Starting phenix.real_space_refine on Sat Dec 16 12:58:38 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xl9_22236/12_2023/6xl9_22236_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xl9_22236/12_2023/6xl9_22236.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xl9_22236/12_2023/6xl9_22236.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xl9_22236/12_2023/6xl9_22236.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xl9_22236/12_2023/6xl9_22236_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xl9_22236/12_2023/6xl9_22236_updated.pdb" } resolution = 2.5 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= -0.004 sd= 0.138 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: 8 Type Number sf(0) Gaussians Sb 3 10.97 5 Zn 2 6.06 5 P 111 5.49 5 Mg 2 5.21 5 S 154 5.16 5 C 21741 2.51 5 N 6169 2.21 5 O 6931 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 12": "NH1" <-> "NH2" Residue "A GLU 17": "OE1" <-> "OE2" Residue "A GLU 67": "OE1" <-> "OE2" Residue "A GLU 72": "OE1" <-> "OE2" Residue "A GLU 97": "OE1" <-> "OE2" Residue "B GLU 7": "OE1" <-> "OE2" Residue "B GLU 29": "OE1" <-> "OE2" Residue "B GLU 58": "OE1" <-> "OE2" Residue "B ARG 91": "NH1" <-> "NH2" Residue "B GLU 122": "OE1" <-> "OE2" Residue "B GLU 163": "OE1" <-> "OE2" Residue "B ARG 170": "NH1" <-> "NH2" Residue "B GLU 181": "OE1" <-> "OE2" Residue "B ARG 191": "NH1" <-> "NH2" Residue "C GLU 7": "OE1" <-> "OE2" Residue "C GLU 40": "OE1" <-> "OE2" Residue "C GLU 77": "OE1" <-> "OE2" Residue "C GLU 84": "OE1" <-> "OE2" Residue "C ARG 97": "NH1" <-> "NH2" Residue "C GLU 106": "OE1" <-> "OE2" Residue "C ARG 201": "NH1" <-> "NH2" Residue "C GLU 231": "OE1" <-> "OE2" Residue "C ARG 268": "NH1" <-> "NH2" Residue "C ARG 332": "NH1" <-> "NH2" Residue "C GLU 334": "OE1" <-> "OE2" Residue "C PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 407": "NH1" <-> "NH2" Residue "C GLU 413": "OE1" <-> "OE2" Residue "C ARG 452": "NH1" <-> "NH2" Residue "C GLU 458": "OE1" <-> "OE2" Residue "C GLU 461": "OE1" <-> "OE2" Residue "C ARG 465": "NH1" <-> "NH2" Residue "C ARG 542": "NH1" <-> "NH2" Residue "C ARG 548": "NH1" <-> "NH2" Residue "C GLU 641": "OE1" <-> "OE2" Residue "C ARG 731": "NH1" <-> "NH2" Residue "C GLU 740": "OE1" <-> "OE2" Residue "C GLU 876": "OE1" <-> "OE2" Residue "C GLU 898": "OE1" <-> "OE2" Residue "C GLU 950": "OE1" <-> "OE2" Residue "C ARG 974": "NH1" <-> "NH2" Residue "C GLU 985": "OE1" <-> "OE2" Residue "C ARG 994": "NH1" <-> "NH2" Residue "C GLU 1024": "OE1" <-> "OE2" Residue "C ARG 1033": "NH1" <-> "NH2" Residue "C GLU 1083": "OE1" <-> "OE2" Residue "C GLU 1114": "OE1" <-> "OE2" Residue "C GLU 1174": "OE1" <-> "OE2" Residue "C ARG 1177": "NH1" <-> "NH2" Residue "C ARG 1216": "NH1" <-> "NH2" Residue "C ARG 1223": "NH1" <-> "NH2" Residue "C TYR 1305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1329": "OE1" <-> "OE2" Residue "D ARG 47": "NH1" <-> "NH2" Residue "D ARG 60": "NH1" <-> "NH2" Residue "D ARG 137": "NH1" <-> "NH2" Residue "D GLU 155": "OE1" <-> "OE2" Residue "D GLU 162": "OE1" <-> "OE2" Residue "D GLU 171": "OE1" <-> "OE2" Residue "D GLU 175": "OE1" <-> "OE2" Residue "D GLU 197": "OE1" <-> "OE2" Residue "D ARG 259": "NH1" <-> "NH2" Residue "D ARG 312": "NH1" <-> "NH2" Residue "D ARG 322": "NH1" <-> "NH2" Residue "D ARG 403": "NH1" <-> "NH2" Residue "D GLU 404": "OE1" <-> "OE2" Residue "D GLU 414": "OE1" <-> "OE2" Residue "D ARG 538": "NH1" <-> "NH2" Residue "D ARG 547": "NH1" <-> "NH2" Residue "D GLU 562": "OE1" <-> "OE2" Residue "D ARG 610": "NH1" <-> "NH2" Residue "D ARG 634": "NH1" <-> "NH2" Residue "D ARG 692": "NH1" <-> "NH2" Residue "D GLU 704": "OE1" <-> "OE2" Residue "D GLU 846": "OE1" <-> "OE2" Residue "D GLU 866": "OE1" <-> "OE2" Residue "D GLU 981": "OE1" <-> "OE2" Residue "D GLU 987": "OE1" <-> "OE2" Residue "D ARG 1174": "NH1" <-> "NH2" Residue "D GLU 1188": "OE1" <-> "OE2" Residue "D ARG 1206": "NH1" <-> "NH2" Residue "D ARG 1262": "NH1" <-> "NH2" Residue "D GLU 1276": "OE1" <-> "OE2" Residue "D ARG 1290": "NH1" <-> "NH2" Residue "D ARG 1330": "NH1" <-> "NH2" Residue "D ARG 1355": "NH1" <-> "NH2" Residue "F ARG 113": "NH1" <-> "NH2" Residue "F GLU 114": "OE1" <-> "OE2" Residue "F GLU 247": "OE1" <-> "OE2" Residue "F GLU 293": "OE1" <-> "OE2" Residue "F GLU 336": "OE1" <-> "OE2" Residue "F GLU 349": "OE1" <-> "OE2" Residue "F ARG 374": "NH1" <-> "NH2" Residue "F GLU 407": "OE1" <-> "OE2" Residue "F ARG 451": "NH1" <-> "NH2" Residue "F ARG 465": "NH1" <-> "NH2" Residue "F GLU 529": "OE1" <-> "OE2" Residue "F ARG 599": "NH1" <-> "NH2" Residue "G ARG 80": "NH1" <-> "NH2" Residue "G ARG 90": "NH1" <-> "NH2" Residue "H ARG 56": "NH1" <-> "NH2" Residue "H GLU 64": "OE1" <-> "OE2" Residue "H ARG 81": "NH1" <-> "NH2" Residue "H GLU 185": "OE1" <-> "OE2" Residue "H PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 220": "NH1" <-> "NH2" Residue "H GLU 257": "OE1" <-> "OE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 35113 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 1786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1786 Classifications: {'peptide': 230} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 220} Chain: "B" Number of atoms: 1774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1774 Classifications: {'peptide': 229} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 219} Chain: "C" Number of atoms: 10560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1339, 10560 Classifications: {'peptide': 1339} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1282} Chain: "D" Number of atoms: 10398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1338, 10398 Classifications: {'peptide': 1338} Link IDs: {'PCIS': 2, 'PTRANS': 53, 'TRANS': 1282} Chain breaks: 2 Chain: "F" Number of atoms: 3789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3789 Classifications: {'peptide': 465} Link IDs: {'PTRANS': 14, 'TRANS': 450} Chain breaks: 1 Chain: "N" Number of atoms: 1109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 1109 Classifications: {'DNA': 54} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 53} Chain: "R" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 77 Unusual residues: {'GTP': 1} Classifications: {'RNA': 2, 'undetermined': 1} Modifications used: {'rna3p_pur': 2} Link IDs: {'rna3p': 1, None: 1} Not linked: pdbres="GTP R 1 " pdbres=" A R 2 " Chain: "T" Number of atoms: 1104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 1104 Classifications: {'DNA': 54} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 53} Chain: "G" Number of atoms: 2208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2208 Classifications: {'peptide': 268} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 255} Chain: "H" Number of atoms: 2208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2208 Classifications: {'peptide': 268} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 255} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'118': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'118': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'118': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "D" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "T" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14569 SG CYS D 70 85.132 87.457 57.321 1.00102.31 S ATOM 14583 SG CYS D 72 82.276 86.475 56.855 1.00105.68 S ATOM 14691 SG CYS D 85 83.243 88.215 53.580 1.00108.22 S ATOM 14715 SG CYS D 88 82.079 89.678 56.335 1.00106.02 S ATOM 20403 SG CYS D 814 120.941 146.289 69.170 1.00 91.18 S ATOM 20968 SG CYS D 888 118.088 144.384 70.703 1.00 80.10 S ATOM 21019 SG CYS D 895 121.672 143.432 71.232 1.00 78.81 S ATOM 21040 SG CYS D 898 120.509 146.033 72.789 1.00 75.95 S Time building chain proxies: 19.31, per 1000 atoms: 0.55 Number of scatterers: 35113 At special positions: 0 Unit cell: (186.16, 213.01, 164.