Starting phenix.real_space_refine on Sat Apr 6 18:31:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tvx_41654/04_2024/8tvx_41654_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tvx_41654/04_2024/8tvx_41654.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tvx_41654/04_2024/8tvx_41654_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tvx_41654/04_2024/8tvx_41654_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tvx_41654/04_2024/8tvx_41654_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tvx_41654/04_2024/8tvx_41654.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tvx_41654/04_2024/8tvx_41654.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tvx_41654/04_2024/8tvx_41654_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tvx_41654/04_2024/8tvx_41654_trim_updated.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.060 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Zn 8 6.06 5 P 56 5.49 5 Mg 1 5.21 5 S 169 5.16 5 C 19019 2.51 5 N 5324 2.21 5 O 5871 1.98 5 H 28608 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 376": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 404": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 478": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 540": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 614": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 636": "OE1" <-> "OE2" Residue "A PHE 646": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 715": "OE1" <-> "OE2" Residue "A PHE 755": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 787": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 833": "OE1" <-> "OE2" Residue "A ASP 1359": "OD1" <-> "OD2" Residue "A TYR 1365": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 1426": "OE1" <-> "OE2" Residue "B PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 209": "OE1" <-> "OE2" Residue "B PHE 286": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 431": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 634": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 698": "OE1" <-> "OE2" Residue "B TYR 785": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 1064": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 1130": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 1180": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 1192": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 61": "OE1" <-> "OE2" Residue "D TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 133": "OE1" <-> "OE2" Residue "F ASP 110": "OD1" <-> "OD2" Residue "F GLU 124": "OE1" <-> "OE2" Residue "F PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 144": "OE1" <-> "OE2" Residue "G PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 27": "OE1" <-> "OE2" Residue "H TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I ASP 113": "OD1" <-> "OD2" Residue "J TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J GLU 58": "OE1" <-> "OE2" Residue "K GLU 64": "OE1" <-> "OE2" Residue "K PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 59056 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 21595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1367, 21595 Classifications: {'peptide': 1367} Link IDs: {'PCIS': 1, 'PTRANS': 61, 'TRANS': 1304} Chain breaks: 6 Chain: "B" Number of atoms: 16378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1041, 16378 Classifications: {'peptide': 1041} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 45, 'TRANS': 995} Chain breaks: 10 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 1, 'PHE:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 38 Chain: "C" Number of atoms: 4146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 4146 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 11, 'TRANS': 254} Chain: "D" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 2066 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 2, 'TRANS': 139} Chain breaks: 1 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "E" Number of atoms: 3548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 3548 Classifications: {'peptide': 215} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 12, 'TRANS': 202} Chain: "F" Number of atoms: 1330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 1330 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 75} Chain: "G" Number of atoms: 1806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1806 Classifications: {'peptide': 171} Modifications used: {'COO': 1, 'NH3': 1} Incomplete info: {'truncation_to_alanine': 76} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 162} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 242 Unresolved non-hydrogen angles: 309 Unresolved non-hydrogen dihedrals: 197 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 5, 'ARG:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 2, 'HIS:plan': 3, 'PHE:plan': 3, 'GLU:plan': 5, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 115 Chain: "H" Number of atoms: 2090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 2090 Classifications: {'peptide': 133} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 128} Chain breaks: 2 Chain: "I" Number of atoms: 1303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 1303 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 5, 'TRANS': 111} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 173 Unresolved non-hydrogen angles: 221 Unresolved non-hydrogen dihedrals: 142 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 5, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 112 Chain: "J" Number of atoms: 1074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 1074 Classifications: {'peptide': 65} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "K" Number of atoms: 1673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 1673 Classifications: {'peptide': 104} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 99} Chain: "L" Number of atoms: 751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 751 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'TRANS': 45} Chain: "N" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 361 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 596 Unusual residues: {'TTD': 1} Classifications: {'DNA': 28, 'undetermined': 1} Link IDs: {'p': 1, 'rna3p': 26, None: 1} Not linked: pdbres=" DC T 17 " pdbres="TTD T 18 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "R" Number of atoms: 330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 330 Classifications: {'RNA': 10} Modifications used: {'3*END': 1, 'rna3p_pur': 8, 'rna3p_pyr': 2} Link IDs: {'rna3p': 9} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2189 SG CYS A 148 99.635 74.158 119.187 1.00210.85 S ATOM 2450 SG CYS A 167 96.358 72.191 122.189 1.00217.84 S ATOM 1041 SG CYS A 77 49.655 70.029 105.084 1.00172.93 S ATOM 36980 SG CYS B1163 59.181 81.706 112.498 1.00166.86 S ATOM 37016 SG CYS B1166 61.912 79.182 111.508 1.00171.06 S ATOM 37266 SG CYS B1182 58.622 78.053 113.038 1.00175.34 S ATOM 37305 SG CYS B1185 61.270 79.841 115.143 1.00180.30 S ATOM 39364 SG CYS C 92 12.004 60.258 49.143 1.00166.19 S ATOM 39408 SG CYS C 95 15.858 62.053 48.818 1.00155.74 S ATOM 53529 SG CYS I 78 119.308 53.480 28.270 1.00255.20 S ATOM 53953 SG CYS I 103 115.824 54.614 29.510 1.00260.00 S ATOM 53992 SG CYS I 106 119.515 53.881 31.613 1.00270.84 S ATOM 54376 SG CYS J 7 43.022 62.632 33.716 1.00106.99 S ATOM 54417 SG CYS J 10 41.658 65.296 31.180 1.00111.36 S ATOM 54973 SG CYS J 45 45.171 64.667 31.212 1.00108.54 S ATOM 54983 SG CYS J 46 42.864 61.872 30.007 1.00111.67 S ATOM 57119 SG CYS L 31 40.103 26.068 62.019 1.00193.43 S ATOM 57154 SG CYS L 34 41.529 24.638 58.482 1.00200.82 S ATOM 57413 SG CYS L 51 42.116 25.363 60.678 1.00191.81 S Time building chain proxies: 19.46, per 1000 atoms: 0.33 Number of scatterers: 59056 At special positions: 0 Unit cell: (156.6, 154.28, 165.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 8 29.99 S 169 16.00 P 56 15.00 Mg 1 11.99 O 5871 8.00 N 5324 7.00 C 19019 6.00 H 28608 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 38.29 Conformation dependent library (CDL) restraints added in 4.