Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 21 01:27:49 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rfl_4868/04_2023/6rfl_4868_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rfl_4868/04_2023/6rfl_4868.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rfl_4868/04_2023/6rfl_4868.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rfl_4868/04_2023/6rfl_4868.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rfl_4868/04_2023/6rfl_4868_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rfl_4868/04_2023/6rfl_4868_updated.pdb" } resolution = 2.76 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3993 atoms to isotropic. 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 4 6.06 5 P 72 5.49 5 Mg 1 5.21 5 S 224 5.16 5 C 32977 2.51 5 N 8569 2.21 5 O 9941 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 29": "NH1" <-> "NH2" Residue "B ARG 45": "NH1" <-> "NH2" Residue "B ARG 65": "NH1" <-> "NH2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B ARG 204": "NH1" <-> "NH2" Residue "B ARG 206": "NH1" <-> "NH2" Residue "B ARG 249": "NH1" <-> "NH2" Residue "B ARG 250": "NH1" <-> "NH2" Residue "B ARG 336": "NH1" <-> "NH2" Residue "B ARG 351": "NH1" <-> "NH2" Residue "B ARG 358": "NH1" <-> "NH2" Residue "B GLU 375": "OE1" <-> "OE2" Residue "B ARG 382": "NH1" <-> "NH2" Residue "B ARG 392": "NH1" <-> "NH2" Residue "B ARG 442": "NH1" <-> "NH2" Residue "B GLU 477": "OE1" <-> "OE2" Residue "B ARG 478": "NH1" <-> "NH2" Residue "B GLU 511": "OE1" <-> "OE2" Residue "B GLU 525": "OE1" <-> "OE2" Residue "B GLU 533": "OE1" <-> "OE2" Residue "B ARG 553": "NH1" <-> "NH2" Residue "B ARG 554": "NH1" <-> "NH2" Residue "B ARG 557": "NH1" <-> "NH2" Residue "B ARG 572": "NH1" <-> "NH2" Residue "B ARG 589": "NH1" <-> "NH2" Residue "B GLU 633": "OE1" <-> "OE2" Residue "B ARG 648": "NH1" <-> "NH2" Residue "B ARG 668": "NH1" <-> "NH2" Residue "B ARG 706": "NH1" <-> "NH2" Residue "B ARG 792": "NH1" <-> "NH2" Residue "B ARG 808": "NH1" <-> "NH2" Residue "B ARG 821": "NH1" <-> "NH2" Residue "B ARG 856": "NH1" <-> "NH2" Residue "B ARG 876": "NH1" <-> "NH2" Residue "B GLU 906": "OE1" <-> "OE2" Residue "B ARG 923": "NH1" <-> "NH2" Residue "B GLU 974": "OE1" <-> "OE2" Residue "B GLU 992": "OE1" <-> "OE2" Residue "B GLU 999": "OE1" <-> "OE2" Residue "B PHE 1010": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1047": "NH1" <-> "NH2" Residue "B ARG 1058": "NH1" <-> "NH2" Residue "B GLU 1072": "OE1" <-> "OE2" Residue "B ARG 1105": "NH1" <-> "NH2" Residue "B ARG 1134": "NH1" <-> "NH2" Residue "E ARG 34": "NH1" <-> "NH2" Residue "E ARG 51": "NH1" <-> "NH2" Residue "E ARG 138": "NH1" <-> "NH2" Residue "E ARG 154": "NH1" <-> "NH2" Residue "E ARG 166": "NH1" <-> "NH2" Residue "F ARG 75": "NH1" <-> "NH2" Residue "F GLU 122": "OE1" <-> "OE2" Residue "F GLU 131": "OE1" <-> "OE2" Residue "G GLU 15": "OE1" <-> "OE2" Residue "G GLU 18": "OE1" <-> "OE2" Residue "G ARG 28": "NH1" <-> "NH2" Residue "G PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 35": "NH1" <-> "NH2" Residue "I ARG 210": "NH1" <-> "NH2" Residue "I ARG 317": "NH1" <-> "NH2" Residue "I GLU 322": "OE1" <-> "OE2" Residue "I GLU 352": "OE1" <-> "OE2" Residue "I ARG 408": "NH1" <-> "NH2" Residue "I ARG 466": "NH1" <-> "NH2" Residue "I ARG 539": "NH1" <-> "NH2" Residue "I ARG 576": "NH1" <-> "NH2" Residue "I ARG 583": "NH1" <-> "NH2" Residue "I ARG 595": "NH1" <-> "NH2" Residue "I ARG 659": "NH1" <-> "NH2" Residue "I ARG 710": "NH1" <-> "NH2" Residue "I ARG 784": "NH1" <-> "NH2" Residue "I GLU 787": "OE1" <-> "OE2" Residue "J GLU 17": "OE1" <-> "OE2" Residue "J ARG 24": "NH1" <-> "NH2" Residue "L GLU 38": "OE1" <-> "OE2" Residue "O GLU 37": "OE1" <-> "OE2" Residue "O GLU 39": "OE1" <-> "OE2" Residue "O GLU 127": "OE1" <-> "OE2" Residue "O TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 207": "OE1" <-> "OE2" Residue "O GLU 211": "OE1" <-> "OE2" Residue "O ARG 217": "NH1" <-> "NH2" Residue "O TYR 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 408": "NH1" <-> "NH2" Residue "O GLU 413": "OE1" <-> "OE2" Residue "O PHE 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 548": "NH1" <-> "NH2" Residue "O PHE 672": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 2": "OE1" <-> "OE2" Residue "R ARG 65": "NH1" <-> "NH2" Residue "K ARG 380": "NH1" <-> "NH2" Residue "K GLU 406": "OE1" <-> "OE2" Residue "K PHE 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 99": "NH1" <-> "NH2" Residue "A ARG 117": "NH1" <-> "NH2" Residue "A GLU 174": "OE1" <-> "OE2" Residue "A GLU 181": "OE1" <-> "OE2" Residue "A ARG 280": "NH1" <-> "NH2" Residue "A ARG 287": "NH1" <-> "NH2" Residue "A ARG 308": "NH1" <-> "NH2" Residue "A PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 347": "NH1" <-> "NH2" Residue "A ARG 386": "NH1" <-> "NH2" Residue "A ARG 395": "NH1" <-> "NH2" Residue "A GLU 461": "OE1" <-> "OE2" Residue "A ARG 488": "NH1" <-> "NH2" Residue "A ARG 537": "NH1" <-> "NH2" Residue "A ARG 567": "NH1" <-> "NH2" Residue "A TYR 568": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 600": "OE1" <-> "OE2" Residue "A ARG 687": "NH1" <-> "NH2" Residue "A GLU 694": "OE1" <-> "OE2" Residue "A ARG 696": "NH1" <-> "NH2" Residue "A ARG 715": "NH1" <-> "NH2" Residue "A GLU 764": "OE1" <-> "OE2" Residue "A ARG 872": "NH1" <-> "NH2" Residue "A ARG 897": "NH1" <-> "NH2" Residue "A ARG 899": "NH1" <-> "NH2" Residue "A GLU 914": "OE1" <-> "OE2" Residue "A GLU 996": "OE1" <-> "OE2" Residue "A GLU 1034": "OE1" <-> "OE2" Residue "A ARG 1043": "NH1" <-> "NH2" Residue "A ARG 1211": "NH1" <-> "NH2" Residue "A PHE 1255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1263": "NH1" <-> "NH2" Residue "Q GLU 74": "OE1" <-> "OE2" Residue "Y ARG 15": "NH1" <-> "NH2" Residue "Y ARG 100": "NH1" <-> "NH2" Residue "Y ARG 120": "NH1" <-> "NH2" Residue "Y ARG 159": "NH1" <-> "NH2" Residue "Y PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 216": "NH1" <-> "NH2" Residue "Y ARG 287": "NH1" <-> "NH2" Residue "Y ARG 328": "NH1" <-> "NH2" Residue "Y ARG 330": "NH1" <-> "NH2" Residue "Y ARG 479": "NH1" <-> "NH2" Residue "Y ARG 490": "NH1" <-> "NH2" Residue "Y GLU 515": "OE1" <-> "OE2" Residue "Y ARG 561": "NH1" <-> "NH2" Residue "Y ARG 588": "NH1" <-> "NH2" Residue "Y ARG 594": "NH1" <-> "NH2" Residue "Y ARG 602": "NH1" <-> "NH2" Residue "Y PHE 631": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 5": "NH1" <-> "NH2" Residue "C GLU 15": "OE1" <-> "OE2" Residue "C GLU 50": "OE1" <-> "OE2" Residue "C GLU 57": "OE1" <-> "OE2" Residue "C ARG 75": "NH1" <-> "NH2" Residue "C GLU 119": "OE1" <-> "OE2" Residue "C ARG 270": "NH1" <-> "NH2" Residue "S GLU 99": "OE1" <-> "OE2" Residue "S ARG 119": "NH1" <-> "NH2" Residue "S GLU 220": "OE1" <-> "OE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 51788 Number of models: 1 Model: "" Number of chains: 29 Chain: "B" Number of atoms: 9091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1129, 9091 Classifications: {'peptide': 1129} Link IDs: {'PCIS': 1, 'PTRANS': 51, 'TRANS': 1076} Chain breaks: 2 Chain: "E" Number of atoms: 1495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1495 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 8, 'TRANS': 175} Chain: "F" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 849 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 2, 'TRANS': 100} Chain: "G" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1192 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 3, 'TRANS': 149} Chain breaks: 1 Chain: "I" Number of atoms: 6446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 773, 6446 Classifications: {'peptide': 773} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 747} Chain breaks: 3 Chain: "J" Number of atoms: 490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 490 Classifications: {'peptide': 61} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 58} Chain: "L" Number of atoms: 2320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2320 Classifications: {'peptide': 284} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 274} Chain breaks: 1 Chain: "O" Number of atoms: 6693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 826, 6693 Classifications: {'peptide': 826} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 794} Chain breaks: 2 Chain: "R" Number of atoms: 1056 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 129, 1050 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 3, 'TRANS': 125} Conformer: "B" Number of residues, atoms: 129, 1050 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 3, 'TRANS': 125} bond proxies already assigned to first conformer: 1065 Chain: "K" Number of atoms: 749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 749 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 4, 'TRANS': 86} Chain breaks: 1 Chain: "U" Number of atoms: 1465 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 63, 1339 Classifications: {'RNA': 63} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 24, 'rna3p_pyr': 26} Link IDs: {'rna2p': 13, 'rna3p': 49} Conformer: "B" Number of residues, atoms: 63, 1339 Classifications: {'RNA': 63} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 24, 'rna3p_pyr': 26} Link IDs: {'rna2p': 13, 'rna3p': 49} bond proxies already assigned to first conformer: 1353 Chain: "A" Number of atoms: 10223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1272, 10223 Classifications: {'peptide': 1272} Link IDs: {'PCIS': 2, 'PTRANS': 42, 'TRANS': 1227} Chain breaks: 1 Chain: "Q" Number of atoms: 1013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1013 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 120} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "Y" Number of atoms: 4845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4845 Classifications: {'peptide': 600} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 588} Chain breaks: 3 Chain: "C" Number of atoms: 2484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2484 Classifications: {'peptide': 304} Link IDs: {'PTRANS': 9, 'TRANS': 294} Chain: "S" Number of atoms: 1311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1311 Classifications: {'peptide': 161} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 150} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 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: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "A" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "Y" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" 