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Sb 3 50.95 Zn 2 29.99 S 154 16.00 P 111 15.00 Mg 2 11.99 O 6931 8.00 N 6169 7.00 C 21741 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 13.84 Conformation dependent library (CDL) restraints added in 6.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1501 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 85 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 72 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 70 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 88 " pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 814 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 888 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 898 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 895 " Number of angles added : 12 8234 Ramachandran restraints generated. 4117 Oldfield, 0 Emsley, 4117 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7706 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 139 helices and 37 sheets defined 35.7% alpha, 12.8% beta 41 base pairs and 83 stacking pairs defined. Time for finding SS restraints: 17.55 Creating SS restraints... Processing helix chain 'A' and resid 36 through 47 removed outlier: 3.882A pdb=" N ALA A 42 " --> pdb=" O THR A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 87 removed outlier: 3.910A pdb=" N GLY A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 114 No H-bonds generated for 'chain 'A' and resid 112 through 114' Processing helix chain 'A' and resid 155 through 158 No H-bonds generated for 'chain 'A' and resid 155 through 158' Processing helix chain 'A' and resid 213 through 232 removed outlier: 3.792A pdb=" N GLU A 229 " --> pdb=" O ALA A 225 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N ALA A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N PHE A 231 " --> pdb=" O GLN A 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 47 removed outlier: 3.703A pdb=" N ASN B 41 " --> pdb=" O HIS B 37 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE B 46 " --> pdb=" O ALA B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 84 removed outlier: 3.608A pdb=" N LEU B 83 " --> pdb=" O LEU B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 114 No H-bonds generated for 'chain 'B' and resid 112 through 114' Processing helix chain 'B' and resid 155 through 160 Processing helix chain 'B' and resid 213 through 225 Processing helix chain 'C' and resid 29 through 35 removed outlier: 3.994A pdb=" N SER C 34 " --> pdb=" O ILE C 30 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N PHE C 35 " --> pdb=" O GLN C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 53 Processing helix chain 'C' and resid 82 through 88 Processing helix chain 'C' and resid 206 through 211 Processing helix chain 'C' and resid 217 through 224 removed outlier: 3.754A pdb=" N PHE C 224 " --> pdb=" O ILE C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 246 Processing helix chain 'C' and resid 271 through 279 Processing helix chain 'C' and resid 319 through 326 Processing helix chain 'C' and resid 346 through 352 removed outlier: 4.137A pdb=" N ARG C 352 " --> pdb=" O SER C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 370 Processing helix chain 'C' and resid 380 through 388 Processing helix chain 'C' and resid 399 through 409 removed outlier: 3.935A pdb=" N MET C 403 " --> pdb=" O ALA C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 436 Processing helix chain 'C' and resid 456 through 459 No H-bonds generated for 'chain 'C' and resid 456 through 459' Processing helix chain 'C' and resid 461 through 478 removed outlier: 4.001A pdb=" N VAL C 466 " --> pdb=" O ASN C 462 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ALA C 474 " --> pdb=" O ARG C 470 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N GLU C 477 " --> pdb=" O ARG C 473 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ARG C 478 " --> pdb=" O ALA C 474 " (cutoff:3.500A) Processing helix chain 'C' and resid 489 through 491 No H-bonds generated for 'chain 'C' and resid 489 through 491' Processing helix chain 'C' and resid 496 through 508 removed outlier: 3.609A pdb=" N PHE C 505 " --> pdb=" O ALA C 501 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 528 removed outlier: 3.605A pdb=" N ARG C 528 " --> pdb=" O ILE C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 540 through 542 No H-bonds generated for 'chain 'C' and resid 540 through 542' Processing helix chain 'C' and resid 552 through 554 No H-bonds generated for 'chain 'C' and resid 552 through 554' Processing helix chain 'C' and resid 610 through 613 removed outlier: 3.576A pdb=" N ASN C 613 " --> pdb=" O GLU C 610 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 610 through 613' Processing helix chain 'C' and resid 671 through 673 No H-bonds generated for 'chain 'C' and resid 671 through 673' Processing helix chain 'C' and resid 676 through 688 removed outlier: 3.917A pdb=" N MET C 681 " --> pdb=" O ASN C 677 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ARG C 687 " --> pdb=" O ALA C 683 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N GLN C 688 " --> pdb=" O ASN C 684 " (cutoff:3.500A) Processing helix chain 'C' and resid 705 through 712 removed outlier: 3.647A pdb=" N SER C 712 " --> pdb=" O VAL C 708 " (cutoff:3.500A) Processing helix chain 'C' and resid 820 through 824 Processing helix chain 'C' and resid 897 through 906 Processing helix chain 'C' and resid 943 through 957 Processing helix chain 'C' and resid 961 through 979 removed outlier: 4.392A pdb=" N GLN C 965 " --> pdb=" O SER C 961 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ILE C 966 " --> pdb=" O GLU C 962 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N GLY C 970 " --> pdb=" O ILE C 966 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU C 971 " --> pdb=" O LEU C 967 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ALA C 977 " --> pdb=" O SER C 973 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL C 978 " --> pdb=" O ARG C 974 " (cutoff:3.500A) Processing helix chain 'C' and resid 986 through 989 No H-bonds generated for 'chain 'C' and resid 986 through 989' Processing helix chain 'C' and resid 1005 through 1036 removed outlier: 4.019A pdb=" N ALA C1015 " --> pdb=" O LEU C1011 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N LYS C1022 " --> pdb=" O TYR C1018 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLU C1026 " --> pdb=" O LYS C1022 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N LYS C1027 " --> pdb=" O HIS C1023 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS C1028 " --> pdb=" O GLU C1024 " (cutoff:3.500A) Processing helix chain 'C' and resid 1082 through 1084 No H-bonds generated for 'chain 'C' and resid 1082 through 1084' Processing helix chain 'C' and resid 1100 through 1102 No H-bonds generated for 'chain 'C' and resid 1100 through 1102' Processing helix chain 'C' and resid 1109 through 1133 removed outlier: 3.674A pdb=" N LEU C1113 " --> pdb=" O GLY C1110 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLU C1114 " --> pdb=" O GLN C1111 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLY C1118 " --> pdb=" O THR C1115 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N MET C1119 " --> pdb=" O HIS C1116 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA C1121 " --> pdb=" O GLY C1118 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLY C1123 " --> pdb=" O ALA C1120 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ASP C1126 " --> pdb=" O GLY C1123 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ASN C1129 " --> pdb=" O ASP C1126 " (cutoff:3.500A) Processing helix chain 'C' and resid 1138 through 1149 Processing helix chain 'C' and resid 1161 through 1163 No H-bonds generated for 'chain 'C' and resid 1161 through 1163' Processing helix chain 'C' and resid 1166 through 1176 Processing helix chain 'C' and resid 1192 through 1201 Processing helix chain 'C' and resid 1239 through 1242 No H-bonds generated for 'chain 'C' and resid 1239 through 1242' Processing helix chain 'C' and resid 1272 through 1281 removed outlier: 3.749A pdb=" N TRP C1276 " --> pdb=" O GLU C1272 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ALA C1277 " --> pdb=" O MET C1273 " (cutoff:3.500A) Processing helix chain 'C' and resid 1284 through 1291 Processing helix chain 'C' and resid 1300 through 1309 removed outlier: 4.075A pdb=" N TYR C1305 " --> pdb=" O ARG C1301 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS C1306 " --> pdb=" O THR C1302 " (cutoff:3.500A) Processing helix chain 'C' and resid 1321 through 1333 removed outlier: 4.102A pdb=" N LEU C1333 " --> pdb=" O GLU C1329 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 32 Processing helix chain 'D' and resid 59 through 62 No H-bonds generated for 'chain 'D' and resid 59 through 62' Processing helix chain 'D' and resid 95 through 99 Processing helix chain 'D' and resid 115 through 118 No H-bonds generated for 'chain 'D' and resid 115 through 118' Processing helix chain 'D' and resid 123 through 128 Processing helix chain 'D' and resid 132 through 140 removed outlier: 4.165A pdb=" N TYR D 140 " --> pdb=" O GLU D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 171 Processing helix chain 'D' and resid 182 through 191 Processing helix chain 'D' and resid 194 through 202 Processing helix chain 'D' and resid 211 through 230 removed outlier: 4.195A pdb=" N LYS D 216 " --> pdb=" O THR D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 237 removed outlier: 3.716A pdb=" N MET D 237 " --> pdb=" O PRO D 234 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 234 through 237' Processing helix chain 'D' and resid 247 through 249 No H-bonds generated for 'chain 'D' and resid 247 through 249' Processing helix chain 'D' and resid 264 through 285 removed outlier: 3.769A pdb=" N ARG D 271 " --> pdb=" O ASP D 267 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL D 272 " --> pdb=" O LEU D 268 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ARG D 278 " --> pdb=" O ASN D 274 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU D 279 " --> pdb=" O ARG D 275 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ASP D 284 " --> pdb=" O LYS D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 307 removed outlier: 3.739A pdb=" N ASN D 294 " --> pdb=" O ILE D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 341 Processing helix chain 'D' and resid 370 through 376 Processing helix chain 'D' and resid 378 through 387 Processing helix chain 'D' and resid 394 through 403 removed outlier: 3.671A pdb=" N LYS D 399 " --> pdb=" O LYS D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 415 removed outlier: 3.723A pdb=" N ASP D 413 " --> pdb=" O TRP D 409 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU D 414 " --> pdb=" O ASP D 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 433 No H-bonds generated for 'chain 'D' and resid 431 through 433' Processing helix chain 'D' and resid 474 through 482 Processing helix chain 'D' and resid 486 through 488 No H-bonds generated for 'chain 'D' and resid 486 through 488' Processing helix chain 'D' and resid 506 through 513 Processing helix chain 'D' and resid 530 through 539 Processing helix chain 'D' and resid 574 through 581 removed outlier: 4.069A pdb=" N MET D 581 " --> pdb=" O ALA D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 589 through 591 No H-bonds generated for 'chain 'D' and resid 589 through 591' Processing helix chain 'D' and resid 598 through 611 Processing helix chain 'D' and resid 615 through 635 removed outlier: 3.805A pdb=" N ASP D 622 " --> pdb=" O VAL D 618 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 665 removed outlier: 3.716A pdb=" N SER D 655 " --> pdb=" O HIS D 651 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLU D 660 " --> pdb=" O GLU D 656 " (cutoff:3.500A) Processing helix chain 'D' and resid 675 through 702 removed outlier: 4.162A pdb=" N ASP D 684 " --> pdb=" O ASN D 680 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ALA D 689 " --> pdb=" O ILE D 685 " (cutoff:3.500A) Processing helix chain 'D' and resid 721 through 727 Processing helix chain 'D' and resid 734 through 741 removed outlier: 4.021A pdb=" N GLN D 739 " --> pdb=" O ALA D 735 " (cutoff:3.500A) Processing helix chain 'D' and resid 769 through 804 removed outlier: 4.095A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ALA D 779 " --> pdb=" O SER D 775 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALA D 787 " --> pdb=" O LEU D 783 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ALA D 791 " --> pdb=" O ALA D 787 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N ASN D 792 " --> pdb=" O LEU D 788 " (cutoff:3.500A) Processing helix chain 'D' and resid 836 through 839 No H-bonds generated for 'chain 'D' and resid 836 through 839' Processing helix chain 'D' and resid 866 through 874 Processing helix chain 'D' and resid 896 through 899 No H-bonds generated for 'chain 'D' and resid 896 through 899' Processing helix chain 'D' and resid 915 through 928 Proline residue: D 926 - end of helix Processing helix chain 'D' and resid 1138 through 1146 Processing helix chain 'D' and resid 1217 through 1223 Processing helix chain 'D' and resid 1226 through 1244 removed outlier: 4.153A pdb=" N VAL D1240 " --> pdb=" O GLU D1236 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR D1241 " --> pdb=" O VAL D1237 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU D1243 " --> pdb=" O ASP D1239 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLN D1244 " --> pdb=" O VAL D1240 " (cutoff:3.500A) Processing helix chain 'D' and resid 1251 through 1261 removed outlier: 3.970A pdb=" N ILE D1256 " --> pdb=" O HIS D1252 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU D1261 " --> pdb=" O VAL D1257 " (cutoff:3.500A) Processing helix chain 'D' and resid 1282 through 1292 removed outlier: 3.892A pdb=" N GLU D1291 " --> pdb=" O ILE D1287 " (cutoff:3.500A) Processing helix chain 'D' and resid 1309 through 1313 Processing helix chain 'D' and resid 1319 through 1325 Processing helix chain 'D' and resid 1328 through 1338 Processing helix chain 'D' and resid 1348 through 1352 Processing helix chain 'D' and resid 1360 through 1375 removed outlier: 4.708A pdb=" N ALA D1364 " --> pdb=" O THR D1361 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N TYR D1365 " --> pdb=" O GLY D1362 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N HIS D1366 " --> pdb=" O TYR D1363 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 104 removed outlier: 3.542A pdb=" N GLU F 104 " --> pdb=" O