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1801 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 167 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 148 " pdb=" ZN A1802 " pdb="ZN ZN A1802 " - pdb=" NE2 HIS A 80 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 77 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1182 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1166 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1163 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1185 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 92 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 95 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 78 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 106 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 103 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 46 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 51 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 31 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 34 " Number of angles added : 12 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7040 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 142 helices and 36 sheets defined 35.5% alpha, 13.2% beta 21 base pairs and 43 stacking pairs defined. Time for finding SS restraints: 26.21 Creating SS restraints... Processing helix chain 'A' and resid 24 through 30 Processing helix chain 'A' and resid 93 through 103 removed outlier: 4.943A pdb=" N ALA A 97 " --> pdb=" O GLY A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 126 Processing helix chain 'A' and resid 131 through 144 removed outlier: 3.621A pdb=" N LEU A 141 " --> pdb=" O ALA A 137 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N THR A 144 " --> pdb=" O THR A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 213 Processing helix chain 'A' and resid 216 through 222 removed outlier: 3.549A pdb=" N SER A 221 " --> pdb=" O LYS A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 234 Processing helix chain 'A' and resid 244 through 247 Processing helix chain 'A' and resid 261 through 281 Processing helix chain 'A' and resid 286 through 304 Processing helix chain 'A' and resid 325 through 329 Processing helix chain 'A' and resid 368 through 371 No H-bonds generated for 'chain 'A' and resid 368 through 371' Processing helix chain 'A' and resid 385 through 394 Processing helix chain 'A' and resid 415 through 417 No H-bonds generated for 'chain 'A' and resid 415 through 417' Processing helix chain 'A' and resid 420 through 422 No H-bonds generated for 'chain 'A' and resid 420 through 422' Processing helix chain 'A' and resid 452 through 454 No H-bonds generated for 'chain 'A' and resid 452 through 454' Processing helix chain 'A' and resid 472 through 478 removed outlier: 3.579A pdb=" N SER A 476 " --> pdb=" O SER A 473 " (cutoff:3.500A) Proline residue: A 477 - end of helix Processing helix chain 'A' and resid 495 through 504 Processing helix chain 'A' and resid 507 through 510 Processing helix chain 'A' and resid 526 through 535 removed outlier: 3.507A pdb=" N ARG A 532 " --> pdb=" O LEU A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 552 removed outlier: 3.600A pdb=" N ASN A 548 " --> pdb=" O ASP A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 581 removed outlier: 3.675A pdb=" N VAL A 580 " --> pdb=" O GLN A 576 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ALA A 581 " --> pdb=" O ILE A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 622 No H-bonds generated for 'chain 'A' and resid 619 through 622' Processing helix chain 'A' and resid 629 through 637 removed outlier: 3.696A pdb=" N ARG A 635 " --> pdb=" O HIS A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 660 removed outlier: 4.245A pdb=" N LYS A 644 " --> pdb=" O GLN A 640 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLY A 647 " --> pdb=" O ALA A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 668 No H-bonds generated for 'chain 'A' and resid 666 through 668' Processing helix chain 'A' and resid 673 through 698 Processing helix chain 'A' and resid 710 through 736 Processing helix chain 'A' and resid 742 through 749 Processing helix chain 'A' and resid 755 through 762 Processing helix chain 'A' and resid 795 through 797 No H-bonds generated for 'chain 'A' and resid 795 through 797' Processing helix chain 'A' and resid 810 through 845 removed outlier: 3.820A pdb=" N ALA A 832 " --> pdb=" O ALA A 828 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N GLY A 835 " --> pdb=" O THR A 831 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR A 836 " --> pdb=" O ALA A 832 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 870 No H-bonds generated for 'chain 'A' and resid 868 through 870' Processing helix chain 'A' and resid 875 through 877 No H-bonds generated for 'chain 'A' and resid 875 through 877' Processing helix chain 'A' and resid 890 through 897 Processing helix chain 'A' and resid 910 through 912 No H-bonds generated for 'chain 'A' and resid 910 through 912' Processing helix chain 'A' and resid 923 through 946 removed outlier: 3.615A pdb=" N GLU A 945 " --> pdb=" O LYS A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 960 through 969 Processing helix chain 'A' and resid 983 through 996 Processing helix chain 'A' and resid 1005 through 1014 Processing helix chain 'A' and resid 1016 through 1025 Processing helix chain 'A' and resid 1028 through 1033 Processing helix chain 'A' and resid 1039 through 1056 Processing helix chain 'A' and resid 1064 through 1076 Proline residue: A1075 - end of helix Processing helix chain 'A' and resid 1099 through 1105 Processing helix chain 'A' and resid 1122 through 1124 No H-bonds generated for 'chain 'A' and resid 1122 through 1124' Processing helix chain 'A' and resid 1128 through 1138 Processing helix chain 'A' and resid 1199 through 1204 Processing helix chain 'A' and resid 1209 through 1219 Processing helix chain 'A' and resid 1258 through 1269 removed outlier: 3.614A pdb=" N MET A1267 " --> pdb=" O ILE A1263 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LEU A1268 " --> pdb=" O GLU A1264 " (cutoff:3.500A) Processing helix chain 'A' and resid 1313 through 1318 removed outlier: 4.561A pdb=" N THR A1318 " --> pdb=" O SER A1314 " (cutoff:3.500A) Processing helix chain 'A' and resid 1324 through 1326 No H-bonds generated for 'chain 'A' and resid 1324 through 1326' Processing helix chain 'A' and resid 1332 through 1338 Processing helix chain 'A' and resid 1341 through 1359 removed outlier: 3.573A pdb=" N VAL A1355 " --> pdb=" O GLU A1351 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASP A1359 " --> pdb=" O VAL A1355 " (cutoff:3.500A) Processing helix chain 'A' and resid 1365 through 1374 removed outlier: 3.741A pdb=" N LEU A1371 " --> pdb=" O HIS A1367 " (cutoff:3.500A) Processing helix chain 'A' and resid 1389 through 1391 No H-bonds generated for 'chain 'A' and resid 1389 through 1391' Processing helix chain 'A' and resid 1396 through 1401 removed outlier: 4.308A pdb=" N SER A1401 " --> pdb=" O LEU A1397 " (cutoff:3.500A) Processing helix chain 'A' and resid 1406 through 1415 removed outlier: 3.729A pdb=" N GLU A1411 " --> pdb=" O GLU A1407 " (cutoff:3.500A) Processing helix chain 'A' and resid 1424 through 1430 Processing helix chain 'A' and resid 1437 through 1439 No H-bonds generated for 'chain 'A' and resid 1437 through 1439' Processing helix chain 'A' and resid 1447 through 1452 Processing helix chain 'B' and resid 27 through 41 removed outlier: 3.582A pdb=" N LYS B 41 " --> pdb=" O PHE B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 64 removed outlier: 4.593A pdb=" N LEU B 59 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N GLN B 60 " --> pdb=" O ASP B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 120 Processing helix chain 'B' and resid 186 through 191 Processing helix chain 'B' and resid 265 through 267 No H-bonds generated for 'chain 'B' and resid 265 through 267' Processing helix chain 'B' and resid 282 through 288 Processing helix chain 'B' and resid 294 through 301 Processing helix chain 'B' and resid 308 through 323 Proline residue: B 316 - end of helix removed outlier: 3.563A pdb=" N PHE B 322 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N VAL B 323 " --> pdb=" O GLU B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 338 Processing helix chain 'B' and resid 349 through 358 Processing helix chain 'B' and resid 368 through 389 removed outlier: 4.905A pdb=" N LYS B 374 " --> pdb=" O GLU B 371 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ALA B 375 " --> pdb=" O SER B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 403 No H-bonds generated for 'chain 'B' and resid 401 through 403' Processing helix chain 'B' and resid 409 through 434 removed outlier: 3.513A pdb=" N THR B 419 " --> pdb=" O GLN B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 463 removed outlier: 3.750A pdb=" N ILE B 448 " --> pdb=" O MET B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 496 Processing helix chain 'B' and resid 516 through 518 No H-bonds generated for 'chain 'B' and resid 516 through 518' Processing helix chain 'B' and resid 530 through 532 No H-bonds generated for 'chain 'B' and resid 530 through 532' Processing helix chain 'B' and resid 552 through 561 Processing helix chain 'B' and resid 566 through 568 No H-bonds generated for 'chain 'B' and resid 566 through 568' Processing helix chain 'B' and resid 593 through 606 Processing helix chain 'B' and resid 655 through 670 Processing helix chain 'B' and resid 681 through 687 Processing helix chain 'B' and resid 695 through 700 removed outlier: 3.655A pdb=" N GLU B 699 " --> pdb=" O ALA B 695 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N SER B 700 " --> pdb=" O GLU B 696 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 695 through 700' Processing helix chain 'B' and resid 707 through 709 No H-bonds generated for 'chain 'B' and resid 707 through 709' Processing helix chain 'B' and resid 712 through 715 No H-bonds generated for 'chain 'B' and resid 712 through 715' Processing helix chain 'B' and resid 745 through 748 Processing helix chain 'B' and resid 751 through 755 removed outlier: 3.839A pdb=" N ILE B 755 " --> pdb=" O VAL B 751 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 751 through 755' Processing helix chain 'B' and resid 759 through 761 No H-bonds generated for 'chain 'B' and resid 759 through 761' Processing helix chain 'B' and resid 764 through 776 removed outlier: 3.783A pdb=" N LYS B 775 " --> pdb=" O SER B 771 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLN B 776 " --> pdb=" O ALA B 772 " (cutoff:3.500A) Processing helix chain 'B' and resid 807 through 812 removed outlier: 3.607A pdb=" N GLU B 810 " --> pdb=" O ARG B 807 " (cutoff:3.500A) Processing helix chain 'B' and resid 843 through 847 Processing helix chain 'B' and resid 1014 through 1020 Proline residue: B1018 - end of helix Processing helix chain 'B' and resid 1023 