.7575 (mmtt) cc_final: 0.7205 (pttm) REVERT: B 345 LYS cc_start: 0.8755 (mmtp) cc_final: 0.8311 (mmmt) REVERT: B 430 ASN cc_start: 0.5449 (t0) cc_final: 0.4773 (p0) REVERT: B 668 LEU cc_start: 0.7994 (pt) cc_final: 0.7738 (tp) REVERT: C 17 GLU cc_start: 0.7521 (pm20) cc_final: 0.7257 (tp30) REVERT: E 91 CYS cc_start: 0.7415 (p) cc_final: 0.7171 (p) REVERT: E 97 GLU cc_start: 0.7557 (tp30) cc_final: 0.7260 (mm-30) REVERT: H 18 GLU cc_start: 0.8010 (mt-10) cc_final: 0.7225 (pt0) REVERT: H 20 LYS cc_start: 0.6933 (tptm) cc_final: 0.6710 (tptm) REVERT: H 136 GLU cc_start: 0.6782 (mp0) cc_final: 0.6582 (mp0) REVERT: I 60 HIS cc_start: 0.5329 (t70) cc_final: 0.5089 (t70) REVERT: K 17 LYS cc_start: 0.8236 (mtpp) cc_final: 0.7766 (mttt) REVERT: R 505 ASN cc_start: 0.6543 (m110) cc_final: 0.5930 (m110) REVERT: R 514 LEU cc_start: 0.6269 (mt) cc_final: 0.5559 (tp) REVERT: R 525 PHE cc_start: 0.4919 (t80) cc_final: 0.4474 (t80) REVERT: R 583 LEU cc_start: 0.7926 (mt) cc_final: 0.7386 (mt) outliers start: 1 outliers final: 1 residues processed: 424 average time/residue: 0.4474 time to fit residues: 303.0659 Evaluate side-chains 369 residues out of total 3479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 368 time to evaluate : 3.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 231 optimal weight: 7.9990 chunk 372 optimal weight: 5.9990 chunk 227 optimal weight: 3.9990 chunk 176 optimal weight: 9.9990 chunk 258 optimal weight: 0.6980 chunk 390 optimal weight: 10.0000 chunk 359 optimal weight: 8.9990 chunk 310 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 240 optimal weight: 1.9990 chunk 190 optimal weight: 0.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN A1093 GLN B 143 GLN B 552 ASN E 92 GLN E 95 GLN I 18 GLN ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 511 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.131214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.102111 restraints weight = 468477.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.102608 restraints weight = 339322.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.102218 restraints weight = 319658.966| |-----------------------------------------------------------------------------| r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 33380 Z= 0.141 Angle : 0.544 11.116 45441 Z= 0.282 Chirality : 0.043 0.164 5130 Planarity : 0.004 0.047 5619 Dihedral : 13.519 169.161 5153 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.03 % Allowed : 0.27 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.14), residues: 3866 helix: 1.59 (0.14), residues: 1402 sheet: -0.05 (0.21), residues: 585 loop : -0.61 (0.15), residues: 1879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A1192 HIS 0.006 0.001 HIS A 465 PHE 0.026 0.001 PHE A 458 TYR 0.028 0.001 TYR B 752 ARG 0.007 0.000 ARG B1064 Details of bonding type rmsd hydrogen bonds : bond 0.03553 ( 1412) hydrogen bonds : angle 4.31439 ( 3988) metal coordination : bond 0.00494 ( 29) metal coordination : angle 3.05549 ( 33) covalent geometry : bond 0.00342 (33351) covalent geometry : angle 0.53804 (45408) ********************** 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 414 residues out of total 3479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 413 time to evaluate : 3.775 Fit side-chains revert: symmetry clash REVERT: A 361 PHE cc_start: 0.7758 (m-80) cc_final: 0.7493 (m-80) REVERT: A 976 LYS cc_start: 0.7475 (tttt) cc_final: 0.7082 (tppt) REVERT: A 1026 ASP cc_start: 0.7482 (t0) cc_final: 0.6944 (t0) REVERT: A 1097 GLU cc_start: 0.7315 (tm-30) cc_final: 0.7018 (tm-30) REVERT: A 1221 MET cc_start: 0.7096 (tpt) cc_final: 0.6686 (tpp) REVERT: A 1306 LYS cc_start: 0.8216 (tptt) cc_final: 0.7861 (tppt) REVERT: B 294 ASP cc_start: 0.7935 (m-30) cc_final: 0.7038 (m-30) REVERT: B 334 LYS cc_start: 0.7594 (mmtt) cc_final: 0.7168 (pttm) REVERT: B 345 LYS cc_start: 0.8781 (mmtp) cc_final: 0.8323 (mmmt) REVERT: B 430 ASN cc_start: 0.5619 (t0) cc_final: 0.4960 (p0) REVERT: B 668 LEU cc_start: 0.8003 (pt) cc_final: 0.7757 (tp) REVERT: C 213 GLU cc_start: 0.6957 (mm-30) cc_final: 0.6634 (tp30) REVERT: E 91 CYS cc_start: 0.7592 (p) cc_final: 0.7321 (p) REVERT: E 97 GLU cc_start: 0.7481 (tp30) cc_final: 0.7172 (mm-30) REVERT: H 18 GLU cc_start: 0.7993 (mt-10) cc_final: 0.7213 (pt0) REVERT: H 20 LYS cc_start: 0.6916 (tptm) cc_final: 0.6675 (tptm) REVERT: H 136 GLU cc_start: 0.6808 (mp0) cc_final: 0.6582 (mp0) REVERT: I 60 HIS cc_start: 0.5417 (t70) cc_final: 0.5156 (t70) REVERT: K 17 LYS cc_start: 0.8190 (mtpp) cc_final: 0.7751 (mttt) REVERT: R 514 LEU cc_start: 0.6342 (mt) cc_final: 0.5688 (tp) REVERT: R 525 PHE cc_start: 0.5008 (t80) cc_final: 0.4559 (t80) REVERT: R 583 LEU cc_start: 0.7889 (mt) cc_final: 0.7360 (mt) outliers start: 1 outliers final: 0 residues processed: 414 average time/residue: 0.4829 time to fit residues: 320.6313 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 : 3.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 247 optimal weight: 0.8980 chunk 331 optimal weight: 0.8980 chunk 95 optimal weight: 0.8980 chunk 286 optimal weight: 2.9990 chunk 45 optimal weight: 0.0570 chunk 86 optimal weight: 2.9990 chunk 311 optimal weight: 0.1980 chunk 130 optimal weight: 5.9990 chunk 319 optimal weight: 0.3980 chunk 39 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN A1093 GLN B 143 GLN E 95 GLN ** E 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 18 GLN ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 509 GLN R 511 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.132874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.103800 restraints weight = 464930.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.104273 restraints weight = 336888.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.103886 restraints weight = 321422.270| |-----------------------------------------------------------------------------| r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 33380 Z= 0.101 Angle : 0.517 11.335 45441 Z= 0.267 Chirality : 0.042 0.180 5130 Planarity : 0.004 0.044 5619 Dihedral : 13.470 168.866 5153 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 0.03 % Allowed : 0.27 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.14), residues: 3866 helix: 1.71 (0.14), residues: 1402 sheet: -0.03 (0.21), residues: 596 loop : -0.57 (0.15), residues: 1868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A1192 HIS 0.005 0.001 HIS D 38 PHE 0.026 0.001 PHE A 458 TYR 0.019 0.001 TYR B 752 ARG 0.007 0.000 ARG B1064 Details of bonding type rmsd hydrogen bonds : bond 0.03139 ( 1412) hydrogen bonds : angle 4.19294 ( 3988) metal coordination : bond 0.00433 ( 29) metal coordination : angle 2.73267 ( 33) covalent geometry : bond 0.00226 (33351) covalent geometry : angle 0.51166 (45408) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8916.59 seconds wall clock time: 158 minutes 19.31 seconds (9499.31 seconds total)