MET F 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 113 through 133 removed outlier: 3.621A pdb=" N ILE F 117 " --> pdb=" O ARG F 113 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG F 122 " --> pdb=" O ASP F 118 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE F 127 " --> pdb=" O ILE F 123 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN F 128 " --> pdb=" O GLU F 124 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN F 131 " --> pdb=" O ILE F 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 147 through 150 No H-bonds generated for 'chain 'F' and resid 147 through 150' Processing helix chain 'F' and resid 214 through 235 removed outlier: 3.690A pdb=" N LYS F 220 " --> pdb=" O LEU F 216 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N PHE F 221 " --> pdb=" O ALA F 217 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ALA F 222 " --> pdb=" O ARG F 218 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLU F 223 " --> pdb=" O GLU F 219 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N LEU F 224 " --> pdb=" O LYS F 220 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ARG F 225 " --> pdb=" O PHE F 221 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N VAL F 230 " --> pdb=" O ALA F 226 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ASP F 233 " --> pdb=" O VAL F 229 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N THR F 234 " --> pdb=" O VAL F 230 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N ILE F 235 " --> pdb=" O THR F 231 " (cutoff:3.500A) Processing helix chain 'F' and resid 243 through 258 removed outlier: 4.759A pdb=" N GLN F 258 " --> pdb=" O GLU F 254 " (cutoff:3.500A) Processing helix chain 'F' and resid 265 through 290 removed outlier: 3.612A pdb=" N SER F 272 " --> pdb=" O TYR F 268 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N MET F 273 " --> pdb=" O LEU F 269 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N MET F 276 " --> pdb=" O SER F 272 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N ARG F 279 " --> pdb=" O VAL F 275 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL F 280 " --> pdb=" O MET F 276 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE F 287 " --> pdb=" O GLN F 283 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N MET F 288 " --> pdb=" O GLU F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 308 removed outlier: 4.007A pdb=" N THR F 304 " --> pdb=" O LYS F 300 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 318 Processing helix chain 'F' and resid 334 through 351 Processing helix chain 'F' and resid 355 through 380 removed outlier: 4.040A pdb=" N ASP F 360 " --> pdb=" O GLU F 356 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARG F 364 " --> pdb=" O ASP F 360 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE F 367 " --> pdb=" O ARG F 363 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLY F 368 " --> pdb=" O ARG F 364 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARG F 373 " --> pdb=" O GLU F 369 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA F 375 " --> pdb=" O LYS F 371 " (cutoff:3.500A) Processing helix chain 'F' and resid 384 through 393 removed outlier: 3.739A pdb=" N LYS F 392 " --> pdb=" O ILE F 388 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N LYS F 393 " --> pdb=" O SER F 389 " (cutoff:3.500A) Processing helix chain 'F' and resid 401 through 415 removed outlier: 4.058A pdb=" N ILE F 410 " --> pdb=" O GLN F 406 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLY F 411 " --> pdb=" O GLU F 407 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LYS F 414 " --> pdb=" O ILE F 410 " (cutoff:3.500A) Processing helix chain 'F' and resid 421 through 423 No H-bonds generated for 'chain 'F' and resid 421 through 423' Processing helix chain 'F' and resid 427 through 445 removed outlier: 4.850A pdb=" N TRP F 433 " --> pdb=" O THR F 429 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N TRP F 434 " --> pdb=" O TYR F 430 " (cutoff:3.500A) Processing helix chain 'F' and resid 454 through 474 removed outlier: 3.613A pdb=" N GLN F 469 " --> pdb=" O ARG F 465 " (cutoff:3.500A) Processing helix chain 'F' and resid 480 through 487 removed outlier: 3.941A pdb=" N ARG F 486 " --> pdb=" O GLU F 482 " (cutoff:3.500A) Processing helix chain 'F' and resid 491 through 499 removed outlier: 3.565A pdb=" N LEU F 498 " --> pdb=" O ILE F 494 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N LYS F 499 " --> pdb=" O ARG F 495 " (cutoff:3.500A) Processing helix chain 'F' and resid 519 through 521 No H-bonds generated for 'chain 'F' and resid 519 through 521' Processing helix chain 'F' and resid 531 through 549 removed outlier: 3.848A pdb=" N ALA F 549 " --> pdb=" O HIS F 545 " (cutoff:3.500A) Processing helix chain 'F' and resid 553 through 563 removed outlier: 3.607A pdb=" N VAL F 558 " --> pdb=" O ARG F 554 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N LEU F 559 " --> pdb=" O GLU F 555 " (cutoff:3.500A) Processing helix chain 'F' and resid 573 through 580 removed outlier: 4.375A pdb=" N GLN F 579 " --> pdb=" O GLU F 575 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE F 580 " --> pdb=" O VAL F 576 " (cutoff:3.500A) Processing helix chain 'F' and resid 584 through 597 removed outlier: 4.365A pdb=" N ARG F 588 " --> pdb=" O ARG F 584 " (cutoff:3.500A) Processing helix chain 'F' and resid 604 through 606 No H-bonds generated for 'chain 'F' and resid 604 through 606' Processing helix chain 'F' and resid 608 through 610 No H-bonds generated for 'chain 'F' and resid 608 through 610' Processing helix chain 'G' and resid 4 through 10 removed outlier: 3.691A pdb=" N LYS G 9 " --> pdb=" O GLY G 5 " (cutoff:3.500A) Processing helix chain 'G' and resid 15 through 24 Processing helix chain 'G' and resid 43 through 58 removed outlier: 3.521A pdb=" N GLN G 51 " --> pdb=" O MET G 47 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N LEU G 58 " --> pdb=" O SER G 54 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 70 Processing helix chain 'G' and resid 75 through 109 removed outlier: 4.123A pdb=" N GLU G 79 " --> pdb=" O HIS G 76 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ARG G 80 " --> pdb=" O ILE G 77 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU G 83 " --> pdb=" O ARG G 80 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE G 85 " --> pdb=" O ARG G 82 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LYS G 87 " --> pdb=" O GLU G 84 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ILE G 89 " --> pdb=" O GLN G 86 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N LEU G 96 " --> pdb=" O ALA G 93 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ILE G 99 " --> pdb=" O LEU G 96 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU G 103 " --> pdb=" O ASN G 100 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N LYS G 107 " --> pdb=" O GLN G 104 " (cutoff:3.500A) Processing helix chain 'G' and resid 136 through 152 Proline residue: G 144 - end of helix removed outlier: 3.797A pdb=" N VAL G 150 " --> pdb=" O ILE G 146 " (cutoff:3.500A) Processing helix chain 'G' and resid 216 through 232 removed outlier: 5.527A pdb=" N ARG G 220 " --> pdb=" O ASP G 217 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ILE G 224 " --> pdb=" O ASN G 221 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N MET G 227 " --> pdb=" O ILE G 224 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N VAL G 230 " --> pdb=" O MET G 227 