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 8500 SG CYS B1087 105.276 115.084 71.255 1.00 25.66 S ATOM 8523 SG CYS B1090 101.695 115.851 71.255 1.00 25.35 S ATOM 8612 SG CYS B1103 103.043 113.484 73.296 1.00 25.51 S ATOM 8637 SG CYS B1106 102.584 112.662 69.532 1.00 25.49 S ATOM 15216 SG CYS I 326 115.098 119.650 107.998 1.00 40.87 S ATOM 15529 SG CYS I 363 112.367 122.550 107.745 1.00 33.08 S ATOM 15553 SG CYS I 366 115.408 122.628 105.707 1.00 34.01 S ATOM 32206 SG CYS A 49 98.438 113.748 87.272 1.00 30.79 S ATOM 32228 SG CYS A 52 101.986 114.152 87.014 1.00 31.60 S ATOM 32280 SG CYS A 59 99.929 117.063 86.284 1.00 30.11 S ATOM 32540 SG CYS A 90 74.287 119.143 45.013 1.00 40.45 S ATOM 32564 SG CYS A 93 75.885 116.030 43.823 1.00 41.41 S ATOM 32862 SG CYS A 130 74.481 118.672 41.406 1.00 51.63 S ATOM 32905 SG CYS A 135 72.134 116.537 43.205 1.00 52.40 S Residues with excluded nonbonded symmetry interactions: 6 residue: pdb=" P A G U 18 " occ=0.50 ... (44 atoms not shown) pdb=" C4 B G U 18 " occ=0.50 residue: pdb=" P A U U 19 " occ=0.50 ... (38 atoms not shown) pdb=" C6 B U U 19 " occ=0.50 residue: pdb=" P A U U 20 " occ=0.50 ... (38 atoms not shown) pdb=" C6 B U U 20 " occ=0.50 residue: pdb=" P A U U 34 " occ=0.50 ... (38 atoms not shown) pdb=" C6 B U U 34 " occ=0.50 residue: pdb=" P A U U 35 " occ=0.50 ... (38 atoms not shown) pdb=" C6 B U U 35 " occ=0.50 residue: pdb=" P A G U 36 " occ=0.50 ... (44 atoms not shown) pdb=" C4 B G U 36 " occ=0.50 Time building chain proxies: 19.95, per 1000 atoms: 0.39 Number of scatterers: 51788 At special positions: 0 Unit cell: (173.351, 214.827, 162.716, 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 4 29.99 S 224 16.00 P 72 15.00 Mg 1 11.99 O 9941 8.00 N 8569 7.00 C 32977 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS J 7 " - pdb=" SG CYS J 39 " distance=2.04 Simple disulfide: pdb=" SG CYS K 372 " - pdb=" SG CYS K 441 " distance=2.03 Simple disulfide: pdb=" SG CYS K 418 " - pdb=" SG CYS K 442 " distance=2.02 Simple disulfide: pdb=" SG CYS K 438 " - pdb=" SG CYS K 456 " distance=2.03 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=0, symmetry=0 Time building additional restraints: 15.01 Conformation dependent library (CDL) restraints added in 5.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1302 " pdb="ZN ZN A1302 " - pdb=" NE2 HIS A 62 " pdb="ZN ZN A1302 " - pdb=" SG CYS A 59 " pdb="ZN ZN A1302 " - pdb=" SG CYS A 49 " pdb="ZN ZN A1302 " - pdb=" SG CYS A 52 " pdb=" ZN A1303 " pdb="ZN ZN A1303 " - pdb=" SG CYS A 130 " pdb="ZN ZN A1303 " - pdb=" SG CYS A 93 " pdb="ZN ZN A1303 " - pdb=" SG CYS A 135 " pdb="ZN ZN A1303 " - pdb=" SG CYS A 90 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1103 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1090 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1087 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1106 " pdb=" ZN I 801 " pdb="ZN ZN I 801 " - pdb=" ND1 HIS I 328 " pdb="ZN ZN I 801 " - pdb=" SG CYS I 366 " pdb="ZN ZN I 801 " - pdb=" SG CYS I 326 " pdb="ZN ZN I 801 " - pdb=" SG CYS I 363 " Number of angles added : 18 12248 Ramachandran restraints generated. 6124 Oldfield, 0 Emsley, 6124 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11878 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 210 helices and 56 sheets defined 33.0% alpha, 13.6% beta 19 base pairs and 33 stacking pairs defined. Time for finding SS restraints: 15.15 Creating SS restraints... Processing helix chain 'B' and resid 9 through 16 Processing helix chain 'B' and resid 29 through 50 removed outlier: 5.530A pdb=" N PHE B 33 " --> pdb=" O PRO B 30 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL B 36 " --> pdb=" O PHE B 33 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASN B 40 " --> pdb=" O SER B 37 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU B 43 " --> pdb=" O ASN B 40 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N HIS B 44 " --> pdb=" O PHE B 41 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ARG B 45 " --> pdb=" O ILE B 42 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU B 46 " --> pdb=" O LEU B 43 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N LEU B 50 " --> pdb=" O HIS B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 87 Processing helix chain 'B' and resid 217 through 219 No H-bonds generated for 'chain 'B' and resid 217 through 219' Processing helix chain 'B' and resid 233 through 240 Processing helix chain 'B' and resid 246 through 252 Processing helix chain 'B' and resid 258 through 277 removed outlier: 3.628A pdb=" N TYR B 262 " --> pdb=" O PRO B 258 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N LEU B 263 " --> pdb=" O GLU B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 297 Processing helix chain 'B' and resid 308 through 312 Processing helix chain 'B' and resid 324 through 343 removed outlier: 3.920A pdb=" N PHE B 343 " --> pdb=" O LEU B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 347 No H-bonds generated for 'chain 'B' and resid 345 through 347' Processing helix chain 'B' and resid 362 through 391 removed outlier: 3.834A pdb=" N PHE B 366 " --> pdb=" O TYR B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 415 Processing helix chain 'B' and resid 434 through 439 Processing helix chain 'B' and resid 464 through 466 No H-bonds generated for 'chain 'B' and resid 464 through 466' Processing helix chain 'B' and resid 499 through 514 removed outlier: 3.667A pdb=" N ASP B 504 " --> pdb=" O SER B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 542 through 557 removed outlier: 3.737A pdb=" N ILE B 545 " --> pdb=" O PRO B 542 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N CYS B 546 " --> pdb=" O ASN B 543 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ASP B 547 " --> pdb=" O MET B 544 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR B 550 " --> pdb=" O ASP B 547 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP B 551 " --> pdb=" O PHE B 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 611 through 613 No H-bonds generated for 'chain 'B' and resid 611 through 613' Processing helix chain 'B' and resid 616 through 622 Processing helix chain 'B' and resid 632 through 636 Processing helix chain 'B' and resid 644 through 648 Processing helix chain 'B' and resid 655 through 657 No H-bonds generated for 'chain 'B' and resid 655 through 657' Processing helix chain 'B' and resid 665 through 668 Processing helix chain 'B' and resid 684 through 694 removed outlier: 4.050A pdb=" N ILE B 688 " --> pdb=" O GLY B 684 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU B 689 " --> pdb=" O PRO B 685 " (cutoff:3.500A) Processing helix chain 'B' and resid 726 through 730 Processing helix chain 'B' and resid 762 through 766 Processing helix chain 'B' and resid 899 through 901 No H-bonds generated for 'chain 'B' and resid 899 through 901' Processing helix chain 'B' and resid 917 through 922 Processing helix chain 'B' and resid 926 through 940 removed outlier: 3.527A pdb=" N LEU B 934 " --> pdb=" O GLU B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 962 through 976 Processing helix chain 'B' and resid 984 through 989 Processing helix chain 'B' and resid 1022 through 1024 No H-bonds generated for 'chain 'B' and resid 1022 through 1024' Processing helix chain 'B' and resid 1055 through 1063 Processing helix chain 'B' and resid 1067 through 1073 Processing helix chain 'B' and resid 1078 through 1080 No H-bonds generated for 'chain 'B' and resid 1078 through 1080' Processing helix chain 'B' and resid 1104 through 1108 Processing helix chain 'B' and resid 1122 through 1133 Processing helix chain 'E' and resid 5 through 21 removed outlier: 3.750A pdb=" N CYS E 14 " --> pdb=" O ALA E 10 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N LEU E 15 " --> pdb=" O LYS E 11 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS E 16 " --> pdb=" O ILE E 12 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N THR E 17 " --> pdb=" O LEU E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 34 Processing helix chain 'E' and resid 97 through 100 Processing helix chain 'E' and resid 119 through 127 Processing helix chain 'E' and resid 147 through 151 Processing helix chain 'F' and resid 63 through 74 Processing helix chain 'F' and resid 79 through 95 Processing helix chain 'F' and resid 113 through 123 Processing helix chain 'F' and resid 144 through 160 Processing helix chain 'G' and resid 16 through 18 No H-bonds generated for 'chain 'G' and resid 16 through 18' Processing helix chain 'G' and resid 23 through 35 Processing helix chain 'I' and resid 4 through 20 removed outlier: 3.712A pdb=" N GLU I 10 " --> pdb=" O THR I 6 " (cutoff:3.500A) Proline residue: I 13 - end of helix Processing helix chain 'I' and resid 29 through 35 Processing helix chain 'I' and resid 38 through 44 removed outlier: 3.513A pdb=" N VAL I 41 " --> pdb=" O ASN I 38 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ILE I 42 " --> pdb=" O ILE I 39 " (cutoff:3.500A) Processing helix chain 'I' and resid 52 through 64 Processing helix chain 'I' and resid 70 through 79 removed outlier: 3.839A pdb=" N VAL I 74 " --> pdb=" O ASP I 70 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ALA I 75 " --> pdb=" O GLN I 71 " (cutoff:3.500A) Processing helix chain 'I' and resid 94 through 96 No H-bonds generated for 'chain 'I' and resid 94 through 96' Processing helix chain 'I' and resid 107 through 118 Processing helix chain 'I' and resid 168 through 185 removed outlier: 3.581A pdb=" N LEU I 171 " --> pdb=" O MET I 168 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N LEU I 172 " --> pdb=" O LYS I 169 " (cutoff:3.500A) Proline residue: I 173 - end of helix removed outlier: 5.142A pdb=" N LEU I 179 " --> pdb=" O GLU I 176 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N ASP I 180 " --> pdb=" O LYS I 177 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER I 185 " --> pdb=" O LEU I 182 " (cutoff:3.500A) Processing helix chain 'I' and resid 189 through 191 No H-bonds generated for 'chain 'I' and resid 189 through 191' Processing helix chain 'I' and resid 255 through 266 removed outlier: 4.315A pdb=" N LYS I 261 " --> pdb=" O SER I 257 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N VAL I 262 " --> pdb=" O ASP I 258 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE I 264 " --> pdb=" O GLY I 260 " (cutoff:3.500A) Proline residue: I 265 - end of