through 1038 Processing helix chain 'B' and resid 1052 through 1062 removed outlier: 3.519A pdb=" N LEU B1058 " --> pdb=" O GLY B1054 " (cutoff:3.500A) Processing helix chain 'B' and resid 1099 through 1101 No H-bonds generated for 'chain 'B' and resid 1099 through 1101' Processing helix chain 'B' and resid 1122 through 1124 No H-bonds generated for 'chain 'B' and resid 1122 through 1124' Processing helix chain 'B' and resid 1132 through 1141 Processing helix chain 'B' and resid 1144 through 1152 Processing helix chain 'B' and resid 1175 through 1177 No H-bonds generated for 'chain 'B' and resid 1175 through 1177' Processing helix chain 'B' and resid 1198 through 1209 Processing helix chain 'C' and resid 27 through 39 Processing helix chain 'C' and resid 60 through 69 removed outlier: 3.572A pdb=" N LEU C 69 " --> pdb=" O HIS C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 79 No H-bonds generated for 'chain 'C' and resid 77 through 79' Processing helix chain 'C' and resid 115 through 117 No H-bonds generated for 'chain 'C' and resid 115 through 117' Processing helix chain 'C' and resid 168 through 170 No H-bonds generated for 'chain 'C' and resid 168 through 170' Processing helix chain 'C' and resid 197 through 200 No H-bonds generated for 'chain 'C' and resid 197 through 200' Processing helix chain 'C' and resid 205 through 209 removed outlier: 3.656A pdb=" N GLU C 208 " --> pdb=" O LYS C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 265 Processing helix chain 'D' and resid 52 through 72 Processing helix chain 'D' and resid 119 through 133 Processing helix chain 'D' and resid 139 through 150 Processing helix chain 'D' and resid 157 through 170 removed outlier: 3.658A pdb=" N ALA D 162 " --> pdb=" O GLU D 158 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N THR D 170 " --> pdb=" O LEU D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 182 removed outlier: 3.974A pdb=" N GLN D 179 " --> pdb=" O PHE D 175 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU D 180 " --> pdb=" O GLU D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 194 Processing helix chain 'D' and resid 196 through 199 Processing helix chain 'D' and resid 204 through 219 removed outlier: 3.515A pdb=" N LYS D 212 " --> pdb=" O GLU D 208 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 26 Processing helix chain 'E' and resid 32 through 35 No H-bonds generated for 'chain 'E' and resid 32 through 35' Processing helix chain 'E' and resid 39 through 46 Processing helix chain 'E' and resid 56 through 58 No H-bonds generated for 'chain 'E' and resid 56 through 58' Processing helix chain 'E' and resid 66 through 71 Processing helix chain 'E' and resid 90 through 103 Processing helix chain 'E' and resid 118 through 125 Proline residue: E 125 - end of helix Processing helix chain 'E' and resid 139 through 141 No H-bonds generated for 'chain 'E' and resid 139 through 141' Processing helix chain 'E' and resid 144 through 146 No H-bonds generated for 'chain 'E' and resid 144 through 146' Processing helix chain 'E' and resid 158 through 168 Processing helix chain 'E' and resid 172 through 174 No H-bonds generated for 'chain 'E' and resid 172 through 174' Processing helix chain 'E' and resid 183 through 188 Processing helix chain 'F' and resid 87 through 102 Processing helix chain 'F' and resid 117 through 126 Processing helix chain 'G' and resid 15 through 17 No H-bonds generated for 'chain 'G' and resid 15 through 17' Processing helix chain 'G' and resid 20 through 34 removed outlier: 3.516A pdb=" N VAL G 34 " --> pdb=" O LEU G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 114 No H-bonds generated for 'chain 'G' and resid 112 through 114' Processing helix chain 'I' and resid 62 through 64 No H-bonds generated for 'chain 'I' and resid 62 through 64' Processing helix chain 'I' and resid 117 through 121 Processing helix chain 'J' and resid 18 through 26 Processing helix chain 'J' and resid 32 through 38 Processing helix chain 'J' and resid 44 through 52 removed outlier: 4.018A pdb=" N MET J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ILE J 50 " --> pdb=" O CYS J 46 " (cutoff:3.500A) Processing helix chain 'J' and resid 57 through 62 removed outlier: 3.576A pdb=" N ARG J 62 " --> pdb=" O GLU J 58 " (cutoff:3.500A) Processing helix chain 'K' and resid 40 through 52 removed outlier: 4.263A pdb=" N LEU K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASN K 52 " --> pdb=" O ALA K 48 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 116 Processing sheet with id= A, first strand: chain 'A' and resid 82 through 85 Processing sheet with id= B, first strand: chain 'A' and resid 151 through 153 Processing sheet with id= C, first strand: chain 'A' and resid 173 through 177 Processing sheet with id= D, first strand: chain 'A' and resid 348 through 352 removed outlier: 3.604A pdb=" N THR A 351 " --> pdb=" O MET A 487 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 353 through 355 removed outlier: 6.022A pdb=" N PHE A 468 " --> pdb=" O SER A 354 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'A' and resid 363 through 367 removed outlier: 6.388A pdb=" N ARG A 459 " --> pdb=" O VAL A 364 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N VAL A 366 " --> pdb=" O ARG A 459 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LYS A 461 " --> pdb=" O VAL A 366 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'A' and resid 375 through 379 Processing sheet with id= H, first strand: chain 'A' and resid 404 through 406 Processing sheet with id= I, first strand: chain 'A' and resid 587 through 590 Processing sheet with id= J, first strand: chain 'A' and resid 878 through 882 Processing sheet with id= K, first strand: chain 'A' and resid 1115 through 1119 Processing sheet with id= L, first strand: chain 'A' and resid 1237 through 1240 removed outlier: 3.967A pdb=" N CYS A1240 " --> pdb=" O LEU A1193 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 68 through 71 Processing sheet with id= N, first strand: chain 'B' and resid 95 through 97 Processing sheet with id= O, first strand: chain 'B' and resid 125 through 127 Processing sheet with id= P, first strand: chain 'B' and resid 203 through 205 Processing sheet with id= Q, first strand: chain 'B' and resid 498 through 500 removed outlier: 6.002A pdb=" N ALA B 214 " --> pdb=" O ASN B 499 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'B' and resid 222 through 227 removed outlier: 3.648A pdb=" N ARG B 241 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N HIS B 236 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL B 256 " --> pdb=" O ALA B 238 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLN B 255 " --> pdb=" O THR B 272 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS B 270 " --> pdb=" O LYS B 257 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'B' and resid 543 through 545 Processing sheet with id= T, first strand: chain 'B' and resid 588 through 590 removed outlier: 3.986A pdb=" N GLY B 588 " --> pdb=" O VAL B 580 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU B 623 " --> pdb=" O ASP B 618 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'B' and resid 793 through 796 removed outlier: 6.078A pdb=" N ARG B 969 " --> pdb=" O VAL B 949 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N VAL B 949 " --> pdb=" O ARG B 969 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'B' and resid 1087 through 1092 removed outlier: 6.702A pdb=" N LEU B1010 " --> pdb=" O ALA B 826 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'B' and resid 979 through 981 Processing sheet with id= X, first strand: chain 'B' and resid 1159 through 1163 removed outlier: 3.519A pdb=" N TYR B1192 " --> pdb=" O ILE B1162 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'B' and resid 839 through 842 removed outlier: 7.598A pdb=" N MET B 841 " --> pdb=" O GLY B 991 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N THR B 993 " --> pdb=" O MET B 841 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'C' and resid 7 through 13 removed outlier: 7.040A pdb=" N ASP C 19 " --> pdb=" O ARG C 11 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N ALA C 13 " --> pdb=" O ASN C 17 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ASN C 17 " --> pdb=" O ALA C 13 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ALA C 175 " --> pdb=" O GLU C 233 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'C' and resid 97 through 104 removed outlier: 6.057A pdb=" N LYS C 160 " --> pdb=" O ILE C 46 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N ILE C 46 " --> pdb=" O LYS C 160 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N GLY C 162 " --> pdb=" O LEU C 44 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N LEU C 44 " --> pdb=" O GLY C 162 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'E' and resid 78 through 82 removed outlier: 7.523A pdb=" N THR E 107 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 8.304A pdb=" N GLU E 81 " --> pdb=" O THR E 107 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ILE E 109 " --> pdb=" O GLU E 81 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N THR E 131 " --> pdb=" O GLY E 108 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N PHE E 110 " --> pdb=" O THR E 131 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N GLU E 133 " --> pdb=" O PHE E 110 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N TYR E 112 " --> pdb=" O GLU E 133 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N PHE E 135 " --> pdb=" O TYR E 112 " (cutoff:3.500A) No H-bonds generated for sheet with id= AB Processing sheet with id= AC, first strand: chain 'E' and resid 152 through 155 Processing sheet with id= AD, first strand: chain 'F' and resid 133 through 137 Processing sheet with id= AE, first strand: chain 'G' and resid 2 through 13 removed outlier: 3.521A pdb=" N ALA G 68 " --> pdb=" O LEU G 13 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ARG G 75 " --> pdb=" O LEU G 49 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N PHE G 79 " --> pdb=" O ILE G 45 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N ILE G 45 " --> pdb=" O PHE G 79 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N SER G 37 " --> pdb=" O ILE G 45 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'G' and resid 142 through 147 removed outlier: 7.065A pdb=" N GLU G 100 " --> pdb=" O VAL G 92 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N CYS G 94 " --> pdb=" O GLY G 98 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N GLY G 98 " --> pdb=" O CYS G 94 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LYS G 107 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N THR G 111 " --> pdb=" O GLY G 161 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'H' and resid 6 through 11 removed outlier: 4.312A pdb=" N PHE H 6 " --> pdb=" O ILE H 59 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA H 140 " --> pdb=" O GLY H 99 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N TYR H 115 " --> pdb=" O TYR H 102 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N PHE H 104 " --> pdb=" O ALA H 113 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N ALA H 113 " --> pdb=" O PHE H 104 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N GLU H 106 " --> pdb=" O LEU H 111 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N LEU H 111 " --> pdb=" O GLU H 106 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N LYS H 37 " --> pdb=" O GLU H 126 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ALA H 29 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N VAL H 12 " --> pdb=" O ALA H 29 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'I' and resid 16 through 19 Processing sheet with id= AI, first strand: chain 'I' and resid 83 through 86 Processing sheet with id= AJ, first strand: chain 'K' and resid 19 through 23 1031 hydrogen bonds defined for protein. 2790 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 48 hydrogen bonds 76 hydrogen bond angles 0 basepair planarities 21 basepair parallelities 43 stacking parallelities Total time for adding SS restraints: 22.99 Time building geometry restraints manager: 40.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 28563 1.03 - 1.23: 158 1.23 - 1.43: 12752 1.43 - 1.62: 17952 1.62 - 1.82: 272 Bond restraints: 59697 Sorted by residual: bond pdb=" C2 TTD T 18 " pdb=" N3 TTD T 18 " ideal model delta sigma weight residual 1.510 1.331 0.179 2.00e-02 2.50e+03 8.00e+01 bond pdb=" C2T TTD T 18 " pdb=" N3T TTD T 18 " ideal model delta sigma weight residual 1.494 1.330 0.164 2.00e-02 2.50e+03 6.69e+01 bond pdb=" C4T TTD T 18 " pdb=" N3T TTD T 18 " ideal model delta sigma weight residual 1.484 1.329 0.155 2.00e-02 2.50e+03 6.04e+01 bond pdb=" N1 TTD T 18 " pdb=" C2 TTD T 18 " ideal model delta sigma weight residual 1.480 1.331 0.149 2.00e-02 2.50e+03 5.54e+01 bond pdb=" N3 TTD T 18 " pdb=" C4 TTD T 18 " ideal model delta sigma weight residual 1.477 1.332 0.145 2.00e-02 2.50e+03 5.26e+01 ... (remaining 59692 not shown) Histogram of bond angle deviations from ideal: 28.33 - 49.48: 1 49.48 - 70.63: 0 70.63 - 91.78: 4 91.78 - 112.94: 70513 112.94 - 134.09: 36924 Bond angle restraints: 107442 Sorted by residual: angle pdb=" O3' TTD T 18 " pdb=" P DT T 19 " pdb=" OP2 DT T 19 " ideal model delta sigma weight residual 108.00 28.33 79.67 3.00e+00 1.11e-01 7.05e+02 angle pdb=" O3' TTD T 18 " pdb=" P DT T 19 " pdb=" O5' DT T 19 " ideal model delta sigma weight residual 103.00 129.89 -26.89 3.00e+00 1.11e-01 8.03e+01 angle pdb=" N PRO G 116 " pdb=" CA PRO G 116 " pdb=" CB PRO G 116 " ideal model delta sigma weight residual 103.19 111.12 -7.93 9.00e-01 1.23e+00 7.76e+01 angle pdb=" N PRO B 877 " pdb=" CA PRO B 877 " pdb=" CB PRO B 877 " ideal model delta sigma weight residual 103.31 111.11 -7.80 8.90e-01 1.26e+00 7.67e+01 angle pdb=" N PRO G 127 " pdb=" CA PRO G 127 " pdb=" CB PRO G 127 " ideal model delta sigma weight residual 102.60 111.08 -8.48 1.10e+00 8.26e-01 5.94e+01 ... (remaining 107437 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.96: 27236 35.96 - 71.92: 708 71.92 - 107.88: 20 107.88 - 143.85: 1 143.85 - 179.81: 5 Dihedral angle restraints: 27970 sinusoidal: 15540 harmonic: 12430 Sorted by residual: dihedral pdb=" C4' TTD T 18 " pdb=" C5R TTD T 18 " pdb=" O5R TTD T 18 " pdb=" PB TTD T 18 " ideal model delta sinusoidal sigma weight residual 241.46 82.29 159.17 1 3.00e+01 1.11e-03 2.06e+01 dihedral pdb=" CA ARG E 7 " pdb=" C ARG E 7 " pdb=" N ASN E 8 " pdb=" CA ASN E 8 " ideal model delta harmonic sigma weight residual 180.00 160.12 19.88 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" O4R TTD T 18 " pdb=" C4' TTD T 18 " pdb=" C5R TTD T 18 " pdb=" O5R TTD T 18 " ideal model delta sinusoidal sigma weight residual -87.02 30.62 -117.64 1 3.00e+01 1.11e-03 1.56e+01 ... (remaining 27967 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 3789 0.045 - 0.089: 677 0.089 - 0.134: 282 0.134 - 0.179: 29 0.179 - 0.223: 8 Chirality restraints: 4785 Sorted by residual: chirality pdb=" CA ILE G 151 " pdb=" N ILE G 151 " pdb=" C ILE G 151 " pdb=" CB ILE G 151 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" C3R TTD T 18 " pdb=" C2' TTD T 18 " pdb=" C4R TTD T 18 " pdb=" O3R TTD T 18 " both_signs ideal model delta sigma weight residual False -2.44 -2.65 0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CA ILE I 49 " pdb=" N ILE I 49 " pdb=" C ILE I 49 " pdb=" CB ILE I 49 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.19 2.00e-01 2.50e+01 9.35e-01 ... (remaining 4782 not shown) Planarity restraints: 8682 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1R TTD T 18 " -0.487 2.00e-02 2.50e+03 2.20e-01 1.09e+03 pdb=" C2T TTD T 18 " 0.125 2.00e-02 2.50e+03 pdb=" C4T TTD T 18 " -0.046 2.00e-02 2.50e+03 pdb=" C5T TTD T 18 " 0.108 2.00e-02 2.50e+03 pdb=" C6T TTD T 18 " 0.109 2.00e-02 2.50e+03 pdb=" N1T TTD T 18 " 0.316 2.00e-02 2.50e+03 pdb=" N3T TTD T 18 " -0.032 2.00e-02 2.50e+03 pdb=" O2T TTD T 18 " 0.114 2.00e-02 2.50e+03 pdb=" O4T TTD T 18 " -0.206 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A1074 " -0.072 5.00e-02 4.00e+02 1.07e-01 1.83e+01 pdb=" N PRO A1075 " 0.185 5.00e-02 4.00e+02 pdb=" CA PRO A1075 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO A1075 " -0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' TTD T 18 " 0.006 2.00e-02 2.50e+03 2.11e-02 1.00e+01 pdb=" N1 TTD T 18 " 0.005 2.00e-02 2.50e+03 pdb=" C2 TTD T 18 " 0.007 2.00e-02 2.50e+03 pdb=" O2 TTD T 18 " -0.005 2.00e-02 2.50e+03 pdb=" N3 TTD T 18 " 0.003 2.00e-02 2.50e+03 pdb=" C4 TTD T 18 " 0.003 2.00e-02 2.50e+03 pdb=" O4 TTD T 18 " -0.017 2.00e-02 2.50e+03 pdb=" C5 TTD T 18 " 0.041 2.00e-02 2.50e+03 pdb=" C6 TTD T 18 " -0.043 2.00e-02 2.50e+03 ... (remaining 8679 not shown) Histogram of nonbonded interaction distances: 1.34 - 1.99: 895 1.99 - 2.64: 79317 2.64 - 3.30: 180401 3.30 - 3.95: 227785 3.95 - 4.60: 356553 Nonbonded interactions: 844951 Sorted by model distance: nonbonded pdb=" O3' DC T 17 " pdb=" O5' TTD T 18 " model vdw 1.340 2.800 nonbonded pdb=" HB2 CYS A 167 " pdb="ZN ZN A1801 " model vdw 1.411 1.544 nonbonded pdb=" OE1 GLU A 795 " pdb=" H GLU A 795 " model vdw 1.520 1.850 nonbonded pdb=" OD1 ASP A 544 " pdb="HH12 ARG K 47 " model vdw 1.520 1.850 nonbonded pdb=" OD2 ASP A 871 " pdb="HH21 ARG A1366 " model vdw 1.522 1.850 ... (remaining 844946 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.660 Extract box with map and model: 13.130 Check model and map are aligned: 0.680 Set scattering table: 0.410 Process input model: 181.470 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.140 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: 0.020 Load rotamer database and sin/cos tables:2.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 203.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 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 : 0.004 0.179 31089 Z= 0.274 Angle : 0.731 79.673 42256 Z= 0.382 Chirality : 0.042 0.223 4785 Planarity : 0.005 0.220 5284 Dihedral : 13.492 159.175 11796 Min Nonbonded Distance : 1.340 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.12 % Favored : 95.79 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.14), residues: 3686 helix: 0.40 (0.14), residues: 1295 sheet: -0.65 (0.22), residues: 526 loop : -0.47 (0.15), residues: 1865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 201 HIS 0.007 0.001 HIS A 877 PHE 0.015 0.001 PHE A 614 TYR 0.015 0.001 TYR B1092 ARG 0.020 0.001 ARG E 7 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 105 is missing expected H atoms. Skipping. Evaluate side-chains 405 residues out of total 3293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 405 time to evaluate : 3.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.8237 (mt-10) cc_final: 0.7882 (mt-10) REVERT: A 146 MET cc_start: 0.8618 (ppp) cc_final: 0.8069 (ppp) REVERT: A 443 LEU cc_start: 0.9040 (tt) cc_final: 0.8735 (tp) REVERT: A 479 ASN cc_start: 0.9430 (t0) cc_final: 0.9161 (t0) REVERT: A 500 GLU cc_start: 0.8784 (tm-30) cc_final: 0.8530 (tm-30) REVERT: A 900 ASP cc_start: 0.7704 (t0) cc_final: 0.6270 (p0) REVERT: A 1075 PRO cc_start: 0.8829 (Cg_exo) cc_final: 0.8442 (Cg_endo) REVERT: A 1111 MET cc_start: 0.7277 (mpp) cc_final: 0.6722 (mmm) REVERT: A 1400 CYS cc_start: 0.9129 (p) cc_final: 0.8877 (p) REVERT: A 1444 MET cc_start: 0.8146 (mmm) cc_final: 0.7528 (mmt) REVERT: B 778 MET cc_start: 0.7997 (mtm) cc_final: 0.7347 (mtm) REVERT: B 789 MET cc_start: 0.8427 (tpp) cc_final: 0.7535 (mmp) REVERT: B 860 MET cc_start: 0.8584 (ppp) cc_final: 0.8320 (tmm) REVERT: G 37 SER cc_start: 0.8750 (t) cc_final: 0.8510 (t) REVERT: G 41 LYS cc_start: 0.9181 (mmmt) cc_final: 0.8770 (mtpp) REVERT: G 56 ILE cc_start: 0.7414 (mt) cc_final: 0.6295 (mm) REVERT: H 105 GLU cc_start: 0.8030 (tm-30) cc_final: 0.7758 (tm-30) REVERT: L 46 VAL cc_start: 0.7201 (m) cc_final: 0.6867 (m) REVERT: L 64 LEU cc_start: 0.8565 (mt) cc_final: 0.8167 (pt) outliers start: 0 outliers final: 0 residues processed: 405 average time/residue: 0.8893 time to fit residues: 563.9195 Evaluate side-chains 312 residues out of total 3293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 312 time to evaluate : 3.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 315 optimal weight: 6.9990 chunk 283 optimal weight: 10.0000 chunk 157 optimal weight: 0.6980 chunk 96 optimal weight: 4.9990 chunk 191 optimal weight: 4.9990 chunk 151 optimal weight: 2.9990 chunk 293 optimal weight: 9.9990 chunk 113 optimal weight: 0.5980 chunk 178 optimal weight: 2.9990 chunk 218 optimal weight: 1.9990 chunk 339 optimal weight: 20.0000 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 282 ASN ** A1078 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 116 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.1157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 31089 Z= 0.232 Angle : 0.545 6.540 42256 Z= 0.295 Chirality : 0.041 0.163 4785 Planarity : 0.004 0.072 5284 Dihedral : 12.644 159.868 4688 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.94 % Favored : 94.98 % Rotamer: Outliers : 0.64 % Allowed : 4.47 % Favored : 94.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.14), residues: 3686 helix: 0.56 (0.14), residues: 1311 sheet: -0.69 (0.22), residues: 499 loop : -0.46 (0.15), residues: 1876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 13 HIS 0.004 0.001 HIS B1104 PHE 0.011 0.001 PHE E 96 TYR 0.013 0.001 TYR B 351 ARG 0.006 0.000 ARG B1135 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 105 is missing expected H atoms. Skipping. Evaluate side-chains 353 residues out of total 3293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 333 time to evaluate : 3.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.8269 (mt-10) cc_final: 0.7894 (mt-10) REVERT: A 146 MET cc_start: 0.8624 (ppp) cc_final: 0.8071 (ppp) REVERT: A 479 ASN cc_start: 0.9411 (t0) cc_final: 0.9132 (t0) REVERT: A 500 GLU cc_start: 0.8822 (tm-30) cc_final: 0.8606 (tm-30) REVERT: A 826 ASP cc_start: 0.9274 (m-30) cc_final: 0.8916 (m-30) REVERT: A 900 ASP cc_start: 0.7778 (t0) cc_final: 0.6280 (p0) REVERT: A 1111 MET cc_start: 0.7010 (mpp) cc_final: 0.6702 (mmm) REVERT: A 1285 MET cc_start: 0.8920 (mmm) cc_final: 0.8687 (mmm) REVERT: A 1400 CYS cc_start: 0.9123 (p) cc_final: 0.8921 (p) REVERT: A 1402 PHE cc_start: 0.8753 (t80) cc_final: 0.7692 (t80) REVERT: A 1444 MET cc_start: 0.8120 (mmm) cc_final: 0.7610 (mmt) REVERT: B 282 ILE cc_start: 0.9588 (pt) cc_final: 0.9223 (mm) REVERT: B 778 MET cc_start: 0.8012 (mtm) cc_final: 0.7418 (mtm) REVERT: B 860 MET cc_start: 0.8574 (ppp) cc_final: 0.8365 (tmm) REVERT: B 1098 MET cc_start: 0.8430 (mpp) cc_final: 0.7936 (mpp) REVERT: D 192 LYS cc_start: 0.6958 (mmtt) cc_final: 0.6671 (mttt) REVERT: E 179 GLN cc_start: 0.9062 (mm110) cc_final: 0.8794 (mm-40) REVERT: G 41 LYS cc_start: 0.9141 (mmmt) cc_final: 0.8725 (mtpp) REVERT: J 26 GLN cc_start: 0.8049 (tm-30) cc_final: 0.7844 (tm-30) REVERT: L 64 LEU cc_start: 0.8601 (mt) cc_final: 0.8275 (pt) outliers start: 20 outliers final: 18 residues processed: 343 average time/residue: 0.8258 time to fit residues: 444.3112 Evaluate side-chains 321 residues out of total 3293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 303 time to evaluate : 3.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 972 HIS Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 995 ARG Chi-restraints excluded: chain B residue 1156 ASP Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 189 ASP Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 215 SER Chi-restraints excluded: chain G residue 47 CYS Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 78 VAL Chi-restraints excluded: chain H residue 109 LYS Chi-restraints excluded: chain I residue 77 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 188 optimal weight: 6.9990 chunk 105 optimal weight: 0.9980 chunk 282 optimal weight: 0.8980 chunk 231 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 chunk 340 optimal weight: 30.0000 chunk 367 optimal weight: 9.9990 chunk 303 optimal weight: 4.9990 chunk 337 optimal weight: 4.9990 chunk 115 optimal weight: 10.0000 chunk 272 optimal weight: 9.9990 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 611 GLN ** A1078 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1130 GLN B 366 GLN ** B1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 ASN ** I 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 31089 Z= 0.361 Angle : 0.573 6.467 42256 Z= 0.311 Chirality : 0.040 0.151 4785 Planarity : 0.004 0.050 5284 Dihedral : 12.727 163.683 4688 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.78 % Favored : 94.14 % Rotamer: Outliers : 0.93 % Allowed : 5.74 % Favored : 93.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.14), residues: 3686 helix: 0.31 (0.14), residues: 1294 sheet: -0.94 (0.22), residues: 513 loop : -0.66 (0.14), residues: 1879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 31 HIS 0.007 0.001 HIS A 786 PHE 0.015 0.001 PHE A 444 TYR 0.012 0.001 TYR B 351 ARG 0.006 0.001 ARG L 47 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 105 is missing expected H atoms. Skipping. Evaluate side-chains 339 residues out of total 3293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 310 time to evaluate : 3.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.8335 (mt-10) cc_final: 0.7838 (mt-10) REVERT: A 146 MET cc_start: 0.8670 (ppp) cc_final: 0.8118 (ppp) REVERT: A 304 MET cc_start: 0.8670 (mtm) cc_final: 0.8451 (mtm) REVERT: A 479 ASN cc_start: 0.9428 (t0) cc_final: 0.9206 (t0) REVERT: A 500 GLU cc_start: 0.8848 (tm-30) cc_final: 0.8647 (tm-30) REVERT: A 826 ASP cc_start: 0.9240 (m-30) cc_final: 0.8791 (m-30) REVERT: A 838 GLN cc_start: 0.9246 (tm-30) cc_final: 0.9031 (tm-30) REVERT: A 1259 MET cc_start: 0.8412 (pmm) cc_final: 0.8202 (pmm) REVERT: A 1285 MET cc_start: 0.8923 (mmm) cc_final: 0.8705 (mmm) REVERT: A 1400 CYS cc_start: 0.9121 (p) cc_final: 0.8852 (p) REVERT: B 282 ILE cc_start: 0.9554 (pt) cc_final: 0.9191 (mm) REVERT: B 860 MET cc_start: 0.8654 (ppp) cc_final: 0.8438 (tmm) REVERT: B 1152 MET cc_start: 0.8299 (mmm) cc_final: 0.8084 (tpt) REVERT: D 192 LYS cc_start: 0.7119 (mmtt) cc_final: 0.6885 (mttt) REVERT: E 179 GLN cc_start: 0.9109 (mm110) cc_final: 0.8867 (mm-40) REVERT: G 1 MET cc_start: 0.8885 (ttm) cc_final: 0.8664 (ttm) REVERT: G 37 SER cc_start: 0.8185 (p) cc_final: 0.7964 (p) REVERT: G 41 LYS cc_start: 0.9156 (mmmt) cc_final: 0.8773 (mtpp) REVERT: J 26 GLN cc_start: 0.8101 (tm-30) cc_final: 0.7870 (tm-30) REVERT: L 64 LEU cc_start: 0.8618 (mt) cc_final: 0.8238 (pt) outliers start: 29 outliers final: 25 residues processed: 324 average time/residue: 0.8484 time to fit residues: 432.3840 Evaluate side-chains 317 residues out of total 3293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 292 time to evaluate : 3.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 517 ASN Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 972 HIS Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 383 ASN Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 533 CYS Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 995 ARG Chi-restraints excluded: chain B residue 1156 ASP Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 215 SER Chi-restraints excluded: chain F residue 145 ASP Chi-restraints excluded: chain G residue 42 PHE Chi-restraints excluded: chain G residue 47 CYS Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 78 VAL Chi-restraints excluded: chain H residue 109 LYS Chi-restraints excluded: chain I residue 77 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 336 optimal weight: 4.9990 chunk 255 optimal weight: 3.9990 chunk 176 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 162 optimal weight: 4.9990 chunk 228 optimal weight: 7.9990 chunk 341 optimal weight: 40.0000 chunk 361 optimal weight: 1.9990 chunk 178 optimal weight: 5.9990 chunk 323 optimal weight: 30.0000 chunk 97 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 281 HIS ** A1078 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 134 ASN ** I 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 31089 Z= 0.398 Angle : 0.590 7.809 42256 Z= 0.321 Chirality : 0.040 0.167 4785 Planarity : 0.004 0.049 5284 Dihedral : 12.836 162.969 4688 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 15.84 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.92 % Favored : 93.03 % Rotamer: Outliers : 1.34 % Allowed : 6.51 % Favored : 92.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.13), residues: 3686 helix: 0.11 (0.14), residues: 1291 sheet: -1.11 (0.22), residues: 511 loop : -0.88 (0.14), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 31 HIS 0.008 0.001 HIS A 399 PHE 0.011 0.001 PHE E 29 TYR 0.012 0.001 TYR B 351 ARG 0.006 0.001 ARG E 26 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 105 is missing expected H atoms. Skipping. Evaluate side-chains 341 residues out of total 3293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 299 time to evaluate : 3.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.8423 (mt-10) cc_final: 0.7914 (mt-10) REVERT: A 146 MET cc_start: 0.8705 (ppp) cc_final: 0.8151 (ppp) REVERT: A 437 MET cc_start: 0.7963 (mtp) cc_final: 0.7756 (mtp) REVERT: A 479 ASN cc_start: 0.9425 (t0) cc_final: 0.9222 (t0) REVERT: A 500 GLU cc_start: 0.8862 (tm-30) cc_final: 0.8657 (tm-30) REVERT: A 826 ASP cc_start: 0.9226 (m-30) cc_final: 0.8789 (m-30) REVERT: A 900 ASP cc_start: 0.8057 (t0) cc_final: 0.6201 (p0) REVERT: A 1259 MET cc_start: 0.8393 (pmm) cc_final: 0.8089 (pmm) REVERT: A 1400 CYS cc_start: 0.9141 (p) cc_final: 0.8824 (p) REVERT: A 1444 MET cc_start: 0.8146 (mmm) cc_final: 0.7773 (mmt) REVERT: B 282 ILE cc_start: 0.9548 (pt) cc_final: 0.9202 (mm) REVERT: B 860 MET cc_start: 0.8701 (ppp) cc_final: 0.8430 (tmm) REVERT: B 1138 MET cc_start: 0.9161 (mmm) cc_final: 0.8938 (mmm) REVERT: D 192 LYS cc_start: 0.7260 (mmtt) cc_final: 0.7030 (mttt) REVERT: E 179 GLN cc_start: 0.9107 (mm110) cc_final: 0.8891 (mm-40) REVERT: G 1 MET cc_start: 0.8779 (ttm) cc_final: 0.8544 (ttm) REVERT: G 41 LYS cc_start: 0.9174 (mmmt) cc_final: 0.8821 (mtpp) REVERT: J 26 GLN cc_start: 0.8206 (tm-30) cc_final: 0.7702 (tm-30) REVERT: L 64 LEU cc_start: 0.8670 (mt) cc_final: 0.8311 (pt) outliers start: 42 outliers final: 35 residues processed: 321 average time/residue: 0.8183 time to fit residues: 413.0810 Evaluate side-chains 321 residues out of total 3293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 286 time to evaluate : 3.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 517 ASN Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 884 ASP Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 895 LYS Chi-restraints excluded: chain A residue 972 HIS Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1373 ASP Chi-restraints excluded: chain B residue 29 ASP Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 383 ASN Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 533 CYS Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 995 ARG Chi-restraints excluded: chain B residue 1136 ASP Chi-restraints excluded: chain B residue 1156 ASP Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 215 SER Chi-restraints excluded: chain F residue 145 ASP Chi-restraints excluded: chain G residue 38 CYS Chi-restraints excluded: chain G residue 42 PHE Chi-restraints excluded: chain G residue 47 CYS Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 78 VAL Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 109 LYS Chi-restraints excluded: chain I residue 77 LYS Chi-restraints excluded: chain I residue 122 SER Chi-restraints excluded: chain K residue 21 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 301 optimal weight: 0.9980 chunk 205 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 269 optimal weight: 20.0000 chunk 149 optimal weight: 2.9990 chunk 308 optimal weight: 0.0980 chunk 249 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 184 optimal weight: 5.9990 chunk 324 optimal weight: 40.0000 chunk 91 optimal weight: 6.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 GLN ** A1078 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 31089 Z= 0.222 Angle : 0.515 6.286 42256 Z= 0.274 Chirality : 0.040 0.150 4785 Planarity : 0.004 0.052 5284 Dihedral : 12.791 159.613 4688 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.59 % Favored : 94.36 % Rotamer: Outliers : 1.05 % Allowed : 7.56 % Favored : 91.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.14), residues: 3686 helix: 0.56 (0.14), residues: 1295 sheet: -0.97 (0.22), residues: 498 loop : -0.69 (0.15), residues: 1893 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 656 HIS 0.005 0.001 HIS A 399 PHE 0.010 0.001 PHE A 22 TYR 0.009 0.001 TYR A 852 ARG 0.006 0.000 ARG B1135 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 105 is missing expected H atoms. Skipping. Evaluate side-chains 331 residues out of total 3293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 298 time to evaluate : 3.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.8370 (mt-10) cc_final: 0.7871 (mt-10) REVERT: A 146 MET cc_start: 0.8707 (ppp) cc_final: 0.8149 (ppp) REVERT: A 437 MET cc_start: 0.7946 (mtp) cc_final: 0.7732 (mtp) REVERT: A 487 MET cc_start: 0.8283 (OUTLIER) cc_final: 0.7842 (ttp) REVERT: A 826 ASP cc_start: 0.9199 (m-30) cc_final: 0.8761 (m-30) REVERT: A 846 GLU cc_start: 0.8447 (mt-10) cc_final: 0.8171 (mt-10) REVERT: A 900 ASP cc_start: 0.8016 (t0) cc_final: 0.6203 (p0) REVERT: A 1259 MET cc_start: 0.8404 (pmm) cc_final: 0.8086 (pmm) REVERT: A 1285 MET cc_start: 0.9066 (mmm) cc_final: 0.8855 (mmm) REVERT: A 1400 CYS cc_start: 0.9175 (p) cc_final: 0.8842 (p) REVERT: A 1444 MET cc_start: 0.8172 (mmm) cc_final: 0.7806 (mmt) REVERT: B 282 ILE cc_start: 0.9549 (pt) cc_final: 0.9207 (mm) REVERT: B 778 MET cc_start: 0.8104 (mtm) cc_final: 0.7674 (mtm) REVERT: B 789 MET cc_start: 0.8474 (tpp) cc_final: 0.8178 (mmp) REVERT: B 860 MET cc_start: 0.8679 (ppp) cc_final: 0.8435 (tmm) REVERT: B 1098 MET cc_start: 0.8460 (mpp) cc_final: 0.8038 (mpp) REVERT: D 192 LYS cc_start: 0.7209 (mmtt) cc_final: 0.6969 (mttt) REVERT: E 179 GLN cc_start: 0.9098 (mm110) cc_final: 0.8888 (mm-40) REVERT: F 100 GLN cc_start: 0.9275 (OUTLIER) cc_final: 0.9054 (mp10) REVERT: G 1 MET cc_start: 0.8810 (ttm) cc_final: 0.8573 (ttm) REVERT: G 41 LYS cc_start: 0.9178 (mmmt) cc_final: 0.8833 (mtpp) REVERT: L 64 LEU cc_start: 0.8673 (mt) cc_final: 0.8338 (pt) outliers start: 33 outliers final: 29 residues processed: 313 average time/residue: 0.8161 time to fit residues: 399.9794 Evaluate side-chains 321 residues out of total 3293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 290 time to evaluate : 3.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 487 MET Chi-restraints excluded: chain A residue 517 ASN Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 972 HIS Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1368 MET Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 995 ARG Chi-restraints excluded: chain B residue 1156 ASP Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 215 SER Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 100 GLN Chi-restraints excluded: chain G residue 42 PHE Chi-restraints excluded: chain G residue 47 CYS Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 78 VAL Chi-restraints excluded: chain H residue 109 LYS Chi-restraints excluded: chain I residue 77 LYS Chi-restraints excluded: chain I residue 122 SER Chi-restraints excluded: chain K residue 21 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 121 optimal weight: 6.9990 chunk 325 optimal weight: 50.0000 chunk 71 optimal weight: 5.9990 chunk 212 optimal weight: 7.9990 chunk 89 optimal weight: 8.9990 chunk 361 optimal weight: 2.9990 chunk 300 optimal weight: 6.9990 chunk 167 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 119 optimal weight: 6.9990 chunk 189 optimal weight: 3.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 299 HIS ** A1078 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 29 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 31089 Z= 0.427 Angle : 0.597 6.294 42256 Z= 0.323 Chirality : 0.040 0.144 4785 Planarity : 0.004 0.058 5284 Dihedral : 12.896 159.395 4688 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 17.31 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.70 % Favored : 92.24 % Rotamer: Outliers : 1.66 % Allowed : 7.47 % Favored : 90.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.14), residues: 3686 helix: 0.16 (0.14), residues: 1291 sheet: -1.17 (0.21), residues: 533 loop : -0.99 (0.14), residues: 1862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 79 HIS 0.009 0.002 HIS A 435 PHE 0.014 0.001 PHE E 29 TYR 0.020 0.001 TYR H 102 ARG 0.005 0.001 ARG A 328 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 105 is missing expected H atoms. Skipping. Evaluate side-chains 330 residues out of total 3293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 278 time to evaluate : 3.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.8477 (mt-10) cc_final: 0.7962 (mt-10) REVERT: A 146 MET cc_start: 0.8765 (ppp) cc_final: 0.8212 (ppp) REVERT: A 257 ARG cc_start: 0.9000 (mmp-170) cc_final: 0.8642 (mmp-170) REVERT: A 437 MET cc_start: 0.8028 (mtp) cc_final: 0.7789 (mtp) REVERT: A 472 LEU cc_start: 0.9550 (tp) cc_final: 0.9322 (tp) REVERT: A 826 ASP cc_start: 0.9214 (m-30) cc_final: 0.8775 (m-30) REVERT: A 900 ASP cc_start: 0.8226 (t0) cc_final: 0.6393 (p0) REVERT: A 1259 MET cc_start: 0.8389 (pmm) cc_final: 0.8093 (pmm) REVERT: A 1400 CYS cc_start: 0.9145 (p) cc_final: 0.8834 (p) REVERT: A 1444 MET cc_start: 0.8106 (mmm) cc_final: 0.7840 (mmt) REVERT: B 860 MET cc_start: 0.8744 (ppp) cc_final: 0.8486 (tmm) REVERT: B 1098 MET cc_start: 0.8514 (mpp) cc_final: 0.8104 (mpp) REVERT: B 1132 GLU cc_start: 0.8077 (tt0) cc_final: 0.7853 (tm-30) REVERT: B 1138 MET cc_start: 0.9095 (mmm) cc_final: 0.8480 (mmm) REVERT: D 192 LYS cc_start: 0.7302 (mmtt) cc_final: 0.7060 (mttt) REVERT: E 179 GLN cc_start: 0.9133 (mm110) cc_final: 0.8929 (mm-40) REVERT: F 100 GLN cc_start: 0.9262 (OUTLIER) cc_final: 0.9041 (mp10) REVERT: G 41 LYS cc_start: 0.9199 (mmmt) cc_final: 0.8865 (mtpp) REVERT: L 64 LEU cc_start: 0.8704 (mt) cc_final: 0.8349 (pt) outliers start: 52 outliers final: 43 residues processed: 306 average time/residue: 0.8026 time to fit residues: 387.1561 Evaluate side-chains 320 residues out of total 3293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 276 time to evaluate : 3.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 517 ASN Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 884 ASP Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 895 LYS Chi-restraints excluded: chain A residue 972 HIS Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1368 MET Chi-restraints excluded: chain A residue 1373 ASP Chi-restraints excluded: chain A residue 1389 PHE Chi-restraints excluded: chain B residue 29 ASP Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 533 CYS Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 683 SER Chi-restraints excluded: chain B residue 781 PHE Chi-restraints excluded: chain B residue 995 ARG Chi-restraints excluded: chain B residue 1137 CYS Chi-restraints excluded: chain B residue 1156 ASP Chi-restraints excluded: chain B residue 1163 CYS Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 200 ASN Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 215 SER Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 100 GLN Chi-restraints excluded: chain G residue 38 CYS Chi-restraints excluded: chain G residue 42 PHE Chi-restraints excluded: chain G residue 47 CYS Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 78 VAL Chi-restraints excluded: chain H residue 67 ASP Chi-restraints excluded: chain H residue 109 LYS Chi-restraints excluded: chain I residue 77 LYS Chi-restraints excluded: chain I residue 122 SER Chi-restraints excluded: chain K residue 21 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 348 optimal weight: 6.9990 chunk 40 optimal weight: 7.9990 chunk 206 optimal weight: 0.9980 chunk 264 optimal weight: 1.9990 chunk 204 optimal weight: 0.0270 chunk 304 optimal weight: 0.9990 chunk 202 optimal weight: 0.6980 chunk 360 optimal weight: 2.9990 chunk 225 optimal weight: 2.9990 chunk 219 optimal weight: 0.9980 chunk 166 optimal weight: 6.9990 overall best weight: 0.7440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1078 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 116 ASN ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 31089 Z= 0.166 Angle : 0.504 9.938 42256 Z= 0.265 Chirality : 0.040 0.148 4785 Planarity : 0.004 0.051 5284 Dihedral : 12.805 155.799 4688 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.05 % Favored : 94.90 % Rotamer: Outliers : 1.08 % Allowed : 8.65 % Favored : 90.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.14), residues: 3686 helix: 0.81 (0.15), residues: 1291 sheet: -0.92 (0.22), residues: 517 loop : -0.62 (0.15), residues: 1878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 656 HIS 0.005 0.001 HIS A 659 PHE 0.012 0.001 PHE A 22 TYR 0.008 0.001 TYR A 852 ARG 0.004 0.000 ARG L 47 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 105 is missing expected H atoms. Skipping. Evaluate side-chains 335 residues out of total 3293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 301 time to evaluate : 3.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.8372 (mt-10) cc_final: 0.7862 (mt-10) REVERT: A 146 MET cc_start: 0.8756 (ppp) cc_final: 0.8196 (ppp) REVERT: A 437 MET cc_start: 0.7963 (mtp) cc_final: 0.7699 (mtp) REVERT: A 826 ASP cc_start: 0.9135 (m-30) cc_final: 0.8690 (m-30) REVERT: A 900 ASP cc_start: 0.8100 (t0) cc_final: 0.6295 (p0) REVERT: A 1111 MET cc_start: 0.8038 (ttp) cc_final: 0.7604 (ttm) REVERT: A 1259 MET cc_start: 0.8396 (pmm) cc_final: 0.8087 (pmm) REVERT: A 1400 CYS cc_start: 0.9168 (p) cc_final: 0.8938 (p) REVERT: A 1444 MET cc_start: 0.8257 (mmm) cc_final: 0.7982 (mmt) REVERT: B 282 ILE cc_start: 0.9537 (pt) cc_final: 0.9243 (mm) REVERT: B 310 MET cc_start: 0.9370 (ttt) cc_final: 0.8564 (tmm) REVERT: B 778 MET cc_start: 0.8003 (mtm) cc_final: 0.7597 (mtm) REVERT: B 860 MET cc_start: 0.8784 (ppp) cc_final: 0.8579 (tmm) REVERT: B 1098 MET cc_start: 0.8431 (mpp) cc_final: 0.8003 (mpp) REVERT: B 1132 GLU cc_start: 0.7942 (tt0) cc_final: 0.7628 (tm-30) REVERT: D 192 LYS cc_start: 0.7242 (mmtt) cc_final: 0.6994 (mttt) REVERT: E 22 MET cc_start: 0.9274 (ttt) cc_final: 0.8957 (tmm) REVERT: F 100 GLN cc_start: 0.9233 (OUTLIER) cc_final: 0.8980 (mp10) REVERT: G 41 LYS cc_start: 0.9112 (mmmt) cc_final: 0.8754 (mtpp) REVERT: L 64 LEU cc_start: 0.8712 (mt) cc_final: 0.8443 (pt) outliers start: 34 outliers final: 30 residues processed: 314 average time/residue: 0.8017 time to fit residues: 398.0575 Evaluate side-chains 326 residues out of total 3293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 295 time to evaluate : 3.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 748 MET Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 972 HIS Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1373 ASP Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 683 SER Chi-restraints excluded: chain B residue 781 PHE Chi-restraints excluded: chain B residue 995 ARG Chi-restraints excluded: chain B residue 1163 CYS Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 215 SER Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 100 GLN Chi-restraints excluded: chain G residue 42 PHE Chi-restraints excluded: chain G residue 47 CYS Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 78 VAL Chi-restraints excluded: chain H residue 67 ASP Chi-restraints excluded: chain H residue 109 LYS Chi-restraints excluded: chain I residue 77 LYS Chi-restraints excluded: chain I residue 122 SER Chi-restraints excluded: chain K residue 21 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 223 optimal weight: 0.8980 chunk 143 optimal weight: 3.9990 chunk 215 optimal weight: 4.9990 chunk 108 optimal weight: 9.9990 chunk 70 optimal weight: 5.9990 chunk 69 optimal weight: 0.9980 chunk 229 optimal weight: 0.5980 chunk 245 optimal weight: 6.9990 chunk 178 optimal weight: 5.9990 chunk 33 optimal weight: 0.6980 chunk 283 optimal weight: 10.0000 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1078 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 31089 Z= 0.192 Angle : 0.504 9.023 42256 Z= 0.264 Chirality : 0.039 0.145 4785 Planarity : 0.004 0.050 5284 Dihedral : 12.736 155.265 4688 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.64 % Favored : 94.30 % Rotamer: Outliers : 1.15 % Allowed : 8.71 % Favored : 90.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.14), residues: 3686 helix: 1.04 (0.15), residues: 1297 sheet: -0.81 (0.22), residues: 506 loop : -0.53 (0.15), residues: 1883 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 656 HIS 0.006 0.001 HIS A 659 PHE 0.010 0.001 PHE A 22 TYR 0.014 0.001 TYR A1349 ARG 0.004 0.000 ARG L 47 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 105 is missing expected H atoms. Skipping. Evaluate side-chains 340 residues out of total 3293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 304 time to evaluate : 3.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.8355 (mt-10) cc_final: 0.7821 (mt-10) REVERT: A 146 MET cc_start: 0.8760 (ppp) cc_final: 0.8199 (ppp) REVERT: A 437 MET cc_start: 0.7994 (mtp) cc_final: 0.7707 (mtp) REVERT: A 900 ASP cc_start: 0.8095 (t0) cc_final: 0.6314 (p0) REVERT: A 1259 MET cc_start: 0.8391 (pmm) cc_final: 0.8077 (pmm) REVERT: A 1285 MET cc_start: 0.9154 (mmm) cc_final: 0.8944 (mmm) REVERT: A 1368 MET cc_start: 0.8533 (mtp) cc_final: 0.7889 (ptp) REVERT: A 1400 CYS cc_start: 0.9159 (p) cc_final: 0.8923 (p) REVERT: A 1444 MET cc_start: 0.8383 (mmm) cc_final: 0.8129 (mmt) REVERT: B 282 ILE cc_start: 0.9536 (pt) cc_final: 0.9229 (mm) REVERT: B 778 MET cc_start: 0.8139 (mtm) cc_final: 0.7748 (mtm) REVERT: B 1098 MET cc_start: 0.8414 (mpp) cc_final: 0.7981 (mpp) REVERT: B 1132 GLU cc_start: 0.7950 (tt0) cc_final: 0.7600 (tm-30) REVERT: D 192 LYS cc_start: 0.7190 (mmtt) cc_final: 0.6939 (mttt) REVERT: D 198 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8940 (mp) REVERT: E 22 MET cc_start: 0.9312 (ttt) cc_final: 0.9004 (tmm) REVERT: E 50 MET cc_start: 0.7004 (ppp) cc_final: 0.6782 (ppp) REVERT: F 100 GLN cc_start: 0.9207 (OUTLIER) cc_final: 0.8952 (mp10) REVERT: G 41 LYS cc_start: 0.9109 (mmmt) cc_final: 0.8750 (mtpp) REVERT: L 64 LEU cc_start: 0.8737 (mt) cc_final: 0.8467 (pt) outliers start: 36 outliers final: 28 residues processed: 321 average time/residue: 0.8328 time to fit residues: 420.9956 Evaluate side-chains 325 residues out of total 3293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 295 time to evaluate : 3.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 299 HIS Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 746 MET Chi-restraints excluded: chain A residue 748 MET Chi-restraints excluded: chain A residue 972 HIS Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 383 ASN Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 995 ARG Chi-restraints excluded: chain B residue 1163 CYS Chi-restraints excluded: chain B residue 1196 ILE Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 215 SER Chi-restraints excluded: chain F residue 100 GLN Chi-restraints excluded: chain G residue 42 PHE Chi-restraints excluded: chain G residue 47 CYS Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 78 VAL Chi-restraints excluded: chain H residue 67 ASP Chi-restraints excluded: chain H residue 109 LYS Chi-restraints excluded: chain I residue 77 LYS Chi-restraints excluded: chain I residue 122 SER Chi-restraints excluded: chain K residue 21 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 327 optimal weight: 4.9990 chunk 345 optimal weight: 0.8980 chunk 315 optimal weight: 9.9990 chunk 335 optimal weight: 5.9990 chunk 202 optimal weight: 4.9990 chunk 146 optimal weight: 0.0670 chunk 263 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 303 optimal weight: 0.8980 chunk 317 optimal weight: 20.0000 chunk 334 optimal weight: 3.9990 overall best weight: 1.3722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 479 ASN ** A1078 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 531 GLN ** I 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 31089 Z= 0.179 Angle : 0.497 8.763 42256 Z= 0.260 Chirality : 0.039 0.147 4785 Planarity : 0.004 0.049 5284 Dihedral : 12.658 154.866 4688 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.07 % Favored : 94.87 % Rotamer: Outliers : 0.99 % Allowed : 8.90 % Favored : 90.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.14), residues: 3686 helix: 1.17 (0.15), residues: 1302 sheet: -0.82 (0.22), residues: 511 loop : -0.47 (0.15), residues: 1873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 656 HIS 0.005 0.001 HIS A 659 PHE 0.011 0.001 PHE A 22 TYR 0.008 0.001 TYR A1349 ARG 0.013 0.000 ARG D 209 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 105 is missing expected H atoms. Skipping. Evaluate side-chains 332 residues out of total 3293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 301 time to evaluate : 3.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.8353 (mt-10) cc_final: 0.7827 (mt-10) REVERT: A 146 MET cc_start: 0.8768 (ppp) cc_final: 0.8209 (ppp) REVERT: A 437 MET cc_start: 0.8039 (mtp) cc_final: 0.7732 (mtp) REVERT: A 752 LYS cc_start: 0.9392 (tppp) cc_final: 0.9143 (tppp) REVERT: A 846 GLU cc_start: 0.8423 (mt-10) cc_final: 0.8172 (mt-10) REVERT: A 900 ASP cc_start: 0.8075 (t0) cc_final: 0.6314 (p0) REVERT: A 1259 MET cc_start: 0.8389 (pmm) cc_final: 0.8076 (pmm) REVERT: A 1400 CYS cc_start: 0.9150 (p) cc_final: 0.8901 (p) REVERT: A 1444 MET cc_start: 0.8497 (mmm) cc_final: 0.8261 (mmt) REVERT: B 282 ILE cc_start: 0.9536 (pt) cc_final: 0.9230 (mm) REVERT: B 778 MET cc_start: 0.8116 (mtm) cc_final: 0.7725 (mtm) REVERT: B 809 MET cc_start: 0.8773 (mtp) cc_final: 0.8515 (mtp) REVERT: B 1098 MET cc_start: 0.8416 (mpp) cc_final: 0.7971 (mpp) REVERT: B 1132 GLU cc_start: 0.7839 (tt0) cc_final: 0.7477 (tm-30) REVERT: D 192 LYS cc_start: 0.7236 (mmtt) cc_final: 0.6994 (mttt) REVERT: D 198 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.8974 (mp) REVERT: E 22 MET cc_start: 0.9305 (ttt) cc_final: 0.9013 (tmm) REVERT: E 50 MET cc_start: 0.7050 (ppp) cc_final: 0.6766 (ppp) REVERT: F 100 GLN cc_start: 0.9207 (OUTLIER) cc_final: 0.8944 (mp10) REVERT: G 41 LYS cc_start: 0.9105 (mmmt) cc_final: 0.8743 (mtpp) REVERT: L 64 LEU cc_start: 0.8748 (mt) cc_final: 0.8484 (pt) outliers start: 31 outliers final: 28 residues processed: 315 average time/residue: 0.8069 time to fit residues: 401.3033 Evaluate side-chains 323 residues out of total 3293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 293 time to evaluate : 3.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 299 HIS Chi-restraints excluded: chain A residue 479 ASN Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 972 HIS Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 531 GLN Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 781 PHE Chi-restraints excluded: chain B residue 1156 ASP Chi-restraints excluded: chain B residue 1163 CYS Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 215 SER Chi-restraints excluded: chain F residue 100 GLN Chi-restraints excluded: chain G residue 38 CYS Chi-restraints excluded: chain G residue 42 PHE Chi-restraints excluded: chain G residue 47 CYS Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 78 VAL Chi-restraints excluded: chain H residue 67 ASP Chi-restraints excluded: chain H residue 109 LYS Chi-restraints excluded: chain I residue 77 LYS Chi-restraints excluded: chain I residue 122 SER Chi-restraints excluded: chain K residue 21 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 220 optimal weight: 2.9990 chunk 355 optimal weight: 2.9990 chunk 216 optimal weight: 0.7980 chunk 168 optimal weight: 0.9980 chunk 246 optimal weight: 2.9990 chunk 372 optimal weight: 10.0000 chunk 342 optimal weight: 50.0000 chunk 296 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 229 optimal weight: 0.9980 chunk 181 optimal weight: 0.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1078 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.272 31089 Z= 0.229 Angle : 0.688 59.175 42256 Z= 0.411 Chirality : 0.040 0.432 4785 Planarity : 0.004 0.073 5284 Dihedral : 12.657 154.865 4688 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.05 % Favored : 94.90 % Rotamer: Outliers : 0.93 % Allowed : 9.06 % Favored : 90.01 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.14), residues: 3686 helix: 1.18 (0.15), residues: 1302 sheet: -0.82 (0.22), residues: 511 loop : -0.47 (0.15), residues: 1873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 656 HIS 0.005 0.001 HIS A 659 PHE 0.012 0.001 PHE A1402 TYR 0.008 0.001 TYR A 852 ARG 0.008 0.000 ARG D 209 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 105 is missing expected H atoms. Skipping. Evaluate side-chains 322 residues out of total 3293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 293 time to evaluate : 3.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.8356 (mt-10) cc_final: 0.7826 (mt-10) REVERT: A 146 MET cc_start: 0.8768 (ppp) cc_final: 0.8209 (ppp) REVERT: A 437 MET cc_start: 0.8040 (mtp) cc_final: 0.7731 (mtp) REVERT: A 479 ASN cc_start: 0.9168 (t0) cc_final: 0.8713 (t0) REVERT: A 752 LYS cc_start: 0.9392 (tppp) cc_final: 0.9148 (tppp) REVERT: A 846 GLU cc_start: 0.8413 (mt-10) cc_final: 0.8189 (mt-10) REVERT: A 900 ASP cc_start: 0.8074 (t0) cc_final: 0.6314 (p0) REVERT: A 1259 MET cc_start: 0.8388 (pmm) cc_final: 0.8076 (pmm) REVERT: A 1400 CYS cc_start: 0.9150 (p) cc_final: 0.8902 (p) REVERT: A 1444 MET cc_start: 0.8497 (mmm) cc_final: 0.8263 (mmt) REVERT: B 282 ILE cc_start: 0.9536 (pt) cc_final: 0.9230 (mm) REVERT: B 778 MET cc_start: 0.8116 (mtm) cc_final: 0.7722 (mtm) REVERT: B 809 MET cc_start: 0.8779 (mtp) cc_final: 0.8513 (mtp) REVERT: B 1098 MET cc_start: 0.8418 (mpp) cc_final: 0.7970 (mpp) REVERT: D 192 LYS cc_start: 0.7233 (mmtt) cc_final: 0.6994 (mttt) REVERT: D 198 LEU cc_start: 0.9253 (OUTLIER) cc_final: 0.8974 (mp) REVERT: E 22 MET cc_start: 0.9305 (ttt) cc_final: 0.9013 (tmm) REVERT: E 50 MET cc_start: 0.7050 (ppp) cc_final: 0.6769 (ppp) REVERT: F 100 GLN cc_start: 0.9207 (OUTLIER) cc_final: 0.8944 (mp10) REVERT: G 41 LYS cc_start: 0.9105 (mmmt) cc_final: 0.8742 (mtpp) REVERT: L 64 LEU cc_start: 0.8749 (mt) cc_final: 0.8484 (pt) outliers start: 29 outliers final: 27 residues processed: 307 average time/residue: 0.8333 time to fit residues: 408.1862 Evaluate side-chains 322 residues out of total 3293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 293 time to evaluate : 3.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 299 HIS Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 748 MET Chi-restraints excluded: chain A residue 972 HIS Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 781 PHE Chi-restraints excluded: chain B residue 1156 ASP Chi-restraints excluded: chain B residue 1163 CYS Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 215 SER Chi-restraints excluded: chain F residue 100 GLN Chi-restraints excluded: chain G residue 38 CYS Chi-restraints excluded: chain G residue 42 PHE Chi-restraints excluded: chain G residue 47 CYS Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 78 VAL Chi-restraints excluded: chain H residue 67 ASP Chi-restraints excluded: chain H residue 109 LYS Chi-restraints excluded: chain I residue 77 LYS Chi-restraints excluded: chain I residue 122 SER Chi-restraints excluded: chain K residue 21 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 235 optimal weight: 2.9990 chunk 316 optimal weight: 9.9990 chunk 90 optimal weight: 1.9990 chunk 273 optimal weight: 8.9990 chunk 43 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 297 optimal weight: 0.7980 chunk 124 optimal weight: 0.6980 chunk 305 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 54 optimal weight: 0.5980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1078 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.078549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.058821 restraints weight = 390772.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.060771 restraints weight = 166689.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.062020 restraints weight = 98158.734| |-----------------------------------------------------------------------------| r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.272 31089 Z= 0.229 Angle : 0.688 59.175 42256 Z= 0.411 Chirality : 0.040 0.432 4785 Planarity : 0.004 0.073 5284 Dihedral : 12.657 154.865 4688 Min Nonbonded Distance : 1.210 Molprobity Statistics. All-atom Clashscore : 14.74 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.05 % Favored : 94.90 % Rotamer: Outliers : 0.93 % Allowed : 9.09 % Favored : 89.98 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.14), residues: 3686 helix: 1.18 (0.15), residues: 1302 sheet: -0.82 (0.22), residues: 511 loop : -0.47 (0.15), residues: 1873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 656 HIS 0.005 0.001 HIS A 659 PHE 0.012 0.001 PHE A1402 TYR 0.008 0.001 TYR A 852 ARG 0.008 0.000 ARG D 209 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9046.92 seconds wall clock time: 158 minutes 16.61 seconds (9496.61 seconds total)