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ASP G 232 " --> pdb=" O TRP G 229 " (cutoff:3.500A) Processing helix chain 'G' and resid 255 through 257 No H-bonds generated for 'chain 'G' and resid 255 through 257' Processing helix chain 'H' and resid 4 through 11 removed outlier: 3.556A pdb=" N LYS H 9 " --> pdb=" O GLY H 5 " (cutoff:3.500A) Processing helix chain 'H' and resid 15 through 24 Processing helix chain 'H' and resid 46 through 58 removed outlier: 4.023A pdb=" N GLN H 51 " --> pdb=" O MET H 47 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU H 58 " --> pdb=" O SER H 54 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 68 Processing helix chain 'H' and resid 76 through 108 removed outlier: 3.638A pdb=" N GLU H 84 " --> pdb=" O ARG H 80 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN H 86 " --> pdb=" O ARG H 82 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER H 97 " --> pdb=" O ALA H 93 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N LYS H 108 " --> pdb=" O GLN H 104 " (cutoff:3.500A) Processing helix chain 'H' and resid 137 through 153 Proline residue: H 144 - end of helix removed outlier: 3.681A pdb=" N GLY H 147 " --> pdb=" O ILE H 143 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N MET H 151 " --> pdb=" O GLY H 147 " (cutoff:3.500A) Processing helix chain 'H' and resid 217 through 232 removed outlier: 4.364A pdb=" N ARG H 220 " --> pdb=" O ASP H 217 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LEU H 226 " --> pdb=" O TYR H 223 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N VAL H 230 " --> pdb=" O MET H 227 " (cutoff:3.500A) Processing helix chain 'H' and resid 255 through 257 No H-bonds generated for 'chain 'H' and resid 255 through 257' Processing sheet with id= A, first strand: chain 'A' and resid 12 through 18 removed outlier: 6.887A pdb=" N THR A 27 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ILE A 16 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LYS A 25 " --> pdb=" O ILE A 16 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N GLN A 18 " --> pdb=" O HIS A 23 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N HIS A 23 " --> pdb=" O GLN A 18 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 170 through 172 removed outlier: 6.835A pdb=" N LYS A 145 " --> pdb=" O THR A 57 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N VAL A 59 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ARG A 143 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N ILE A 61 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N SER A 141 " --> pdb=" O ILE A 61 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 90 through 92 Processing sheet with id= D, first strand: chain 'A' and resid 108 through 111 Processing sheet with id= E, first strand: chain 'B' and resid 17 through 20 removed outlier: 6.504A pdb=" N HIS B 23 " --> pdb=" O VAL B 19 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU B 198 " --> pdb=" O ALA B 190 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 170 through 172 removed outlier: 7.033A pdb=" N LYS B 145 " --> pdb=" O THR B 57 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N VAL B 59 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ARG B 143 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N ILE B 61 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N SER B 141 " --> pdb=" O ILE B 61 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ASP B 135 " --> pdb=" O GLY B 106 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLY B 106 " --> pdb=" O ASP B 135 " (cutoff:3.500A) removed outlier: 8.917A pdb=" N ASN B 137 " --> pdb=" O LYS B 104 " (cutoff:3.500A) removed outlier: 10.247A pdb=" N LYS B 104 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 9.990A pdb=" N SER B 139 " --> pdb=" O LEU B 102 " (cutoff:3.500A) removed outlier: 11.292A pdb=" N LEU B 102 " --> pdb=" O SER B 139 " (cutoff:3.500A) removed outlier: 10.021A pdb=" N SER B 141 " --> pdb=" O LEU B 100 " (cutoff:3.500A) removed outlier: 11.220A pdb=" N LEU B 100 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 9.923A pdb=" N ARG B 143 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 10.594A pdb=" N VAL B 98 " --> pdb=" O ARG B 143 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 90 through 92 Processing sheet with id= H, first strand: chain 'C' and resid 136 through 138 Processing sheet with id= I, first strand: chain 'C' and resid 148 through 151 Processing sheet with id= J, first strand: chain 'C' and resid 154 through 160 removed outlier: 3.732A pdb=" N LEU C 184 " --> pdb=" O ILE C 176 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 227 through 231 Processing sheet with id= L, first strand: chain 'C' and resid 529 through 531 Processing sheet with id= M, first strand: chain 'C' and resid 603 through 607 Processing sheet with id= N, first strand: chain 'C' and resid 634 through 638 Processing sheet with id= O, first strand: chain 'C' and resid 748 through 752 removed outlier: 6.237A pdb=" N LYS C 735 " --> pdb=" O VAL C 724 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N VAL C 724 " --> pdb=" O LYS C 735 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 1227 through 1232 removed outlier: 6.688A pdb=" N ILE C1096 " --> pdb=" O ALA C 803 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 876 through 878 removed outlier: 7.922A pdb=" N SER C 925 " --> pdb=" O LYS C1057 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N LYS C1057 " --> pdb=" O SER C 925 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N TYR C1053 " --> pdb=" O ILE C 929 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N VAL C 931 " --> pdb=" O LYS C1051 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N LYS C1051 " --> pdb=" O VAL C 931 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N VAL C 933 " --> pdb=" O ILE C1049 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILE C1049 " --> pdb=" O VAL C 933 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N THR C 935 " --> pdb=" O LEU C1047 " (cutoff:3.500A) removed outlier: 8.339A pdb=" N LEU C1047 " --> pdb=" O THR C 935 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N SER C 840 " --> pdb=" O LEU C1047 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ILE C1049 " --> pdb=" O CYS C 838 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N CYS C 838 " --> pdb=" O ILE C1049 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N LYS C1051 " --> pdb=" O LEU C 836 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N LEU C 836 " --> pdb=" O LYS C1051 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N TYR C1053 " --> pdb=" O GLN C 834 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N GLN C 834 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ALA C1055 " --> pdb=" O HIS C 832 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N HIS C 832 " --> pdb=" O ALA C1055 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N LYS C1057 " --> pdb=" O THR C 830 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N THR C 830 " --> pdb=" O LYS C1057 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 887 through 889 Processing sheet with id= S, first strand: chain 'C' and resid 1065 through 1067 Processing sheet with id= T, first strand: chain 'C' and resid 66 through 75 removed outlier: 6.918A pdb=" N LYS C 99 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N TYR C 73 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N ARG C 97 " --> pdb=" O TYR C 73 