helix Processing helix chain 'I' and resid 270 through 278 removed outlier: 3.550A pdb=" N TYR I 273 " --> pdb=" O ARG I 270 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N SER I 274 " --> pdb=" O HIS I 271 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N TYR I 275 " --> pdb=" O LEU I 272 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE I 276 " --> pdb=" O TYR I 273 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU I 278 " --> pdb=" O TYR I 275 " (cutoff:3.500A) Processing helix chain 'I' and resid 284 through 290 removed outlier: 4.618A pdb=" N THR I 288 " --> pdb=" O SER I 285 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASP I 289 " --> pdb=" O TYR I 286 " (cutoff:3.500A) Processing helix chain 'I' and resid 327 through 335 Processing helix chain 'I' and resid 343 through 353 Processing helix chain 'I' and resid 371 through 373 No H-bonds generated for 'chain 'I' and resid 371 through 373' Processing helix chain 'I' and resid 405 through 420 removed outlier: 3.534A pdb=" N ARG I 408 " --> pdb=" O HIS I 405 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N PHE I 411 " --> pdb=" O ARG I 408 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ASN I 412 " --> pdb=" O PHE I 409 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER I 416 " --> pdb=" O ILE I 413 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASN I 419 " --> pdb=" O SER I 416 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE I 420 " --> pdb=" O PHE I 417 " (cutoff:3.500A) Processing helix chain 'I' and resid 426 through 445 removed outlier: 3.649A pdb=" N LYS I 429 " --> pdb=" O TRP I 426 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N TYR I 430 " --> pdb=" O VAL I 427 " (cutoff:3.500A) Processing helix chain 'I' and resid 447 through 453 removed outlier: 3.727A pdb=" N LYS I 452 " --> pdb=" O GLN I 448 " (cutoff:3.500A) Processing helix chain 'I' and resid 455 through 458 No H-bonds generated for 'chain 'I' and resid 455 through 458' Processing helix chain 'I' and resid 483 through 500 Processing helix chain 'I' and resid 504 through 513 Processing helix chain 'I' and resid 523 through 537 Processing helix chain 'I' and resid 546 through 556 Processing helix chain 'I' and resid 562 through 580 removed outlier: 3.805A pdb=" N VAL I 579 " --> pdb=" O LEU I 575 " (cutoff:3.500A) Processing helix chain 'I' and resid 639 through 648 Processing helix chain 'I' and resid 706 through 709 No H-bonds generated for 'chain 'I' and resid 706 through 709' Processing helix chain 'I' and resid 724 through 741 Processing helix chain 'I' and resid 757 through 770 removed outlier: 3.629A pdb=" N LYS I 770 " --> pdb=" O ILE I 766 " (cutoff:3.500A) Processing helix chain 'I' and resid 774 through 792 removed outlier: 5.824A pdb=" N THR I 783 " --> pdb=" O ASP I 779 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ARG I 784 " --> pdb=" O GLU I 780 " (cutoff:3.500A) Processing helix chain 'J' and resid 16 through 19 No H-bonds generated for 'chain 'J' and resid 16 through 19' Processing helix chain 'J' and resid 28 through 35 removed outlier: 4.583A pdb=" N SER J 34 " --> pdb=" O ASP J 30 " (cutoff:3.500A) Processing helix chain 'J' and resid 38 through 45 Processing helix chain 'L' and resid 3 through 10 Processing helix chain 'L' and resid 37 through 39 No H-bonds generated for 'chain 'L' and resid 37 through 39' Processing helix chain 'L' and resid 44 through 54 removed outlier: 5.969A pdb=" N ARG L 49 " --> pdb=" O LEU L 45 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N VAL L 50 " --> pdb=" O GLN L 46 " (cutoff:3.500A) Processing helix chain 'L' and resid 58 through 65 Processing helix chain 'L' and resid 74 through 81 Processing helix chain 'L' and resid 133 through 135 No H-bonds generated for 'chain 'L' and resid 133 through 135' Processing helix chain 'L' and resid 139 through 145 removed outlier: 3.652A pdb=" N ARG L 142 " --> pdb=" O ASP L 139 " (cutoff:3.500A) Proline residue: L 143 - end of helix No H-bonds generated for 'chain 'L' and resid 139 through 145' Processing helix chain 'L' and resid 164 through 175 Processing helix chain 'L' and resid 203 through 217 Processing helix chain 'L' and resid 239 through 266 removed outlier: 4.149A pdb=" N PHE L 248 " --> pdb=" O LYS L 244 " (cutoff:3.500A) Processing helix chain 'L' and resid 277 through 286 Processing helix chain 'O' and resid 11 through 22 Processing helix chain 'O' and resid 48 through 54 Processing helix chain 'O' and resid 92 through 97 Processing helix chain 'O' and resid 135 through 137 No H-bonds generated for 'chain 'O' and resid 135 through 137' Processing helix chain 'O' and resid 175 through 181 Processing helix chain 'O' and resid 205 through 220 removed outlier: 3.850A pdb=" N HIS O 218 " --> pdb=" O THR O 214 " (cutoff:3.500A) Processing helix chain 'O' and resid 247 through 249 No H-bonds generated for 'chain 'O' and resid 247 through 249' Processing helix chain 'O' and resid 327 through 337 removed outlier: 3.721A pdb=" N LYS O 332 " --> pdb=" O LEU O 328 " (cutoff:3.500A) Processing helix chain 'O' and resid 359 through 369 removed outlier: 3.851A pdb=" N VAL O 363 " --> pdb=" O THR O 359 " (cutoff:3.500A) Processing helix chain 'O' and resid 385 through 387 No H-bonds generated for 'chain 'O' and resid 385 through 387' Processing helix chain 'O' and resid 466 through 468 No H-bonds generated for 'chain 'O' and resid 466 through 468' Processing helix chain 'O' and resid 494 through 502 Processing helix chain 'O' and resid 511 through 521 Processing helix chain 'O' and resid 525 through 527 No H-bonds generated for 'chain 'O' and resid 525 through 527' Processing helix chain 'O' and resid 534 through 543 Processing helix chain 'O' and resid 564 through 580 removed outlier: 3.911A pdb=" N MET O 579 " --> pdb=" O LEU O 575 " (cutoff:3.500A) Processing helix chain 'O' and resid 605 through 610 Processing helix chain 'O' and resid 624 through 636 removed outlier: 3.775A pdb=" N ARG O 632 " --> pdb=" O ARG O 628 " (cutoff:3.500A) Processing helix chain 'O' and resid 663 through 665 No H-bonds generated for 'chain 'O' and resid 663 through 665' Processing helix chain 'O' and resid 681 through 683 No H-bonds generated for 'chain 'O' and resid 681 through 683' Processing helix chain 'O' and resid 687 through 689 No H-bonds generated for 'chain 'O' and resid 687 through 689' Processing helix chain 'O' and resid 691 through 699 removed outlier: 4.045A pdb=" N ASN O 696 " --> pdb=" O THR O 692 " (cutoff:3.500A) Processing helix chain 'O' and resid 714 through 717 No H-bonds generated for 'chain 'O' and resid 714 through 717' Processing helix chain 'O' and resid 768 through 777 Processing helix chain 'O' and resid 788 through 801 removed outlier: 4.696A pdb=" N LYS O 797 " --> pdb=" O GLU O 793 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N PHE O 798 " --> pdb=" O ARG O 794 " (cutoff:3.500A) Processing helix chain 'O' and resid 809 through 822 removed outlier: 3.576A pdb=" N ASN O 813 " --> pdb=" O PRO O 809 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N PHE O 814 " --> pdb=" O SER O 810 " (cutoff:3.500A) Processing helix chain 'O' and resid 829 through 832 No H-bonds generated for 'chain 'O' and resid 829 through 832' Processing helix chain 'R' and resid 27 through 39 removed outlier: 4.774A pdb=" N ASN R 32 " --> pdb=" O SER R 28 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N LYS R 33 " --> pdb=" O GLU R 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 44 through 46 No H-bonds generated for 'chain 'R' and resid 44 through 46' Processing helix chain 'K' and resid 451 through 456 Processing helix chain 'A' and resid 14 through 18 Processing helix chain 'A' and resid 76 through 88 removed outlier: 4.062A pdb=" N ILE A 79 " --> pdb=" O PRO A 76 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N SER A 80 " --> pdb=" O GLU A 77 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU A 81 " --> pdb=" O PHE A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 126 Processing helix chain 'A' and resid 162 through 170 Processing helix chain 'A' and resid 174 through 180 removed outlier: 3.532A pdb=" N TRP A 177 " --> pdb=" O GLU A 174 " (cutoff:3.500A) Proline residue: A 178 - end of helix No H-bonds generated for 'chain 'A' and resid 174 through 180' Processing helix chain 'A' and resid 219 through 232 Processing helix chain 'A' and resid 237 through 248 Processing helix chain 'A' and resid 250 through 252 No H-bonds generated for 'chain 'A' and resid 250 through 252' Processing helix chain 'A' and resid 262 through 266 removed outlier: 4.271A pdb=" N ILE A 265 " --> pdb=" O LEU A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 276 No H-bonds generated for 'chain 'A' and resid 273 through 276' Processing helix chain 'A' and resid 305 through 310 Processing helix chain 'A' and resid 322 through 330 Processing helix chain 'A' and resid 355 through 357 No H-bonds generated for 'chain 'A' and resid 355 through 357' Processing helix chain 'A' and resid 429 through 438 Processing helix chain 'A' and resid 459 through 470 removed outlier: 4.255A pdb=" N VAL A 463 " --> pdb=" O GLN A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 487 removed outlier: 6.710A pdb=" N LYS A 485 " --> pdb=" O ASN A 481 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N TYR A 486 " --> pdb=" O ILE A 482 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N GLY A 487 " --> pdb=" O LEU A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 507 Processing helix chain 'A' and resid 530 through 533 No H-bonds generated for 'chain 'A' and resid 530 through 533' Processing helix chain 'A' and resid 541 through 548 Processing helix chain 'A' and resid 551 through 571 Processing helix chain 'A' and resid 578 through 580 No H-bonds generated for 'chain 'A' and resid 578 through 580' Processing helix chain 'A' and resid 586 through 614 Processing helix chain 'A' and resid 623 through 655 Processing helix chain 'A' and resid 660 through 667 Processing helix chain 'A' and resid 673 through 680 Processing helix chain 'A' and resid 712 through 715 Processing helix chain 'A' and resid 728 through 762 Processing helix chain 'A' and resid 810 through 820 Processing helix chain 'A' and resid 842 through 844 No H-bonds generated for 'chain 'A' and resid 842 through 844' Processing helix chain 'A' and resid 857 through 875 Processing helix chain 'A' and resid 883 through 892 Processing helix chain 'A' and resid 902 through 918 Processing helix chain 'A' and resid 926 through 945 removed outlier: 4.587A pdb=" N SER A 944 " --> pdb=" O GLN A 940 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N SER A 945 " --> pdb=" O GLN A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 961 through 969 Processing helix chain 'A' and resid 986 through 995 Processing helix chain 'A' and resid 1000 through 1003 Processing helix chain 'A' and resid 1024 through 1029 Processing helix chain 'A' and resid 1036 through 1045 Processing helix chain 'A' and resid 1078 through 1092 Proline residue: A1090 - end of helix Processing helix chain 'A' and resid 1130 through 1133 Processing helix chain 'A' and resid 1147 through 1154 Processing helix chain 'A' and resid 1156 through 1171 Processing helix chain 'A' and resid 1176 through 1189 removed outlier: 4.220A pdb=" N GLN A1180 " --> pdb=" O TYR A1177 " (cutoff:3.500A) Proline residue: A1181 - end of helix Processing helix chain 'A' and resid 1208 through 1214 Processing helix chain 'A' and resid 1219 through 1226 Processing helix chain 'A' and resid 1236 through 1240 Processing helix chain 'A' and resid 1248 through 1251 Processing helix chain 'A' and resid 1259 through 1262 No H-bonds generated for 'chain 'A' and resid 1259 through 1262' Processing helix chain 'Q' and resid 30 through 41 Processing helix chain 'Q' and resid 44 through 46 No H-bonds generated for 'chain 'Q' and resid 44 through 46' Processing helix chain 'Y' and resid 5 through 16 Processing helix chain 'Y' and resid 33 through 44 Processing helix chain 'Y' and resid 61 through 74 removed outlier: 4.951A pdb=" N LYS Y 73 " --> pdb=" O LEU Y 69 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N ASP Y 74 " --> pdb=" O LYS Y 70 " (cutoff:3.500A) Processing helix chain 'Y' and resid 87 through 89 No H-bonds generated for 'chain 'Y' and resid 87 through 89' Processing helix chain 'Y' and resid 93 through 101 Processing helix chain 'Y' and resid 103 through 105 No H-bonds generated for 'chain 'Y' and resid 103 through 105' Processing helix chain 'Y' and resid 119 through 128 Processing helix chain 'Y' and resid 143 through 151 Processing helix chain 'Y' and resid 162 through 174 removed outlier: 4.051A pdb=" N LYS Y 170 " --> pdb=" O ASN Y 166 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ALA Y 173 " --> pdb=" O SER Y 169 " (cutoff:3.500A) Processing helix chain 'Y' and resid 192 through 201 Processing helix chain 'Y' and resid 220 through 226 Processing helix chain 'Y' and resid 265 through 281 Processing helix chain 'Y' and resid 288 through 295 Processing helix chain 'Y' and resid 322 through 327 Processing helix chain 'Y' and resid 335 through 341 Processing helix chain 'Y' and resid 352 through 364 Processing helix chain 'Y' and resid 366 through 377 Processing helix chain 'Y' and resid 393 through 404 Processing helix chain 'Y' and resid 419 through 426 Processing helix chain 'Y' and resid 467 through 477 Processing helix chain 'Y' and resid 509 through 533 removed outlier: 3.857A pdb=" N PHE Y 514 " --> pdb=" O ASP Y 510 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLN Y 526 " --> pdb=" O LYS Y 522 " (cutoff:3.500A) Processing helix chain 'Y' and resid 536 through 542 Processing helix chain 'Y' and resid 555 through 559 Processing helix chain 'C' and resid 16 through 29 Processing helix chain 'C' and resid 49 through 58 removed outlier: 4.143A pdb=" N HIS C 58 " --> pdb=" O THR C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 63 No H-bonds generated for 'chain 'C' and resid 61 through 63' Processing helix chain 'C' and resid 66 through 73 removed outlier: 4.122A pdb=" N ILE C 69 " --> pdb=" O TYR C 66 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N HIS C 70 " --> pdb=" O LYS C 67 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LYS C 71 " --> pdb=" O HIS C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 122 Processing helix chain 'C' and resid 163 through 176 Processing helix chain 'C' and resid 208 through 228 Processing helix chain 'C' and resid 256 through 264 Processing helix chain 'C' and resid 279 through 281 No H-bonds generated for 'chain 'C' and resid 279 through 281' Processing helix chain 'C' and resid 284 through 302 Processing helix chain 'S' and resid 37 through 50 Processing helix chain 'S' and resid 73 through 79 Processing helix chain 'S' and resid 82 through 84 No H-bonds generated for 'chain 'S' and resid 82 through 84' Processing helix chain 'S' and resid 103 through 109 Processing helix chain 'S' and resid 113 through 130 Processing helix chain 'S' and resid 214 through 216 No H-bonds generated for 'chain 'S' and resid 214 through 216' Processing sheet with id= A, first strand: chain 'B' and resid 54 through 59 removed outlier: 6.551A pdb=" N ILE B 66 " --> pdb=" O LEU B 56 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N SER B 58 " --> pdb=" O GLU B 64 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N GLU B 64 " --> pdb=" O SER B 58 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N THR B 99 " --> pdb=" O SER B 71 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N LYS B 104 " --> pdb=" O LYS B 116 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N LYS B 116 " --> pdb=" O LYS B 104 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N VAL B 106 " --> pdb=" O ILE B 114 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N ILE B 114 " --> pdb=" O VAL B 106 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 74 through 76 Processing sheet with id= C, first strand: chain 'B' and resid 156 through 158 Processing sheet with id= D, first strand: chain 'B' and resid 221 through 223 removed outlier: 3.514A pdb=" N ASN B 221 " --> pdb=" O SER B 211 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER B 187 " --> pdb=" O LYS B 184 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS B 184 " --> pdb=" O SER B 187 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N THR B 189 " --> pdb=" O VAL B 182 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N VAL B 182 " --> pdb=" O THR B 189 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N SER B 191 " --> pdb=" O PHE B 180 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N PHE B 180 " --> pdb=" O SER B 191 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 443 through 445 Processing sheet with id= F, first strand: chain 'B' and resid 567 through 571 removed outlier: 7.324A pdb=" N ILE B 580 " --> pdb=" O PRO B 529 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N THR B 531 " --> pdb=" O ILE B 580 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA B 538 " --> pdb=" O ILE B 530 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ILE B 532 " --> pdb=" O LEU B 536 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N LEU B 536 " --> pdb=" O ILE B 532 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 588 through 592 Processing sheet with id= H, first strand: chain 'B' and resid 712 through 715 removed outlier: 3.809A pdb=" N ILE B 772 " --> pdb=" O ARG B 875 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 1009 through 1015 removed outlier: 4.485A pdb=" N PHE B1009 " --> pdb=" O LEU B 746 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N VAL B 913 " --> pdb=" O ALA B 745 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N THR B 892 " --> pdb=" O ILE B 758 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N ILE B 760 " --> pdb=" O THR B 892 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N ALA B 894 " --> pdb=" O ILE B 760 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 858 through 860 Processing sheet with id= K, first strand: chain 'B' and resid 1095 through 1097 Processing sheet with id= L, first strand: chain 'E' and resid 63 through 65 removed outlier: 6.233A pdb=" N ILE E 82 " --> pdb=" O PHE E 64 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 113 through 115 removed outlier: 7.186A pdb=" N ILE E 181 " --> pdb=" O PRO E 140 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N MET E 142 " --> pdb=" O ILE E 181 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'G' and resid 3 through 14 removed outlier: 6.897A pdb=" N ALA G 77 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N ALA G 45 " --> pdb=" O ALA G 77 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'G' and resid 136 through 140 removed outlier: 5.097A pdb=" N VAL G 97 " --> pdb=" O LEU G 108 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N PHE G 152 " --> pdb=" O ILE G 105 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N LYS G 107 " --> pdb=" O PHE G 152 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N PHE G 154 " --> pdb=" O LYS G 107 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N VAL G 153 " --> pdb=" O GLN G 145 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ASN G 157 " --> pdb=" O LEU G 141 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N LEU G 141 " --> pdb=" O ASN G 157 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'G' and resid 124 through 126 Processing sheet with id= Q, first strand: chain 'I' and resid 121 through 124 removed outlier: 4.132A pdb=" N TYR I 234 " --> pdb=" O ARG I 124 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYS I 242 " --> pdb=" O LEU I 237 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'I' and resid 161 through 166 removed outlier: 6.599A pdb=" N ILE I 128 " --> pdb=" O LYS I 162 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N ILE I 164 " --> pdb=" O ILE I 128 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ILE I 130 " --> pdb=" O ILE I 164 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N PHE I 166 " --> pdb=" O ILE I 130 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N VAL I 132 " --> pdb=" O PHE I 166 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'I' and resid 209 through 217 removed outlier: 3.932A pdb=" N VAL I 209 " --> pdb=" O ASP I 228 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASP I 228 " --> pdb=" O VAL I 209 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'I' and resid 354 through 357 Processing sheet with id= U, first strand: chain 'I' and resid 656 through 659 Processing sheet with id= V, first strand: chain 'I' and resid 668 through 670 Processing sheet with id= W, first strand: chain 'L' and resid 12 through 16 removed outlier: 4.524A pdb=" N VAL L 179 " --> pdb=" O LEU L 16 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL L 99 " --> pdb=" O TYR L 152 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'O' and resid 122 through 124 removed outlier: 4.421A pdb=" N LEU O 38 " --> pdb=" O PHE O 195 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N LEU O 143 " --> pdb=" O LEU O 166 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N LYS O 152 " --> pdb=" O SER O 57 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N SER O 57 " --> pdb=" O LYS O 152 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N LYS O 79 " --> pdb=" O VAL O 103 " (cutoff:3.500A) removed outlier: 9.871A pdb=" N VAL O 103 " --> pdb=" O LYS O 79 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N SER O 108 " --> pdb=" O THR O 125 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N LEU O 123 " --> pdb=" O VAL O 110 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'O' and resid 227 through 229 removed outlier: 4.394A pdb=" N TYR O 284 " --> pdb=" O PHE O 279 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE O 279 " --> pdb=" O TYR O 284 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL O 298 " --> pdb=" O VAL O 270 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL O 299 " --> pdb=" O ILE O 318 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N GLU O 303 " --> pdb=" O LEU O 314 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N LEU O 314 " --> pdb=" O GLU O 303 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N VAL O 305 " --> pdb=" O VAL O 312 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N VAL O 312 " --> pdb=" O VAL O 305 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'O' and resid 255 through 259 Processing sheet with id= AA, first strand: chain 'O' and resid 436 through 445 removed outlier: 6.384A pdb=" N LYS O 428 " --> pdb=" O TYR O 439 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N SER O 441 " --> pdb=" O TYR O 426 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N TYR O 426 " --> pdb=" O SER O 441 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N LYS O 443 " --> pdb=" O VAL O 424 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N VAL O 424 " --> pdb=" O LYS O 443 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ASN O 431 " --> pdb=" O ASP O 400 " (cutoff:3.500A) removed outlier: 10.625A pdb=" N ASP O 400 " --> pdb=" O ASN O 431 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LYS O 491 " --> pdb=" O GLU O 482 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N LEU O 484 " --> pdb=" O ILE O 489 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ILE O 489 " --> pdb=" O LEU O 484 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'O' and resid 415 through 417 Processing sheet with id= AC, first strand: chain 'O' and resid 450 through 453 Processing sheet with id= AD, first strand: chain 'O' and resid 780 through 787 removed outlier: 6.498A pdb=" N VAL O 840 " --> pdb=" O VAL O 783 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ASN O 785 " --> pdb=" O VAL O 838 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N VAL O 838 " --> pdb=" O ASN O 785 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ASP O 787 " --> pdb=" O TYR O 836 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N TYR O 836 " --> pdb=" O ASP O 787 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR O 710 " --> pdb=" O TRP O 677 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE O 674 " --> pdb=" O LYS O 593 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N GLN O 678 " --> pdb=" O ILE O 597 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N LEU O 615 " --> pdb=" O VAL O 594 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N ALA O 596 " --> pdb=" O LEU O 615 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N VAL O 617 " --> pdb=" O ALA O 596 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N LYS O 646 " --> pdb=" O LEU O 616 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N ALA O 618 " --> pdb=" O LYS O 646 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ASP O 648 " --> pdb=" O ALA O 618 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'O' and resid 724 through 727 Processing sheet with id= AF, first strand: chain 'R' and resid 14 through 16 removed outlier: 6.230A pdb=" N ALA R 113 " --> pdb=" O VAL R 94 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N PHE R 96 " --> pdb=" O ALA R 113 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N ILE R 115 " --> pdb=" O PHE R 96 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N VAL R 98 " --> pdb=" O ILE R 115 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N VAL R 117 " --> pdb=" O VAL R 98 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'R' and resid 48 through 54 Processing sheet with id= AH, first strand: chain 'K' and resid 383 through 385 removed outlier: 4.009A pdb=" N MET K 415 " --> pdb=" O ILE K 385 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'K' and resid 399 through 401 Processing sheet with id= AJ, first strand: chain 'K' and resid 427 through 431 removed outlier: 3.813A pdb=" N LYS K 427 " --> pdb=" O PHE K 443 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'A' and resid 6 through 8 Processing sheet with id= AL, first strand: chain 'A' and resid 22 through 24 removed outlier: 4.361A pdb=" N SER A 67 " --> pdb=" O ILE A 24 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'A' and resid 142 through 144 removed outlier: 4.195A pdb=" N PHE A 151 " --> pdb=" O VAL A 160 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ILE A 158 " --> pdb=" O ASN A 153 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'A' and resid 285 through 289 Processing sheet with id= AO, first strand: chain 'A' and resid 290 through 292 removed outlier: 5.994A pdb=" N ILE A 402 " --> pdb=" O GLY A 291 " (cutoff:3.500A) No H-bonds generated for sheet with id= AO Processing sheet with id= AP, first strand: chain 'A' and resid 312 through 316 removed outlier: 7.209A pdb=" N ALA A 369 " --> pdb=" O VAL A 334 " (cutoff:3.500A) removed outlier: 8.298A pdb=" N VAL A 334 " --> pdb=" O ALA A 369 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'A' and resid 796 through 799 Processing sheet with id= AR, first strand: chain 'A' and resid 976 through 978 Processing sheet with id= AS, first strand: chain 'A' and resid 979 through 981 Processing sheet with id= AT, first strand: chain 'A' and resid 1008 through 1012 removed outlier: 3.641A pdb=" N LYS A1015 " --> pdb=" O GLU A1012 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'Q' and resid 48 through 54 Processing sheet with id= AV, first strand: chain 'Q' and resid 113 through 118 removed outlier: 6.494A pdb=" N GLU Q 9 " --> pdb=" O THR Q 92 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N VAL Q 94 " --> pdb=" O PHE Q 7 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N PHE Q 7 " --> pdb=" O VAL Q 94 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'Y' and resid 22 through 24 Processing sheet with id= AX, first strand: chain 'Y' and resid 231 through 234 removed outlier: 8.150A pdb=" N SER Y 232 " --> pdb=" O SER Y 50 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LEU Y 52 " --> pdb=" O SER Y 232 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N ILE Y 234 " --> pdb=" O LEU Y 52 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N PHE Y 54 " --> pdb=" O ILE Y 234 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N MET Y 179 " --> pdb=" O LEU Y 51 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N LEU Y 53 " --> pdb=" O MET Y 179 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N CYS Y 181 " --> pdb=" O LEU Y 53 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N HIS Y 55 " --> pdb=" O CYS Y 181 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'Y' and resid 253 through 262 removed outlier: 4.498A pdb=" N ASN Y 456 " --> pdb=" O TYR Y 492 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N LYS Y 381 " --> pdb=" O ASN Y 456 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N ILE Y 458 " --> pdb=" O LYS Y 381 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LEU Y 383 " --> pdb=" O ILE Y 458 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N ILE Y 460 " --> pdb=" O LEU Y 383 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N PHE Y 385 " --> pdb=" O ILE Y 460 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL Y 384 " --> pdb=" O CYS Y 440 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ILE Y 409 " --> pdb=" O VAL Y 441 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N SER Y 443 " --> pdb=" O ILE Y 409 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N PHE Y 411 " --> pdb=" O SER Y 443 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'Y' and resid 592 through 598 removed outlier: 8.136A pdb=" N LEU Y 627 " --> pdb=" O ASN Y 580 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N TRP Y 582 " --> pdb=" O LEU Y 627 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'Y' and resid 602 through 604 removed outlier: 3.688A pdb=" N HIS Y 612 " --> pdb=" O VAL Y 603 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'C' and resid 5 through 13 Processing sheet with id= BC, first strand: chain 'C' and resid 99 through 104 removed outlier: 7.103A pdb=" N ILE C 142 " --> pdb=" O VAL C 40 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N VAL C 40 " --> pdb=" O ILE C 142 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N PHE C 144 " --> pdb=" O GLY C 38 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N GLY C 38 " --> pdb=" O PHE C 144 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'C' and resid 251 through 253 1640 hydrogen bonds defined for protein. 4479 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 49 hydrogen bonds 88 hydrogen bond angles 0 basepair planarities 19 basepair parallelities 33 stacking parallelities Total time for adding SS restraints: 18.80 Time building geometry restraints manager: 16.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 16081 1.34 - 1.47: 12785 1.47 - 1.59: 23597 1.59 - 1.72: 96 1.72 - 1.85: 355 Bond restraints: 52914 Sorted by residual: bond pdb=" CB THR L 12 " pdb=" OG1 THR L 12 " ideal model delta sigma weight residual 1.433 1.505 -0.072 1.60e-02 3.91e+03 2.03e+01 bond pdb=" CB THR L 12 " pdb=" CG2 THR L 12 " ideal model delta sigma weight residual 1.521 1.432 0.089 3.30e-02 9.18e+02 7.20e+00 bond pdb=" CA PRO B1146 " pdb=" C PRO B1146 " ideal model delta sigma weight residual 1.517 1.533 -0.016 6.70e-03 2.23e+04 5.93e+00 bond pdb=" C ASP Y 92 " pdb=" N PRO Y 93 " ideal model delta sigma weight residual 1.334 1.388 -0.054 2.34e-02 1.83e+03 5.40e+00 bond pdb=" C ILE B 909 " pdb=" N THR B 910 " ideal model delta sigma weight residual 1.331 1.283 0.048 2.07e-02 2.33e+03 5.30e+00 ... (remaining 52909 not shown) Histogram of bond angle deviations from ideal: 99.19 - 106.30: 1477 106.30 - 113.41: 29150 113.41 - 120.52: 21520 120.52 - 127.63: 19230 127.63 - 134.74: 471 Bond angle restraints: 71848 Sorted by residual: angle pdb=" N HIS A 92 " pdb=" CA HIS A 92 " pdb=" C HIS A 92 " ideal model delta sigma weight residual 114.62 108.12 6.50 1.14e+00 7.69e-01 3.25e+01 angle pdb=" N LYS A1122 " pdb=" CA LYS A1122 " pdb=" C LYS A1122 " ideal model delta sigma weight residual 110.91 117.21 -6.30 1.17e+00 7.31e-01 2.90e+01 angle pdb=" N THR A1124 " pdb=" CA THR A1124 " pdb=" C THR A1124 " ideal model delta sigma weight residual 110.91 116.91 -6.00 1.17e+00 7.31e-01 2.63e+01 angle pdb=" C TYR B 467 " pdb=" N LEU B 468 " pdb=" CA LEU B 468 " ideal model delta sigma weight residual 121.54 130.72 -9.18 1.91e+00 2.74e-01 2.31e+01 angle pdb=" CA TRP A1054 " pdb=" CB TRP A1054 " pdb=" CG TRP A1054 " ideal model delta sigma weight residual 113.60 122.59 -8.99 1.90e+00 2.77e-01 2.24e+01 ... (remaining 71843 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.61: 31206 35.61 - 71.22: 726 71.22 - 106.83: 29 106.83 - 142.44: 0 142.44 - 178.05: 2 Dihedral angle restraints: 31963 sinusoidal: 13614 harmonic: 18349 Sorted by residual: dihedral pdb=" CA ARG A 582 " pdb=" C ARG A 582 " pdb=" N PRO A 583 " pdb=" CA PRO A 583 " ideal model delta harmonic sigma weight residual 180.00 -124.18 -55.82 0 5.00e+00 4.00e-02 1.25e+02 dihedral pdb=" CA ILE B1097 " pdb=" C ILE B1097 " pdb=" N LYS B1098 " pdb=" CA LYS B1098 " ideal model delta harmonic sigma weight residual -180.00 -134.46 -45.54 0 5.00e+00 4.00e-02 8.29e+01 dihedral pdb=" CA LEU E 116 " pdb=" C LEU E 116 " pdb=" N ASP E 117 " pdb=" CA ASP E 117 " ideal model delta harmonic sigma weight residual 180.00 134.62 45.38 0 5.00e+00 4.00e-02 8.24e+01 ... (remaining 31960 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.017: 8209 1.017 - 2.034: 0 2.034 - 3.051: 0 3.051 - 4.068: 0 4.068 - 5.085: 1 Chirality restraints: 8210 Sorted by residual: chirality pdb=" CB THR L 12 " pdb=" CA THR L 12 " pdb=" OG1 THR L 12 " pdb=" CG2 THR L 12 " both_signs ideal model delta sigma weight residual False 2.55 -2.53 5.08 2.00e-01 2.50e+01 6.46e+02 chirality pdb=" CB VAL B 152 " pdb=" CA VAL B 152 " pdb=" CG1 VAL B 152 " pdb=" CG2 VAL B 152 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" CA THR E 136 " pdb=" N THR E 136 " pdb=" C THR E 136 " pdb=" CB THR E 136 " both_signs ideal model delta sigma weight residual False 2.53 2.24 0.29 2.00e-01 2.50e+01 2.08e+00 ... (remaining 8207 not shown) Planarity restraints: 8821 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE B 42 " -0.024 2.00e-02 2.50e+03 4.88e-02 2.38e+01 pdb=" C ILE B 42 " 0.084 2.00e-02 2.50e+03 pdb=" O ILE B 42 " -0.031 2.00e-02 2.50e+03 pdb=" N LEU B 43 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG A 582 " 0.066 5.00e-02 4.00e+02 1.02e-01 1.68e+01 pdb=" N PRO A 583 " -0.177 5.00e-02 4.00e+02 pdb=" CA PRO A 583 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO A 583 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 594 " -0.018 2.00e-02 2.50e+03 3.58e-02 1.28e+01 pdb=" C VAL B 594 " 0.062 2.00e-02 2.50e+03 pdb=" O VAL B 594 " -0.024 2.00e-02 2.50e+03 pdb=" N ASP B 595 " -0.021 2.00e-02 2.50e+03 ... (remaining 8818 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.29: 13 2.29 - 2.94: 21685 2.94 - 3.60: 72258 3.60 - 4.25: 129064 4.25 - 4.90: 213170 Nonbonded interactions: 436190 Sorted by model distance: nonbonded pdb=" OD1 ASP A 415 " pdb=" OD1 ASP A 417 " model vdw 1.641 3.040 nonbonded pdb=" OD1 ASP A 415 " pdb="MG MG A1301 " model vdw 2.062 2.170 nonbonded pdb=" OD1 ASP A 417 " pdb="MG MG A1301 " model vdw 2.075 2.170 nonbonded pdb=" OD1 ASP A 419 " pdb="MG MG A1301 " model vdw 2.083 2.170 nonbonded pdb=" O PRO Y 20 " pdb=" OH TYR Y 67 " model vdw 2.253 2.440 ... (remaining 436185 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 'Q' and (resid 1 through 15 or resid 17 through 124)) selection = (chain 'R' and (resid 1 through 15 or resid 17 through 29 or (resid 30 and (name \ N or name CA or name C or name O or name CB )) or resid 31 through 124)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.250 Construct map_model_manager: 0.020 Extract box with map and model: 26.200 Check model and map are aligned: 0.560 Set scattering table: 0.330 Process input model: 113.280 Find NCS groups from input model: 1.330 Set up NCS constraints: 0.170 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:9.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 156.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 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 : 0.005 0.089 52914 Z= 0.316 Angle : 0.761 13.929 71848 Z= 0.431 Chirality : 0.076 5.085 8210 Planarity : 0.006 0.102 8821 Dihedral : 14.264 178.048 20073 Min Nonbonded Distance : 1.641 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.24 % Favored : 93.71 % Rotamer Outliers : 4.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.08 % 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: -3.54 (0.09), residues: 6124 helix: -2.43 (0.08), residues: 2212 sheet: -1.70 (0.15), residues: 997 loop : -2.45 (0.10), residues: 2915 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12248 Ramachandran restraints generated. 6124 Oldfield, 0 Emsley, 6124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12248 Ramachandran restraints generated. 6124 Oldfield, 0 Emsley, 6124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1244 residues out of total 5702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 275 poor density : 969 time to evaluate : 4.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 275 outliers final: 77 residues processed: 1186 average time/residue: 1.3208 time to fit residues: 1983.0081 Evaluate side-chains 759 residues out of total 5702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 682 time to evaluate : 4.548 Switching outliers to nearest non-outliers outliers start: 77 outliers final: 70 residues processed: 9 average time/residue: 0.6831 time to fit residues: 15.6907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 620 random chunks: chunk 523 optimal weight: 0.8980 chunk 469 optimal weight: 2.9990 chunk 260 optimal weight: 3.9990 chunk 160 optimal weight: 5.9990 chunk 316 optimal weight: 6.9990 chunk 251 optimal weight: 3.9990 chunk 485 optimal weight: 1.9990 chunk 188 optimal weight: 1.9990 chunk 295 optimal weight: 4.9990 chunk 361 optimal weight: 1.9990 chunk 563 optimal weight: 0.9980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 11 GLN B 40 ASN B 169 ASN B 325 GLN B 371 HIS B 388 ASN B 429 HIS B 431 HIS B 563 ASN B 639 ASN B 681 HIS B 693 GLN ** B 754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 779 GLN B 858 GLN B 967 GLN B 971 GLN B1040 GLN B1064 HIS B1101 ASN B1110 ASN E 125 ASN E 129 GLN E 168 ASN F 112 ASN F 115 HIS F 140 ASN G 17 HIS G 100 GLN G 133 ASN I 46 ASN I 99 ASN I 253 ASN I 271 HIS I 329 GLN I 348 ASN I 419 ASN I 438 ASN I 489 ASN I 567 HIS I 589 ASN I 644 ASN ** I 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 728 GLN ** I 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 740 HIS I 776 GLN J 51 GLN J 53 ASN L 7 ASN L 46 GLN L 229 GLN L 234 ASN L 243 ASN L 276 ASN O 52 ASN O 147 ASN O 463 ASN O 509 ASN O 521 GLN O 601 ASN O 630 ASN O 634 ASN O 678 GLN K 374 ASN K 386 ASN ** K 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 412 ASN K 445 HIS ** K 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 137 GLN ** A 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 167 GLN A 271 ASN A 309 ASN A 318 ASN A 381 GLN A 388 ASN A 450 HIS A 589 ASN A 611 ASN A 636 ASN A 641 ASN A 686 GLN A 741 GLN A 865 HIS A 932 GLN A 941 GLN A 994 ASN A1023 ASN A1142 ASN A1169 ASN A1199 ASN A1235 ASN ** A1239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 78 ASN ** Y 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 177 HIS Y 236 ASN Y 272 GLN Y 391 GLN ** Y 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 466 ASN ** Y 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 551 ASN C 129 GLN C 137 GLN C 171 ASN C 226 ASN C 236 ASN C 260 ASN S 58 ASN S 72 ASN S 73 ASN Total number of N/Q/H flips: 104 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.092 52914 Z= 0.429 Angle : 0.666 11.770 71848 Z= 0.357 Chirality : 0.049 0.350 8210 Planarity : 0.005 0.104 8821 Dihedral : 8.625 175.917 7581 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.84 % Favored : 93.11 % Rotamer Outliers : 5.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.08 % 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: -2.38 (0.10), residues: 6124 helix: -1.03 (0.10), residues: 2197 sheet: -1.28 (0.16), residues: 978 loop : -2.08 (0.10), residues: 2949 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12248 Ramachandran restraints generated. 6124 Oldfield, 0 Emsley, 6124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12248 Ramachandran restraints generated. 6124 Oldfield, 0 Emsley, 6124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 996 residues out of total 5702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 288 poor density : 708 time to evaluate : 4.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 288 outliers final: 139 residues processed: 913 average time/residue: 1.3123 time to fit residues: 1529.7384 Evaluate side-chains 799 residues out of total 5702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 660 time to evaluate : 4.536 Switching outliers to nearest non-outliers outliers start: 139 outliers final: 112 residues processed: 29 average time/residue: 0.7330 time to fit residues: 37.8733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 620 random chunks: chunk 312 optimal weight: 0.9980 chunk 174 optimal weight: 0.5980 chunk 468 optimal weight: 0.6980 chunk 383 optimal weight: 0.5980 chunk 155 optimal weight: 2.9990 chunk 564 optimal weight: 0.7980 chunk 609 optimal weight: 0.0980 chunk 502 optimal weight: 0.9980 chunk 559 optimal weight: 4.9990 chunk 192 optimal weight: 0.7980 chunk 452 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 387 ASN ** B 754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 779 GLN B 944 ASN B 967 GLN E 168 ASN ** F 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 140 ASN ** I 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 776 GLN L 46 GLN L 234 ASN ** O 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 785 ASN K 386 ASN ** K 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 412 ASN K 432 ASN A 26 HIS A 107 ASN ** A 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 238 GLN A 318 ASN A 435 GLN A 538 HIS A1199 ASN A1222 ASN ** A1239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 78 ASN ** Y 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 166 ASN Y 391 GLN ** Y 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 623 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.071 52914 Z= 0.192 Angle : 0.547 10.272 71848 Z= 0.293 Chirality : 0.044 0.268 8210 Planarity : 0.004 0.093 8821 Dihedral : 8.283 174.073 7581 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.72 % Favored : 94.25 % Rotamer Outliers : 4.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.05 % 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: -1.72 (0.10), residues: 6124 helix: -0.35 (0.11), residues: 2190 sheet: -0.94 (0.16), residues: 976 loop : -1.81 (0.10), residues: 2958 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12248 Ramachandran restraints generated. 6124 Oldfield, 0 Emsley, 6124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12248 Ramachandran restraints generated. 6124 Oldfield, 0 Emsley, 6124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 952 residues out of total 5702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 247 poor density : 705 time to evaluate : 4.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 247 outliers final: 126 residues processed: 889 average time/residue: 1.2724 time to fit residues: 1457.6080 Evaluate side-chains 782 residues out of total 5702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 656 time to evaluate : 4.523 Switching outliers to nearest non-outliers outliers start: 126 outliers final: 101 residues processed: 27 average time/residue: 0.7023 time to fit residues: 34.9037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 620 random chunks: chunk 557 optimal weight: 1.9990 chunk 424 optimal weight: 0.6980 chunk 292 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 269 optimal weight: 0.7980 chunk 378 optimal weight: 1.9990 chunk 566 optimal weight: 0.4980 chunk 599 optimal weight: 1.9990 chunk 295 optimal weight: 5.9990 chunk 536 optimal weight: 1.9990 chunk 161 optimal weight: 5.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 161 GLN B 387 ASN B 576 ASN ** B 754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 779 GLN B 944 ASN B 967 GLN B1096 GLN E 168 ASN ** F 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 140 ASN ** I 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 776 GLN I 795 ASN L 13 HIS L 46 GLN L 234 ASN ** L 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 386 ASN ** K 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 26 HIS ** A 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 238 GLN A 318 ASN A 659 ASN A1199 ASN ** A1239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 27 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.072 52914 Z= 0.294 Angle : 0.585 10.377 71848 Z= 0.311 Chirality : 0.046 0.211 8210 Planarity : 0.004 0.095 8821 Dihedral : 8.282 173.901 7581 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.37 % Favored : 93.60 % Rotamer Outliers : 4.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.05 % 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: -1.49 (0.10), residues: 6124 helix: -0.14 (0.11), residues: 2199 sheet: -0.85 (0.16), residues: 972 loop : -1.68 (0.11), residues: 2953 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12248 Ramachandran restraints generated. 6124 Oldfield, 0 Emsley, 6124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12248 Ramachandran restraints generated. 6124 Oldfield, 0 Emsley, 6124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 940 residues out of total 5702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 265 poor density : 675 time to evaluate : 4.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 265 outliers final: 151 residues processed: 869 average time/residue: 1.3076 time to fit residues: 1456.4880 Evaluate side-chains 796 residues out of total 5702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 645 time to evaluate : 4.558 Switching outliers to nearest non-outliers outliers start: 151 outliers final: 124 residues processed: 28 average time/residue: 0.6143 time to fit residues: 33.5240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 620 random chunks: chunk 499 optimal weight: 0.9980 chunk 340 optimal weight: 7.9990 chunk 8 optimal weight: 1.9990 chunk 446 optimal weight: 2.9990 chunk 247 optimal weight: 7.9990 chunk 511 optimal weight: 2.9990 chunk 414 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 306 optimal weight: 1.9990 chunk 537 optimal weight: 2.9990 chunk 151 optimal weight: 2.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 779 GLN B 889 GLN B 944 ASN B 967 GLN E 65 ASN E 168 ASN ** F 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 140 ASN ** I 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 776 GLN L 46 GLN L 234 ASN O 35 ASN O 601 ASN O 813 ASN ** K 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 447 GLN A 26 HIS ** A 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 238 GLN A 318 ASN A1199 ASN A1239 HIS ** Y 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 208 HIS ** Y 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.098 52914 Z= 0.437 Angle : 0.654 12.283 71848 Z= 0.347 Chirality : 0.049 0.213 8210 Planarity : 0.005 0.098 8821 Dihedral : 8.496 174.013 7581 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.04 % Favored : 92.94 % Rotamer Outliers : 4.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.07 % 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: -1.48 (0.10), residues: 6124 helix: -0.15 (0.11), residues: 2179 sheet: -0.82 (0.16), residues: 975 loop : -1.66 (0.11), residues: 2970 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12248 Ramachandran restraints generated. 6124 Oldfield, 0 Emsley, 6124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12248 Ramachandran restraints generated. 6124 Oldfield, 0 Emsley, 6124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 928 residues out of total 5702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 272 poor density : 656 time to evaluate : 4.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 272 outliers final: 168 residues processed: 856 average time/residue: 1.3188 time to fit residues: 1447.7362 Evaluate side-chains 804 residues out of total 5702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 636 time to evaluate : 4.566 Switching outliers to nearest non-outliers outliers start: 168 outliers final: 138 residues processed: 32 average time/residue: 0.6760 time to fit residues: 39.3496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 620 random chunks: chunk 201 optimal weight: 0.9980 chunk 539 optimal weight: 0.7980 chunk 118 optimal weight: 1.9990 chunk 351 optimal weight: 0.4980 chunk 147 optimal weight: 0.8980 chunk 599 optimal weight: 0.9990 chunk 497 optimal weight: 0.3980 chunk 277 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 198 optimal weight: 0.6980 chunk 314 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 779 GLN B 944 ASN B 967 GLN E 168 ASN ** F 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 140 ASN ** I 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 776 GLN L 46 GLN L 234 ASN ** L 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 785 ASN ** K 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 238 GLN A 318 ASN A1199 ASN ** Y 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 391 GLN ** Y 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.064 52914 Z= 0.220 Angle : 0.558 10.359 71848 Z= 0.297 Chirality : 0.044 0.199 8210 Planarity : 0.004 0.093 8821 Dihedral : 8.207 173.186 7581 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.09 % Favored : 93.89 % Rotamer Outliers : 3.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.05 % 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: -1.24 (0.10), residues: 6124 helix: 0.11 (0.11), residues: 2194 sheet: -0.66 (0.17), residues: 968 loop : -1.59 (0.11), residues: 2962 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12248 Ramachandran restraints generated. 6124 Oldfield, 0 Emsley, 6124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12248 Ramachandran restraints generated. 6124 Oldfield, 0 Emsley, 6124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 902 residues out of total 5702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 226 poor density : 676 time to evaluate : 4.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 226 outliers final: 145 residues processed: 863 average time/residue: 1.2936 time to fit residues: 1443.3587 Evaluate side-chains 787 residues out of total 5702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 642 time to evaluate : 4.555 Switching outliers to nearest non-outliers outliers start: 145 outliers final: 136 residues processed: 11 average time/residue: 0.7834 time to fit residues: 19.0079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 620 random chunks: chunk 578 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 341 optimal weight: 3.9990 chunk 438 optimal weight: 0.8980 chunk 339 optimal weight: 3.9990 chunk 504 optimal weight: 0.0980 chunk 334 optimal weight: 7.9990 chunk 597 optimal weight: 0.0870 chunk 373 optimal weight: 5.9990 chunk 364 optimal weight: 2.9990 chunk 275 optimal weight: 0.7980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 779 GLN ** B 944 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 967 GLN E 168 ASN ** F 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 776 GLN L 46 GLN L 205 ASN L 234 ASN ** L 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 785 ASN K 386 ASN ** K 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 238 GLN A 318 ASN ** Y 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 97 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.062 52914 Z= 0.194 Angle : 0.540 11.560 71848 Z= 0.286 Chirality : 0.044 0.192 8210 Planarity : 0.004 0.092 8821 Dihedral : 8.016 172.741 7581 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.24 % Favored : 93.74 % Rotamer Outliers : 3.