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N LEU C 75 " --> pdb=" O PRO C 95 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLY C 125 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N VAL C 98 " --> pdb=" O TYR C 123 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N TYR C 123 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N LEU C 100 " --> pdb=" O GLU C 121 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N GLU C 121 " --> pdb=" O LEU C 100 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N LEU C 102 " --> pdb=" O GLU C 119 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N GLU C 119 " --> pdb=" O LEU C 102 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N ILE C 104 " --> pdb=" O ILE C 117 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ILE C 117 " --> pdb=" O ILE C 104 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 816 through 819 removed outlier: 7.562A pdb=" N VAL C 818 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ILE C1079 " --> pdb=" O VAL C 818 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 103 through 106 Processing sheet with id= W, first strand: chain 'D' and resid 252 through 254 Processing sheet with id= X, first strand: chain 'D' and resid 350 through 354 Processing sheet with id= Y, first strand: chain 'D' and resid 355 through 357 removed outlier: 5.956A pdb=" N ILE D 447 " --> pdb=" O THR D 356 " (cutoff:3.500A) No H-bonds generated for sheet with id= Y Processing sheet with id= Z, first strand: chain 'D' and resid 547 through 556 Processing sheet with id= AA, first strand: chain 'D' and resid 820 through 822 Processing sheet with id= AB, first strand: chain 'D' and resid 957 through 961 removed outlier: 3.991A pdb=" N GLU D 993 " --> pdb=" O LEU D 984 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'D' and resid 965 through 967 Processing sheet with id= AD, first strand: chain 'D' and resid 1034 through 1036 Processing sheet with id= AE, first strand: chain 'D' and resid 1162 through 1165 Processing sheet with id= AF, first strand: chain 'D' and resid 1279 through 1281 removed outlier: 6.845A pdb=" N THR D1301 " --> pdb=" O VAL D1267 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'D' and resid 145 through 148 removed outlier: 6.710A pdb=" N ASP D 177 " --> pdb=" O ILE D 147 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'D' and resid 1024 through 1028 Processing sheet with id= AI, first strand: chain 'G' and resid 117 through 121 removed outlier: 6.799A pdb=" N GLU G 261 " --> pdb=" O TYR G 245 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N TYR G 245 " --> pdb=" O GLU G 261 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N GLN G 263 " --> pdb=" O GLU G 243 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N GLU G 243 " --> pdb=" O GLN G 263 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N CYS G 165 " --> pdb=" O TYR G 245 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ILE G 125 " --> pdb=" O VAL G 187 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'G' and resid 235 through 237 Processing sheet with id= AK, first strand: chain 'H' and resid 117 through 121 removed outlier: 7.153A pdb=" N GLU H 261 " --> pdb=" O TYR H 245 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N TYR H 245 " --> pdb=" O GLU H 261 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N GLN H 263 " --> pdb=" O GLU H 243 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N GLU H 243 " --> pdb=" O GLN H 263 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N CYS H 165 " --> pdb=" O TYR H 245 " (cutoff:3.500A) 1068 hydrogen bonds defined for protein. 2874 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 110 hydrogen bonds 220 hydrogen bond angles 0 basepair planarities 41 basepair parallelities 83 stacking parallelities Total time for adding SS restraints: 14.84 Time building geometry restraints manager: 14.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.39: 14155 1.39 - 1.58: 21245 1.58 - 1.76: 220 1.76 - 1.95: 267 1.95 - 2.13: 12 Bond restraints: 35899 Sorted by residual: bond pdb=" O3' DG T 19 " pdb=" P DG T 20 " ideal model delta sigma weight residual 1.607 1.646 -0.039 1.50e-02 4.44e+03 6.86e+00 bond pdb=" CG1 ILE H 202 " pdb=" CD1 ILE H 202 " ideal model delta sigma weight residual 1.513 1.415 0.098 3.90e-02 6.57e+02 6.28e+00 bond pdb=" O3' DA T 12 " pdb=" P DC T 13 " ideal model delta sigma weight residual 1.607 1.645 -0.038 1.50e-02 4.44e+03 6.27e+00 bond pdb=" C VAL C 550 " pdb=" N HIS C 551 " ideal model delta sigma weight residual 1.333 1.295 0.038 1.59e-02 3.96e+03 5.62e+00 bond pdb=" CA ASP F 581 " pdb=" C ASP F 581 " ideal model delta sigma weight residual 1.527 1.497 0.030 1.30e-02 5.92e+03 5.30e+00 ... (remaining 35894 not shown) Histogram of bond angle deviations from ideal: 98.02 - 105.25: 1072 105.25 - 112.48: 18288 112.48 - 119.71: 12861 119.71 - 126.93: 16203 126.93 - 134.16: 543 Bond angle restraints: 48967 Sorted by residual: angle pdb=" N GLU F 585 " pdb=" CA GLU F 585 " pdb=" C GLU F 585 " ideal model delta sigma weight residual 112.90 120.54 -7.64 1.31e+00 5.83e-01 3.40e+01 angle pdb=" N LEU C 397 " pdb=" CA LEU C 397 " pdb=" C LEU C 397 " ideal model delta sigma weight residual 109.25 101.44 7.81 1.53e+00 4.27e-01 2.61e+01 angle pdb=" N ASP F 581 " pdb=" CA ASP F 581 " pdb=" C ASP F 581 " ideal model delta sigma weight residual 111.39 104.67 6.72 1.38e+00 5.25e-01 2.37e+01 angle pdb=" N ASP C 396 " pdb=" CA ASP C 396 " pdb=" C ASP C 396 " ideal model delta sigma weight residual 107.20 114.63 -7.43 1.70e+00 3.46e-01 1.91e+01 angle pdb=" N ASP H 180 " pdb=" CA ASP H 180 " pdb=" C ASP H 180 " ideal model delta sigma weight residual 108.41 101.56 6.85 1.61e+00 3.86e-01 1.81e+01 ... (remaining 48962 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.46: 20859 35.46 - 70.92: 795 70.92 - 106.39: 42 106.39 - 141.85: 1 141.85 - 177.31: 3 Dihedral angle restraints: 21700 sinusoidal: 9737 harmonic: 11963 Sorted by residual: dihedral pdb=" CA SER C1295 " pdb=" C SER C1295 " pdb=" N ASP C1296 " pdb=" CA ASP C1296 " ideal model delta harmonic sigma weight residual -180.00 -150.00 -30.00 0 5.00e+00 4.00e-02 3.60e+01 dihedral pdb=" CA VAL C 261 " pdb=" C VAL C 261 " pdb=" N TYR C 262 " pdb=" CA TYR C 262 " ideal model delta harmonic sigma weight residual 180.00 -150.52 -29.48 0 5.00e+00 4.00e-02 3.48e+01 dihedral pdb=" CA LYS D 850 " pdb=" C LYS D 850 " pdb=" N PRO D 851 " pdb=" CA PRO D 851 " ideal model delta harmonic sigma weight residual 180.00 -150.81 -29.19 0 5.00e+00 4.00e-02 3.41e+01 ... (remaining 21697 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 4462 0.071 - 0.142: 983 0.142 - 0.212: 72 0.212 - 0.283: 10 0.283 - 0.354: 2 Chirality restraints: 5529 Sorted by residual: chirality pdb=" CA LYS H 141 " pdb=" N LYS H 141 " pdb=" C LYS H 141 " pdb=" CB LYS H 141 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.13e+00 chirality pdb=" CB VAL H 126 " pdb=" CA VAL H 126 " pdb=" CG1 VAL H 126 " pdb=" CG2 VAL H 126 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" CA LEU B 65 " pdb=" N LEU B 65 " pdb=" C LEU B 65 " pdb=" CB LEU B 65 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.96e+00 ... (remaining 5526 not shown) Planarity restraints: 5981 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO D 851 " -0.017 2.00e-02 2.50e+03 3.45e-02 1.19e+01 pdb=" C PRO D 851 " 0.060 2.00e-02 2.50e+03 pdb=" O PRO D 851 " -0.022 2.00e-02 2.50e+03 pdb=" N GLY D 852 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE G 131 " 0.022 2.00e-02 2.50e+03 2.28e-02 9.07e+00 pdb=" CG PHE G 131 " -0.051 2.00e-02 2.50e+03 pdb=" CD1 PHE G 131 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 PHE G 131 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE G 131 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE G 131 " 0.012 2.00e-02 2.50e+03 pdb=" CZ PHE G 131 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS D 881 " 0.015 2.00e-02 2.50e+03 2.98e-02 8.91e+00 pdb=" C LYS D 881 " -0.052 2.00e-02 2.50e+03 pdb=" O LYS D 881 " 0.019 2.00e-02 2.50e+03 pdb=" N VAL D 882 " 0.017 2.00e-02 2.50e+03 ... (remaining 5978 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 268 2.60 - 3.18: 27994 3.18 - 3.75: 49575 3.75 - 4.32: 72568 4.32 - 4.90: 118352 Nonbonded interactions: 268757 Sorted by model distance: nonbonded pdb=" OD1 ASP D 464 " pdb="MG MG D1503 " model vdw 2.025 2.170 nonbonded pdb=" OD1 ASP D 460 " pdb="MG MG D1503 " model vdw 2.102 2.170 nonbonded pdb=" OD1 ASP D 462 " pdb="MG MG D1503 " model vdw 2.121 2.170 nonbonded pdb=" N7 GTP R 1 " pdb="MG MG R 101 " model vdw 2.123 2.250 nonbonded pdb=" O ASP G 135 " pdb=" OG SER G 138 " model vdw 2.204 2.440 ... (remaining 268752 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 6 through 233) selection = (chain 'B' and resid 6 through 233) } ncs_group { reference = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.930 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: 0.040 Extract box with map and model: 14.240 Check model and map are aligned: 0.610 Set scattering table: 0.380 Process input model: 108.920 Find NCS groups from input model: 1.380 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 142.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 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 : 0.008 0.101 35899 Z= 0.521 Angle : 0.899 13.324 48967 Z= 0.507 Chirality : 0.057 0.354 5529 Planarity : 0.006 0.065 5981 Dihedral : 17.123 177.311 13994 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.04 % Favored : 98.91 % Rotamer: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.19 % 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: -3.38 (0.11), residues: 4117 helix: -2.40 (0.11), residues: 1540 sheet: -0.76 (0.22), residues: 473 loop : -2.48 (0.11), residues: 2104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP G 258 HIS 0.021 0.002 HIS C 526 PHE 0.051 0.003 PHE G 131 TYR 0.025 0.002 TYR G 127 ARG 0.017 0.001 ARG D 352 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8234 Ramachandran restraints generated. 4117 Oldfield, 0 Emsley, 4117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8234 Ramachandran restraints generated. 4117 Oldfield, 0 Emsley, 4117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 3573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 409 time to evaluate : 4.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 409 average time/residue: 1.8787 time to fit residues: 892.3150 Evaluate side-chains 271 residues out of total 3573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 271 time to evaluate : 3.702 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.1049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 353 optimal weight: 10.0000 chunk 317 optimal weight: 0.8980 chunk 176 optimal weight: 3.9990 chunk 108 optimal weight: 5.9990 chunk 214 optimal weight: 2.9990 chunk 169 optimal weight: 0.8980 chunk 328 optimal weight: 20.0000 chunk 127 optimal weight: 1.9990 chunk 199 optimal weight: 3.9990 chunk 244 optimal weight: 3.9990 chunk 380 optimal weight: 5.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN A 84 ASN A 137 ASN A 160 HIS B 23 HIS B 66 HIS B 75 GLN B 117 HIS B 147 GLN C 139 ASN C 447 HIS C 462 ASN C 518 ASN C 519 ASN C 568 ASN C 620 ASN C 894 GLN C 932 GLN ** C1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1023 HIS C1070 HIS C1307 ASN D 186 GLN D 209 ASN D 266 ASN D 364 HIS D 419 HIS D 430 HIS D 465 GLN D 667 GLN D 720 ASN D 736 GLN D 951 GLN D 979 ASN D1235 ASN F 128 ASN F 317 ASN F 362 ASN F 383 ASN F 400 GLN F 461 ASN F 472 GLN F 579 GLN G 22 ASN ** G 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 148 GLN G 233 ASN H 50 HIS H 76 HIS ** H 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 154 ASN ** H 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.1175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 35899 Z= 0.273 Angle : 0.623 11.898 48967 Z= 0.331 Chirality : 0.045 0.172 5529 Planarity : 0.005 0.061 5981 Dihedral : 15.813 178.111 5752 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.79 % Allowed : 13.13 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.19 % 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: -2.27 (0.12), residues: 4117 helix: -1.28 (0.13), residues: 1549 sheet: -0.33 (0.23), residues: 491 loop : -1.97 (0.12), residues: 2077 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D1020 HIS 0.008 0.001 HIS C 526 PHE 0.019 0.002 PHE C 405 TYR 0.021 0.001 TYR G 127 ARG 0.012 0.000 ARG D 133 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8234 Ramachandran restraints generated. 4117 Oldfield, 0 Emsley, 4117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8234 Ramachandran restraints generated. 4117 Oldfield, 0 Emsley, 4117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 3573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 295 time to evaluate : 3.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 64 outliers final: 22 residues processed: 334 average time/residue: 1.7439 time to fit residues: 690.1858 Evaluate side-chains 280 residues out of total 3573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 258 time to evaluate : 4.384 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 14 residues processed: 8 average time/residue: 1.0980 time to fit residues: 16.9459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 211 optimal weight: 3.9990 chunk 118 optimal weight: 5.9990 chunk 316 optimal weight: 7.9990 chunk 259 optimal weight: 6.9990 chunk 104 optimal weight: 6.9990 chunk 381 optimal weight: 8.9990 chunk 411 optimal weight: 20.0000 chunk 339 optimal weight: 0.8980 chunk 378 optimal weight: 3.9990 chunk 129 optimal weight: 6.9990 chunk 305 optimal weight: 3.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 HIS A 137 ASN B 18 GLN ** B 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 620 ASN C 894 GLN ** C1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 196 GLN D 200 GLN D 294 ASN D 897 HIS ** G 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.078 35899 Z= 0.434 Angle : 0.685 12.453 48967 Z= 0.363 Chirality : 0.048 0.187 5529 Planarity : 0.006 0.070 5981 Dihedral : 15.925 177.736 5752 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.69 % Allowed : 14.67 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.19 % 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: -2.03 (0.12), residues: 4117 helix: -1.04 (0.13), residues: 1554 sheet: -0.30 (0.23), residues: 502 loop : -1.84 (0.12), residues: 2061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D1020 HIS 0.013 0.001 HIS C 526 PHE 0.020 0.002 PHE C 514 TYR 0.021 0.002 TYR D 631 ARG 0.008 0.000 ARG D 133 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8234 Ramachandran restraints generated. 4117 Oldfield, 0 Emsley, 4117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8234 Ramachandran restraints generated. 4117 Oldfield, 0 Emsley, 4117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 3573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 275 time to evaluate : 3.