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.05 % 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: -1.02 (0.11), residues: 6124 helix: 0.32 (0.11), residues: 2198 sheet: -0.47 (0.17), residues: 957 loop : -1.50 (0.11), residues: 2969 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12248 Ramachandran restraints generated. 6124 Oldfield, 0 Emsley, 6124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12248 Ramachandran restraints generated. 6124 Oldfield, 0 Emsley, 6124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 885 residues out of total 5702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 208 poor density : 677 time to evaluate : 4.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 208 outliers final: 144 residues processed: 854 average time/residue: 1.2951 time to fit residues: 1433.5684 Evaluate side-chains 788 residues out of total 5702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 644 time to evaluate : 4.552 Switching outliers to nearest non-outliers outliers start: 144 outliers final: 133 residues processed: 13 average time/residue: 0.7799 time to fit residues: 21.3191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 620 random chunks: chunk 369 optimal weight: 6.9990 chunk 238 optimal weight: 0.9990 chunk 356 optimal weight: 0.8980 chunk 180 optimal weight: 0.9980 chunk 117 optimal weight: 0.5980 chunk 115 optimal weight: 0.8980 chunk 379 optimal weight: 0.7980 chunk 407 optimal weight: 0.7980 chunk 295 optimal weight: 0.0370 chunk 55 optimal weight: 0.7980 chunk 469 optimal weight: 0.0020 overall best weight: 0.4466 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 779 GLN ** B 944 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 967 GLN B1096 GLN E 168 ASN F 112 ASN ** I 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 776 GLN L 46 GLN L 234 ASN ** L 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 530 ASN O 651 GLN K 386 ASN ** K 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 107 ASN ** A 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 238 GLN A 271 ASN A 318 ASN A 659 ASN ** Y 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 428 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.072 52914 Z= 0.176 Angle : 0.533 10.399 71848 Z= 0.282 Chirality : 0.043 0.192 8210 Planarity : 0.004 0.091 8821 Dihedral : 7.917 172.688 7581 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.17 % Favored : 93.81 % Rotamer Outliers : 3.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.05 % 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: -0.89 (0.11), residues: 6124 helix: 0.43 (0.11), residues: 2199 sheet: -0.37 (0.17), residues: 964 loop : -1.45 (0.11), residues: 2961 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12248 Ramachandran restraints generated. 6124 Oldfield, 0 Emsley, 6124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12248 Ramachandran restraints generated. 6124 Oldfield, 0 Emsley, 6124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 866 residues out of total 5702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 676 time to evaluate : 4.629 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 190 outliers final: 142 residues processed: 840 average time/residue: 1.2708 time to fit residues: 1382.4937 Evaluate side-chains 790 residues out of total 5702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 648 time to evaluate : 4.514 Switching outliers to nearest non-outliers outliers start: 142 outliers final: 133 residues processed: 11 average time/residue: 0.7308 time to fit residues: 18.3498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 620 random chunks: chunk 543 optimal weight: 2.9990 chunk 572 optimal weight: 7.9990 chunk 522 optimal weight: 1.9990 chunk 556 optimal weight: 4.9990 chunk 335 optimal weight: 4.9990 chunk 242 optimal weight: 5.9990 chunk 437 optimal weight: 0.8980 chunk 170 optimal weight: 0.7980 chunk 503 optimal weight: 0.0060 chunk 526 optimal weight: 0.0270 chunk 554 optimal weight: 1.9990 overall best weight: 0.7456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 967 GLN B1096 GLN E 168 ASN ** I 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 46 GLN ** L 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 517 HIS O 651 GLN K 386 ASN ** K 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 238 GLN A 271 ASN A 318 ASN A 659 ASN ** Y 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 52914 Z= 0.238 Angle : 0.564 11.697 71848 Z= 0.297 Chirality : 0.045 0.182 8210 Planarity : 0.004 0.091 8821 Dihedral : 7.948 172.791 7581 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.42 % Favored : 93.57 % Rotamer Outliers : 3.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.05 % 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: -0.88 (0.11), residues: 6124 helix: 0.44 (0.11), residues: 2193 sheet: -0.38 (0.17), residues: 970 loop : -1.42 (0.11), residues: 2961 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12248 Ramachandran restraints generated. 6124 Oldfield, 0 Emsley, 6124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12248 Ramachandran restraints generated. 6124 Oldfield, 0 Emsley, 6124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 831 residues out of total 5702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 650 time to evaluate : 5.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 181 outliers final: 135 residues processed: 807 average time/residue: 1.2995 time to fit residues: 1356.9266 Evaluate side-chains 774 residues out of total 5702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 639 time to evaluate : 4.638 Switching outliers to nearest non-outliers outliers start: 135 outliers final: 126 residues processed: 11 average time/residue: 0.6727 time to fit residues: 18.1155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 620 random chunks: chunk 365 optimal weight: 3.9990 chunk 588 optimal weight: 0.6980 chunk 359 optimal weight: 1.9990 chunk 279 optimal weight: 2.9990 chunk 409 optimal weight: 0.0970 chunk 617 optimal weight: 0.9990 chunk 568 optimal weight: 6.9990 chunk 491 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 379 optimal weight: 1.9990 chunk 301 optimal weight: 0.4980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 967 GLN B1096 GLN E 168 ASN G 69 ASN ** I 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 46 GLN ** L 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 279 GLN ** O 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 465 HIS K 386 ASN ** K 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 107 ASN ** A 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 238 GLN ** A 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 318 ASN A 659 ASN ** Y 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 428 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.065 52914 Z= 0.210 Angle : 0.552 14.513 71848 Z= 0.290 Chirality : 0.044 0.343 8210 Planarity : 0.004 0.090 8821 Dihedral : 7.898 172.885 7581 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.26 % Favored : 93.73 % Rotamer Outliers : 2.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.05 % 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: -0.83 (0.11), residues: 6124 helix: 0.47 (0.11), residues: 2196 sheet: -0.36 (0.17), residues: 969 loop : -1.40 (0.11), residues: 2959 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12248 Ramachandran restraints generated. 6124 Oldfield, 0 Emsley, 6124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12248 Ramachandran restraints generated. 6124 Oldfield, 0 Emsley, 6124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 802 residues out of total 5702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 654 time to evaluate : 4.833 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 148 outliers final: 133 residues processed: 792 average time/residue: 1.2719 time to fit residues: 1310.0753 Evaluate side-chains 773 residues out of total 5702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 640 time to evaluate : 4.531 Switching outliers to nearest non-outliers outliers start: 133 outliers final: 127 residues processed: 7 average time/residue: 0.7770 time to fit residues: 14.4053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 620 random chunks: chunk 390 optimal weight: 0.8980 chunk 523 optimal weight: 0.9990 chunk 150 optimal weight: 0.0870 chunk 453 optimal weight: 0.8980 chunk 72 optimal weight: 0.8980 chunk 136 optimal weight: 0.8980 chunk 492 optimal weight: 0.2980 chunk 206 optimal weight: 1.9990 chunk 505 optimal weight: 0.8980 chunk 62 optimal weight: 0.1980 chunk 90 optimal weight: 0.9980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 967 GLN B1096 GLN E 168 ASN ** I 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 46 GLN ** L 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 386 ASN ** K 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 107 ASN ** A 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 238 GLN ** A 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 318 ASN A 659 ASN ** Y 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 192 GLN ** Y 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.163351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.123842 restraints weight = 110420.063| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.75 r_work: 0.3165 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2994 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2994 r_free = 0.2994 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2994 r_free = 0.2994 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2994 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.084 52914 Z= 0.185 Angle : 0.545 13.751 71848 Z= 0.287 Chirality : 0.044 0.336 8210 Planarity : 0.004 0.089 8821 Dihedral : 7.814 172.768 7581 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.14 % Favored : 93.84 % Rotamer Outliers : 2.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.47 % 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: -0.76 (0.11), residues: 6124 helix: 0.54 (0.11), residues: 2192 sheet: -0.28 (0.17), residues: 964 loop : -1.37 (0.11), residues: 2968 =============================================================================== Job complete usr+sys time: 20576.21 seconds wall clock time: 357 minutes 53.17 seconds (21473.17 seconds total)