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 96 outliers final: 50 residues processed: 350 average time/residue: 1.5799 time to fit residues: 661.4008 Evaluate side-chains 305 residues out of total 3573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 255 time to evaluate : 4.271 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 42 residues processed: 8 average time/residue: 0.8344 time to fit residues: 14.2814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 376 optimal weight: 6.9990 chunk 286 optimal weight: 0.3980 chunk 197 optimal weight: 4.9990 chunk 42 optimal weight: 0.8980 chunk 181 optimal weight: 1.9990 chunk 255 optimal weight: 6.9990 chunk 382 optimal weight: 0.0040 chunk 405 optimal weight: 0.0570 chunk 199 optimal weight: 3.9990 chunk 362 optimal weight: 6.9990 chunk 109 optimal weight: 8.9990 overall best weight: 0.6712 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN A 137 ASN A 147 GLN ** B 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 628 HIS ** C1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 736 GLN ** G 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN ** G 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 105 HIS ** H 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 35899 Z= 0.146 Angle : 0.528 9.863 48967 Z= 0.282 Chirality : 0.041 0.164 5529 Planarity : 0.004 0.056 5981 Dihedral : 15.469 175.744 5752 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.80 % Allowed : 15.79 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.19 % 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: -1.36 (0.12), residues: 4117 helix: -0.38 (0.13), residues: 1539 sheet: 0.10 (0.24), residues: 469 loop : -1.53 (0.12), residues: 2109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 33 HIS 0.012 0.001 HIS G 101 PHE 0.017 0.001 PHE H 183 TYR 0.026 0.001 TYR G 127 ARG 0.010 0.000 ARG A 12 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8234 Ramachandran restraints generated. 4117 Oldfield, 0 Emsley, 4117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8234 Ramachandran restraints generated. 4117 Oldfield, 0 Emsley, 4117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 3573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 279 time to evaluate : 4.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 100 outliers final: 40 residues processed: 356 average time/residue: 1.5754 time to fit residues: 677.4292 Evaluate side-chains 294 residues out of total 3573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 254 time to evaluate : 4.232 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 34 residues processed: 6 average time/residue: 0.5862 time to fit residues: 11.3422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 337 optimal weight: 3.9990 chunk 229 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 301 optimal weight: 0.8980 chunk 167 optimal weight: 0.0470 chunk 345 optimal weight: 0.0970 chunk 279 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 206 optimal weight: 3.9990 chunk 363 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 overall best weight: 1.1478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN A 147 GLN B 18 GLN ** B 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 628 HIS C 799 ASN ** C1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 200 GLN F 464 ASN ** G 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN ** G 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 35899 Z= 0.178 Angle : 0.535 11.821 48967 Z= 0.282 Chirality : 0.042 0.156 5529 Planarity : 0.004 0.057 5981 Dihedral : 15.419 175.699 5752 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.24 % Allowed : 17.44 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.19 % 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: -1.08 (0.13), residues: 4117 helix: -0.14 (0.14), residues: 1541 sheet: 0.15 (0.23), residues: 502 loop : -1.36 (0.13), residues: 2074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D1020 HIS 0.012 0.001 HIS G 101 PHE 0.014 0.001 PHE C 405 TYR 0.013 0.001 TYR D 631 ARG 0.009 0.000 ARG D 133 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8234 Ramachandran restraints generated. 4117 Oldfield, 0 Emsley, 4117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8234 Ramachandran restraints generated. 4117 Oldfield, 0 Emsley, 4117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 3573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 263 time to evaluate : 4.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 80 outliers final: 49 residues processed: 322 average time/residue: 1.5703 time to fit residues: 608.0811 Evaluate side-chains 306 residues out of total 3573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 257 time to evaluate : 4.114 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 40 residues processed: 9 average time/residue: 1.0811 time to fit residues: 18.8366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 136 optimal weight: 7.9990 chunk 364 optimal weight: 7.9990 chunk 80 optimal weight: 0.3980 chunk 237 optimal weight: 3.9990 chunk 99 optimal weight: 7.9990 chunk 405 optimal weight: 0.0030 chunk 336 optimal weight: 3.9990 chunk 187 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 134 optimal weight: 8.9990 chunk 212 optimal weight: 0.4980 overall best weight: 1.7794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN B 18 GLN C 628 HIS F 464 ASN ** G 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 35899 Z= 0.230 Angle : 0.557 10.753 48967 Z= 0.293 Chirality : 0.043 0.163 5529 Planarity : 0.004 0.063 5981 Dihedral : 15.466 176.125 5752 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.38 % Allowed : 17.60 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.19 % 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: -1.00 (0.13), residues: 4117 helix: -0.09 (0.14), residues: 1544 sheet: 0.13 (0.23), residues: 518 loop : -1.31 (0.13), residues: 2055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D1020 HIS 0.006 0.001 HIS G 101 PHE 0.016 0.001 PHE C 514 TYR 0.025 0.001 TYR G 127 ARG 0.016 0.000 ARG D1173 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8234 Ramachandran restraints generated. 4117 Oldfield, 0 Emsley, 4117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8234 Ramachandran restraints generated. 4117 Oldfield, 0 Emsley, 4117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 3573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 259 time to evaluate : 4.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 85 outliers final: 53 residues processed: 324 average time/residue: 1.5491 time to fit residues: 604.8209 Evaluate side-chains 298 residues out of total 3573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 245 time to evaluate : 3.976 Switching outliers to nearest non-outliers outliers start: 53 outliers final: 44 residues processed: 10 average time/residue: 0.8700 time to fit residues: 17.0535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 390 optimal weight: 30.0000 chunk 45 optimal weight: 2.9990 chunk 230 optimal weight: 4.9990 chunk 296 optimal weight: 6.9990 chunk 229 optimal weight: 4.9990 chunk 341 optimal weight: 0.9990 chunk 226 optimal weight: 8.9990 chunk 403 optimal weight: 30.0000 chunk 252 optimal weight: 4.9990 chunk 246 optimal weight: 6.9990 chunk 186 optimal weight: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: