Starting phenix.real_space_refine on Fri Feb 23 03:52:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7du2_30865/02_2024/7du2_30865_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7du2_30865/02_2024/7du2_30865.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7du2_30865/02_2024/7du2_30865.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7du2_30865/02_2024/7du2_30865.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7du2_30865/02_2024/7du2_30865_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7du2_30865/02_2024/7du2_30865_updated.pdb" } resolution = 3.35 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= 0.065 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 Fe 4 7.16 5 Zn 6 6.06 5 P 36 5.49 5 Mg 1 5.21 5 S 249 5.16 5 C 23095 2.51 5 N 6366 2.21 5 O 6859 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 4": "OE1" <-> "OE2" Residue "A GLU 27": "OE1" <-> "OE2" Residue "A GLU 120": "OE1" <-> "OE2" Residue "A GLU 177": "OE1" <-> "OE2" Residue "A ARG 254": "NH1" <-> "NH2" Residue "A ARG 366": "NH1" <-> "NH2" Residue "A GLU 379": "OE1" <-> "OE2" Residue "A GLU 443": "OE1" <-> "OE2" Residue "A ARG 452": "NH1" <-> "NH2" Residue "A ARG 479": "NH1" <-> "NH2" Residue "A GLU 490": "OE1" <-> "OE2" Residue "A ASP 544": "OD1" <-> "OD2" Residue "A ARG 669": "NH1" <-> "NH2" Residue "A ARG 694": "NH1" <-> "NH2" Residue "A ARG 769": "NH1" <-> "NH2" Residue "A ARG 816": "NH1" <-> "NH2" Residue "A GLU 822": "OE1" <-> "OE2" Residue "A GLU 846": "OE1" <-> "OE2" Residue "A GLU 880": "OE1" <-> "OE2" Residue "A GLU 996": "OE1" <-> "OE2" Residue "A ARG 998": "NH1" <-> "NH2" Residue "A ARG 1069": "NH1" <-> "NH2" Residue "A GLU 1072": "OE1" <-> "OE2" Residue "A ARG 1136": "NH1" <-> "NH2" Residue "A ARG 1141": "NH1" <-> "NH2" Residue "A GLU 1143": "OE1" <-> "OE2" Residue "A GLU 1170": "OE1" <-> "OE2" Residue "A ARG 1178": "NH1" <-> "NH2" Residue "A GLU 1179": "OE1" <-> "OE2" Residue "A GLU 1206": "OE1" <-> "OE2" Residue "A ARG 1245": "NH1" <-> "NH2" Residue "B GLU 88": "OE1" <-> "OE2" Residue "B ARG 103": "NH1" <-> "NH2" Residue "B GLU 154": "OE1" <-> "OE2" Residue "B ARG 188": "NH1" <-> "NH2" Residue "B GLU 192": "OE1" <-> "OE2" Residue "B ARG 213": "NH1" <-> "NH2" Residue "B GLU 246": "OE1" <-> "OE2" Residue "B GLU 258": "OE1" <-> "OE2" Residue "B ARG 310": "NH1" <-> "NH2" Residue "B GLU 311": "OE1" <-> "OE2" Residue "B ARG 329": "NH1" <-> "NH2" Residue "B ARG 361": "NH1" <-> "NH2" Residue "B GLU 374": "OE1" <-> "OE2" Residue "B ARG 454": "NH1" <-> "NH2" Residue "B GLU 486": "OE1" <-> "OE2" Residue "B GLU 529": "OE1" <-> "OE2" Residue "B GLU 530": "OE1" <-> "OE2" Residue "B ARG 591": "NH1" <-> "NH2" Residue "B GLU 622": "OE1" <-> "OE2" Residue "B PHE 624": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 726": "OE1" <-> "OE2" Residue "B ARG 764": "NH1" <-> "NH2" Residue "B ARG 781": "NH1" <-> "NH2" Residue "B ARG 1041": "NH1" <-> "NH2" Residue "B ARG 1052": "NH1" <-> "NH2" Residue "B GLU 1066": "OE1" <-> "OE2" Residue "C GLU 9": "OE1" <-> "OE2" Residue "C PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 50": "NH1" <-> "NH2" Residue "C GLU 58": "OE1" <-> "OE2" Residue "C GLU 90": "OE1" <-> "OE2" Residue "C GLU 131": "OE1" <-> "OE2" Residue "C GLU 187": "OE1" <-> "OE2" Residue "C ASP 196": "OD1" <-> "OD2" Residue "C ARG 234": "NH1" <-> "NH2" Residue "C GLU 246": "OE1" <-> "OE2" Residue "C ARG 279": "NH1" <-> "NH2" Residue "C ARG 298": "NH1" <-> "NH2" Residue "G ARG 12": "NH1" <-> "NH2" Residue "G GLU 19": "OE1" <-> "OE2" Residue "G ARG 73": "NH1" <-> "NH2" Residue "G PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 48": "OD1" <-> "OD2" Residue "K GLU 115": "OE1" <-> "OE2" Residue "L GLU 21": "OE1" <-> "OE2" Residue "L GLU 38": "OE1" <-> "OE2" Residue "P GLU 233": "OE1" <-> "OE2" Residue "P GLU 257": "OE1" <-> "OE2" Residue "P ASP 294": "OD1" <-> "OD2" Residue "P GLU 301": "OE1" <-> "OE2" Residue "P GLU 312": "OE1" <-> "OE2" Residue "E GLU 78": "OE1" <-> "OE2" Residue "E GLU 154": "OE1" <-> "OE2" Residue "F GLU 82": "OE1" <-> "OE2" Residue "H GLU 7": "OE1" <-> "OE2" Residue "H GLU 33": "OE1" <-> "OE2" Residue "J GLU 28": "OE1" <-> "OE2" Residue "J GLU 31": "OE1" <-> "OE2" Residue "J TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 5": "OE1" <-> "OE2" Residue "O TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 134": "OE1" <-> "OE2" Residue "O ARG 159": "NH1" <-> "NH2" Residue "O ARG 258": "NH1" <-> "NH2" Residue "O GLU 408": "OE1" <-> "OE2" Residue "O ARG 419": "NH1" <-> "NH2" Residue "O PHE 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 448": "OE1" <-> "OE2" Residue "O GLU 453": "OE1" <-> "OE2" Residue "O GLU 456": "OE1" <-> "OE2" Residue "O GLU 500": "OE1" <-> "OE2" Residue "O GLU 513": "OE1" <-> "OE2" Residue "O ARG 533": "NH1" <-> "NH2" Residue "Q TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 52": "OE1" <-> "OE2" Residue "Q GLU 79": "OE1" <-> "OE2" Residue "Q ASP 83": "OD1" <-> "OD2" Residue "Q GLU 85": "OE1" <-> "OE2" Residue "Q ARG 105": "NH1" <-> "NH2" Residue "Q ARG 108": "NH1" <-> "NH2" Residue "D TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 59": "NH1" <-> "NH2" Residue "D GLU 64": "OE1" <-> "OE2" Residue "D PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 96": "OE1" <-> "OE2" Residue "D GLU 102": "OE1" <-> "OE2" Residue "D GLU 106": "OE1" <-> "OE2" Residue "D GLU 110": "OE1" <-> "OE2" Residue "D GLU 114": "OE1" <-> "OE2" Residue "M TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 75": "OE1" <-> "OE2" Residue "M ARG 113": "NH1" <-> "NH2" Residue "M ARG 136": "NH1" <-> "NH2" Residue "M ASP 146": "OD1" <-> "OD2" Residue "I GLU 16": "OE1" <-> "OE2" Residue "I PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 36616 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 10152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1293, 10152 Classifications: {'peptide': 1293} Link IDs: {'PTRANS': 60, 'TRANS': 1232} Chain breaks: 5 Chain: "B" Number of atoms: 8254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1044, 8254 Classifications: {'peptide': 1044} Link IDs: {'PTRANS': 47, 'TRANS': 996} Chain breaks: 6 Chain: "C" Number of atoms: 2641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2641 Classifications: {'peptide': 330} Link IDs: {'PTRANS': 17, 'TRANS': 312} Chain breaks: 1 Chain: "G" Number of atoms: 1337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1337 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 10, 'TRANS': 155} Chain breaks: 2 Chain: "K" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 822 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 4, 'TRANS': 98} Chain: "L" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 372 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "P" Number of atoms: 1008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1008 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 7, 'TRANS': 122} Chain: "E" Number of atoms: 1590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1590 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 9, 'TRANS': 184} Chain breaks: 2 Chain: "F" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 610 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 5, 'TRANS': 70} Chain: "H" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1002 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain breaks: 2 Chain: "J" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 507 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "O" Number of atoms: 3546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3546 Classifications: {'peptide': 443} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 19, 'TRANS': 423} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "Q" Number of atoms: 724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 724 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 11, 'TRANS': 74} Chain breaks: 1 Chain: "D" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 985 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "M" Number of atoms: 1272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1272 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 8, 'TRANS': 145} Chain breaks: 2 Chain: "N" Number of atoms: 697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 697 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 3, 'TRANS': 88} Chain breaks: 1 Chain: "I" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 340 Classifications: {'peptide': 47} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 3, 'TRANS': 43} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "X" Number of atoms: 288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 288 Classifications: {'DNA': 14} Link IDs: {'rna3p': 13} Chain: "Y" Number of atoms: 392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 392 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Chain: "R" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 62 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 1, 'rna3p_pyr': 2} Link IDs: {'rna3p': 2} 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: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 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: "I" 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 534 SG CYS A 69 37.114 116.929 102.648 1.00 96.02 S ATOM 556 SG CYS A 72 39.723 120.654 103.407 1.00 94.46 S ATOM 604 SG CYS A 79 40.355 117.388 101.110 1.00 88.70 S ATOM 1236 SG CYS A 156 70.720 101.445 138.825 1.00118.39 S ATOM 1262 SG CYS A 159 68.454 102.675 141.276 1.00121.42 S ATOM 17993 SG CYS B1080 52.590 123.736 109.949 1.00 81.64 S ATOM 18012 SG CYS B1083 53.162 122.878 113.406 1.00 81.49 S ATOM 18078 SG CYS B1092 49.345 122.184 110.556 1.00 86.49 S ATOM 18106 SG CYS B1095 50.974 125.773 114.312 1.00 88.09 S ATOM 23248 SG CYS L 19 15.681 76.308 66.250 1.00 81.26 S ATOM 23410 SG CYS L 39 16.216 71.055 68.141 1.00 97.98 S ATOM 24369 SG CYS P 287 44.367 116.956 137.878 1.00121.28 S ATOM 27843 SG CYS J 7 51.989 82.339 42.122 1.00 54.01 S ATOM 27867 SG CYS J 10 55.193 84.642 38.723 1.00 57.92 S ATOM 28131 SG CYS J 44 55.248 81.631 40.751 1.00 57.10 S ATOM 28137 SG CYS J 45 52.330 81.199 38.745 1.00 54.89 S ATOM 35552 SG CYS I 5 80.387 40.108 126.364 1.00122.02 S ATOM 35700 SG CYS I 25 78.034 43.451 129.299 1.00125.31 S Time building chain proxies: 19.72, per 1000 atoms: 0.54 Number of scatterers: 36616 At special positions: 0 Unit cell: (135.966, 193.936, 193.936, 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 6 29.99 Fe 4 26.01 S 249 16.00 P 36 15.00 Mg 1 11.99 O 6859 8.00 N 6366 7.00 C 23095 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 14.68 Conformation dependent library (CDL) restraints added in 6.9 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 P 401 " pdb="FE1 SF4 P 401 " - pdb=" SG CYS P 287 " pdb="FE2 SF4 P 401 " - pdb=" SG CYS P 307 " Number of angles added : 6 Zn2+ tetrahedral coordination pdb=" ZN A1902 " pdb="ZN ZN A1902 " - pdb=" NE2 HIS A 82 " pdb="ZN ZN A1902 " - pdb=" SG CYS A 69 " pdb="ZN ZN A1902 " - pdb=" SG CYS A 79 " pdb="ZN ZN A1902 " - pdb=" SG CYS A 72 " pdb=" ZN A1903 " pdb="ZN ZN A1903 " - pdb=" SG CYS A 159 " pdb="ZN ZN A1903 " - pdb=" SG CYS A 156 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1083 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1080 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1092 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1095 " pdb=" ZN I2000 " pdb="ZN ZN I2000 " - pdb=" SG CYS I 5 " pdb="ZN ZN I2000 " - pdb=" SG CYS I 25 " pdb=" ZN J2000 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 45 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 7 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 44 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 10 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 39 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 19 " Number of angles added : 15 8852 Ramachandran restraints generated. 4426 Oldfield, 0 Emsley, 4426 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8486 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 150 helices and 39 sheets defined 31.8% alpha, 8.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.57 Creating SS restraints... Processing helix chain 'A' and resid 29 through 31 No H-bonds generated for 'chain 'A' and resid 29 through 31' Processing helix chain 'A' and resid 98 through 105 Processing helix chain 'A' and resid 121 through 129 Processing helix chain 'A' and resid 137 through 150 removed outlier: 4.430A pdb=" N LEU A 142 " --> pdb=" O GLN A 138 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS A 144 " --> pdb=" O ARG A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 226 removed outlier: 3.743A pdb=" N LEU A 224 " --> pdb=" O PRO A 220 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ASN A 225 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 238 Proline residue: A 236 - end of helix No H-bonds generated for 'chain 'A' and resid 232 through 238' Processing helix chain 'A' and resid 247 through 250 Processing helix chain 'A' and resid 260 through 262 No H-bonds generated for 'chain 'A' and resid 260 through 262' Processing helix chain 'A' and resid 279 through 295 removed outlier: 3.728A pdb=" N LYS A 294 " --> pdb=" O ASN A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 319 removed outlier: 3.920A pdb=" N GLU A 308 " --> pdb=" O GLN A 304 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TRP A 310 " --> pdb=" O ILE A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 355 No H-bonds generated for 'chain 'A' and resid 352 through 355' Processing helix chain 'A' and resid 384 through 387 No H-bonds generated for 'chain 'A' and resid 384 through 387' Processing helix chain 'A' and resid 401 through 408 Processing helix chain 'A' and resid 437 through 442 Processing helix chain 'A' and resid 470 through 472 No H-bonds generated for 'chain 'A' and resid 470 through 472' Processing helix chain 'A' and resid 513 through 520 Processing helix chain 'A' and resid 543 through 552 removed outlier: 4.368A pdb=" N TYR A 550 " --> pdb=" O THR A 547 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU A 552 " --> pdb=" O ALA A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 570 removed outlier: 3.659A pdb=" N CYS A 565 " --> pdb=" O ARG A 561 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER A 570 " --> pdb=" O GLN A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 605 removed outlier: 4.004A pdb=" N VAL A 603 " --> pdb=" O GLN A 599 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE A 604 " --> pdb=" O ILE A 600 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU A 605 " --> pdb=" O PHE A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 670 Processing helix chain 'A' and resid 674 through 694 removed outlier: 3.841A pdb=" N ARG A 685 " --> pdb=" O SER A 681 " (cutoff:3.500A) Proline residue: A 688 - end of helix removed outlier: 3.801A pdb=" N ASN A 693 " --> pdb=" O VAL A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 700 through 702 No H-bonds generated for 'chain 'A' and resid 700 through 702' Processing helix chain 'A' and resid 707 through 732 removed outlier: 3.600A pdb=" N LYS A 711 " --> pdb=" O GLN A 707 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLU A 715 " --> pdb=" O LYS A 711 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TYR A 721 " --> pdb=" O LEU A 717 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LYS A 723 " --> pdb=" O ALA A 719 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N CYS A 724 " --> pdb=" O GLY A 720 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU A 731 " --> pdb=" O TYR A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 770 removed outlier: 3.707A pdb=" N LYS A 754 " --> pdb=" O ALA A 750 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU A 755 " --> pdb=" O LEU A 751 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASP A 761 " --> pdb=" O SER A 757 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU A 768 " --> pdb=" O GLY A 764 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLU A 770 " --> pdb=" O ALA A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 776 through 782 Processing helix chain 'A' and resid 789 through 795 Processing helix chain 'A' and resid 844 through 876 removed outlier: 3.859A pdb=" N GLU A 856 " --> pdb=" O MET A 852 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLY A 857 " --> pdb=" O ALA A 853 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU A 858 " --> pdb=" O GLY A 854 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA A 862 " --> pdb=" O LEU A 858 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N THR A 865 " --> pdb=" O THR A 861 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA A 866 " --> pdb=" O ALA A 862 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N TYR A 870 " --> pdb=" O ALA A 866 " (cutoff:3.500A) Processing helix chain 'A' and resid 902 through 904 No H-bonds generated for 'chain 'A' and resid 902 through 904' Processing helix chain 'A' and resid 921 through 931 Processing helix chain 'A' and resid 945 through 951 Processing helix chain 'A' and resid 966 through 986 removed outlier: 3.685A pdb=" N LYS A 970 " --> pdb=" O LEU A 966 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LYS A 979 " --> pdb=" O GLY A 975 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS A 986 " --> pdb=" O LYS A 982 " (cutoff:3.500A) Processing helix chain 'A' and resid 998 through 1002 removed outlier: 3.552A pdb=" N TYR A1001 " --> pdb=" O ARG A 998 " (cutoff:3.500A) Processing helix chain 'A' and resid 1008 through 1024 removed outlier: 3.805A pdb=" N GLU A1012 " --> pdb=" O PRO A1008 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASP A1020 " --> pdb=" O GLU A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1033 through 1046 removed outlier: 3.528A pdb=" N GLN A1039 " --> pdb=" O ALA A1035 " (cutoff:3.500A) Proline residue: A1044 - end of helix Processing helix chain 'A' and resid 1067 through 1075 removed outlier: 3.591A pdb=" N GLU A1072 " --> pdb=" O PRO A1068 " (cutoff:3.500A) Processing helix chain 'A' and resid 1097 through 1105 Processing helix chain 'A' and resid 1111 through 1113 No H-bonds generated for 'chain 'A' and resid 1111 through 1113' Processing helix chain 'A' and resid 1134 through 1139 Processing helix chain 'A' and resid 1146 through 1153 Processing helix chain 'A' and resid 1187 through 1198 removed outlier: 4.278A pdb=" N GLU A1194 " --> pdb=" O GLN A1190 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASP A1195 " --> pdb=" O PHE A1191 " (cutoff:3.500A) Proline residue: A1197 - end of helix Processing helix chain 'A' and resid 1232 through 1236 Processing helix chain 'A' and resid 1251 through 1255 Processing helix chain 'A' and resid 1261 through 1277 removed outlier: 3.501A pdb=" N ILE A1267 " --> pdb=" O ALA A1263 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE A1271 " --> pdb=" O ILE A1267 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR A1274 " --> pdb=" O GLU A1270 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL A1276 " --> pdb=" O GLN A1272 " (cutoff:3.500A) Processing helix chain 'A' and resid 1284 through 1294 removed outlier: 3.725A pdb=" N ASP A1292 " --> pdb=" O MET A1288 " (cutoff:3.500A) Processing helix chain 'A' and resid 1305 through 1309 removed outlier: 3.868A pdb=" N ALA A1309 " --> pdb=" O ARG A1305 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1305 through 1309' Processing helix chain 'A' and resid 1315 through 1319 Processing helix chain 'A' and resid 1324 through 1333 removed outlier: 3.525A pdb=" N LEU A1328 " --> pdb=" O THR A1324 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA A1331 " --> pdb=" O HIS A1327 " (cutoff:3.500A) Processing helix chain 'A' and resid 1346 through 1349 No H-bonds generated for 'chain 'A' and resid 1346 through 1349' Processing helix chain 'B' and resid 27 through 37 Proline residue: B 31 - end of helix removed outlier: 3.940A pdb=" N LEU B 34 " --> pdb=" O PRO B 31 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS B 35 " --> pdb=" O ALA B 32 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N LYS B 37 " --> pdb=" O LEU B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 52 removed outlier: 3.611A pdb=" N SER B 46 " --> pdb=" O GLN B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 102 No H-bonds generated for 'chain 'B' and resid 99 through 102' Processing helix chain 'B' and resid 152 through 157 removed outlier: 3.654A pdb=" N ALA B 156 " --> pdb=" O PRO B 152 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LYS B 157 " --> pdb=" O ALA B 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 152 through 157' Processing helix chain 'B' and resid 236 through 242 Processing helix chain 'B' and resid 248 through 255 Processing helix chain 'B' and resid 266 through 275 removed outlier: 5.274A pdb=" N GLU B 271 " --> pdb=" O PRO B 267 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N CYS B 272 " --> pdb=" O SER B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 291 removed outlier: 3.879A pdb=" N GLY B 288 " --> pdb=" O LEU B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 314 No H-bonds generated for 'chain 'B' and resid 311 through 314' Processing helix chain 'B' and resid 329 through 344 removed outlier: 3.640A pdb=" N ILE B 333 " --> pdb=" O ARG B 329 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N TYR B 334 " --> pdb=" O ALA B 330 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL B 342 " --> pdb=" O MET B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 391 removed outlier: 3.595A pdb=" N LEU B 372 " --> pdb=" O LEU B 368 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU B 374 " --> pdb=" O SER B 370 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ASP B 375 " --> pdb=" O LEU B 371 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N MET B 384 " --> pdb=" O PHE B 380 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS B 385 " --> pdb=" O ASN B 381 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLN B 390 " --> pdb=" O LYS B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 420 removed outlier: 3.628A pdb=" N ASP B 409 " --> pdb=" O MET B 406 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ILE B 411 " --> pdb=" O GLN B 408 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N THR B 412 " --> pdb=" O ASP B 409 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ASN B 413 " --> pdb=" O GLN B 410 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N VAL B 416 " --> pdb=" O ASN B 413 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASN B 417 " --> pdb=" O GLY B 414 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N SER B 420 " --> pdb=" O ASN B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 452 removed outlier: 3.940A pdb=" N MET B 451 " --> pdb=" O SER B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 475 No H-bonds generated for 'chain 'B' and resid 473 through 475' Processing helix chain 'B' and resid 509 through 518 removed outlier: 3.684A pdb=" N ASN B 517 " --> pdb=" O LYS B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 565 Processing helix chain 'B' and resid 609 through 616 removed outlier: 3.707A pdb=" N ALA B 615 " --> pdb=" O MET B 611 " (cutoff:3.500A) Processing helix chain 'B' and resid 621 through 626 removed outlier: 3.676A pdb=" N LEU B 625 " --> pdb=" O PHE B 621 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N HIS B 626 " --> pdb=" O GLU B 622 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 621 through 626' Processing helix chain 'B' and resid 637 through 640 Processing helix chain 'B' and resid 661 through 664 removed outlier: 3.910A pdb=" N LEU B 664 " --> pdb=" O PRO B 661 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 661 through 664' Processing helix chain 'B' and resid 680 through 691 removed outlier: 3.639A pdb=" N THR B 684 " --> pdb=" O SER B 680 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N TYR B 685 " --> pdb=" O PRO B 681 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLN B 686 " --> pdb=" O ARG B 682 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA B 688 " --> pdb=" O THR B 684 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LYS B 691 " --> pdb=" O CYS B 687 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 727 No H-bonds generated for 'chain 'B' and resid 724 through 727' Processing helix chain 'B' and resid 761 through 764 No H-bonds generated for 'chain 'B' and resid 761 through 764' Processing helix chain 'B' and resid 913 through 915 No H-bonds generated for 'chain 'B' and resid 913 through 915' Processing helix chain 'B' and resid 931 through 937 removed outlier: 3.613A pdb=" N PHE B 934 " --> pdb=" O PRO B 931 " (cutoff:3.500A) Proline residue: B 935 - end of helix No H-bonds generated for 'chain 'B' and resid 931 through 937' Processing helix chain 'B' and resid 940 through 955 removed outlier: 3.792A pdb=" N LEU B 947 " --> pdb=" O LEU B 943 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS B 950 " --> pdb=" O LEU B 946 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU B 954 " --> pdb=" O LYS B 950 " (cutoff:3.500A) Processing helix chain 'B' and resid 969 through 976 removed outlier: 4.458A pdb=" N GLU B 974 " --> pdb=" O LYS B 970 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASP B 975 " --> pdb=" O ASP B 971 " (cutoff:3.500A) Processing helix chain 'B' and resid 1016 through 1018 No H-bonds generated for 'chain 'B' and resid 1016 through 1018' Processing helix chain 'B' and resid 1049 through 1057 removed outlier: 3.550A pdb=" N CYS B1054 " --> pdb=" O MET B1050 " (cutoff:3.500A) Processing helix chain 'B' and resid 1061 through 1068 Processing helix chain 'B' and resid 1108 through 1117 Processing helix chain 'C' and resid 42 through 47 Processing helix chain 'C' and resid 73 through 82 removed outlier: 3.525A pdb=" N ARG C 78 " --> pdb=" O ASN C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 109 Processing helix chain 'C' and resid 223 through 225 No H-bonds generated for 'chain 'C' and resid 223 through 225' Processing helix chain 'C' and resid 249 through 256 Processing helix chain 'C' and resid 259 through 261 No H-bonds generated for 'chain 'C' and resid 259 through 261' Processing helix chain 'C' and resid 278 through 280 No H-bonds generated for 'chain 'C' and resid 278 through 280' Processing helix chain 'C' and resid 287 through 289 No H-bonds generated for 'chain 'C' and resid 287 through 289' Processing helix chain 'C' and resid 293 through 295 No H-bonds generated for 'chain 'C' and resid 293 through 295' Processing helix chain 'C' and resid 318 through 342 removed outlier: 3.923A pdb=" N SER C 323 " --> pdb=" O ASP C 319 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS C 327 " --> pdb=" O SER C 323 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N PHE C 336 " --> pdb=" O LYS C 332 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU C 339 " --> pdb=" O ARG C 335 " (cutoff:3.500A) 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 22 through 33 removed outlier: 3.751A pdb=" N ALA G 27 " --> pdb=" O ASN G 23 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU G 29 " --> pdb=" O SER G 25 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LYS G 32 " --> pdb=" O GLU G 28 " (cutoff:3.500A) Processing helix chain 'K' and resid 49 through 60 removed outlier: 4.218A pdb=" N SER K 54 " --> pdb=" O THR K 50 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N TYR K 57 " --> pdb=" O ASN K 53 " (cutoff:3.500A) Processing helix chain 'K' and resid 94 through 125 removed outlier: 3.780A pdb=" N ASN K 101 " --> pdb=" O GLN K 97 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER K 117 " --> pdb=" O LYS K 113 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASP K 123 " --> pdb=" O LYS K 119 " (cutoff:3.500A) Processing helix chain 'P' and resid 202 through 205 No H-bonds generated for 'chain 'P' and resid 202 through 205' Processing helix chain 'P' and resid 220 through 227 Processing helix chain 'P' and resid 242 through 254 removed outlier: 4.827A pdb=" N LYS P 247 " --> pdb=" O ILE P 243 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N VAL P 248 " --> pdb=" O TYR P 244 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N GLU P 249 " --> pdb=" O ASP P 245 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N MET P 250 " --> pdb=" O GLY P 246 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ALA P 254 " --> pdb=" O MET P 250 " (cutoff:3.500A) Processing helix chain 'P' and resid 286 through 289 No H-bonds generated for 'chain 'P' and resid 286 through 289' Processing helix chain 'P' and resid 292 through 294 No H-bonds generated for 'chain 'P' and resid 292 through 294' Processing helix chain 'P' and resid 304 through 306 No H-bonds generated for 'chain 'P' and resid 304 through 306' Processing helix chain 'P' and resid 308 through 313 Processing helix chain 'E' and resid 12 through 23 removed outlier: 4.010A pdb=" N HIS E 22 " --> pdb=" O MET E 18 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 33 No H-bonds generated for 'chain 'E' and resid 30 through 33' Processing helix chain 'E' and resid 37 through 40 No H-bonds generated for 'chain 'E' and resid 37 through 40' Processing helix chain 'E' and resid 44 through 48 Proline residue: E 48 - end of helix No H-bonds generated for 'chain 'E' and resid 44 through 48' Processing helix chain 'E' and resid 84 through 96 removed outlier: 3.958A pdb=" N TYR E 90 " --> pdb=" O THR E 86 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N GLN E 92 " --> pdb=" O LYS E 88 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ARG E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 114 through 120 removed outlier: 3.624A pdb=" N LEU E 118 " --> pdb=" O ALA E 114 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL E 119 " --> pdb=" O LYS E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 135 No H-bonds generated for 'chain 'E' and resid 132 through 135' Processing helix chain 'E' and resid 153 through 163 removed outlier: 3.674A pdb=" N THR E 157 " --> pdb=" O LYS E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 183 Processing helix chain 'F' and resid 59 through 75 removed outlier: 3.545A pdb=" N ARG F 64 " --> pdb=" O TYR F 60 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N MET F 75 " --> pdb=" O LEU F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 98 removed outlier: 3.503A pdb=" N LYS F 95 " --> pdb=" O LEU F 91 " (cutoff:3.500A) Processing helix chain 'J' and resid 15 through 17 No H-bonds generated for 'chain 'J' and resid 15 through 17' Processing helix chain 'J' and resid 19 through 26 Processing helix chain 'J' and resid 31 through 37 removed outlier: 4.257A pdb=" N LEU J 35 " --> pdb=" O GLU J 31 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASP J 36 " --> pdb=" O GLY J 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 47 through 50 No H-bonds generated for 'chain 'J' and resid 47 through 50' Processing helix chain 'J' and resid 55 through 62 removed outlier: 3.981A pdb=" N LEU J 59 " --> pdb=" O ILE J 56 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N LEU J 60 " --> pdb=" O GLU J 57 " (cutoff:3.500A) Processing helix chain 'O' and resid 3 through 16 removed outlier: 3.528A pdb=" N GLN O 14 " --> pdb=" O SER O 10 " (cutoff:3.500A) Processing helix chain 'O' and resid 20 through 31 Processing helix chain 'O' and resid 36 through 42 Processing helix chain 'O' and resid 47 through 59 Processing helix chain 'O' and resid 79 through 97 removed outlier: 3.899A pdb=" N LEU O 83 " --> pdb=" O CYS O 79 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ARG O 84 " --> pdb=" O SER O 80 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N MET O 85 " --> pdb=" O ARG O 81 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N LEU O 86 " --> pdb=" O VAL O 82 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ARG O 87 " --> pdb=" O LEU O 83 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TYR O 88 " --> pdb=" O ARG O 84 " (cutoff:3.500A) Proline residue: O 89 - end of helix removed outlier: 3.543A pdb=" N THR O 94 " --> pdb=" O ARG O 90 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N THR O 95 " --> pdb=" O TYR O 91 " (cutoff:3.500A) Processing helix chain 'O' and resid 101 through 112 Processing helix chain 'O' and resid 118 through 132 removed outlier: 4.284A pdb=" N LYS O 123 " --> pdb=" O SER O 119 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASP O 127 " --> pdb=" O LYS O 123 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N THR O 130 " --> pdb=" O ALA O 126 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR O 132 " --> pdb=" O ARG O 128 " (cutoff:3.500A) Processing helix chain 'O' and resid 142 through 153 removed outlier: 3.571A pdb=" N VAL O 149 " --> pdb=" O SER O 145 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA O 152 " --> pdb=" O PHE O 148 " (cutoff:3.500A) Processing helix chain 'O' and resid 171 through 174 No H-bonds generated for 'chain 'O' and resid 171 through 174' Processing helix chain 'O' and resid 239 through 256 Processing helix chain 'O' and resid 261 through 272 removed outlier: 3.597A pdb=" N GLU O 265 " --> pdb=" O GLN O 261 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE O 266 " --> pdb=" O THR O 262 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL O 267 " --> pdb=" O SER O 263 " (cutoff:3.500A) Processing helix chain 'O' and resid 290 through 295 Processing helix chain 'O' and resid 305 through 316 Processing helix chain 'O' and resid 338 through 357 removed outlier: 3.678A pdb=" N LEU O 342 " --> pdb=" O LEU O 338 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N THR O 347 " --> pdb=" O ALA O 343 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA O 348 " --> pdb=" O SER O 344 " (cutoff:3.500A) Processing helix chain 'O' and resid 359 through 371 removed outlier: 3.538A pdb=" N ILE O 365 " --> pdb=" O ARG O 361 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU O 368 " --> pdb=" O ARG O 364 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL O 369 " --> pdb=" O ILE O 365 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU O 370 " --> pdb=" O PHE O 366 " (cutoff:3.500A) Processing helix chain 'O' and resid 380 through 383 No H-bonds generated for 'chain 'O' and resid 380 through 383' Processing helix chain 'O' and resid 388 through 400 removed outlier: 3.653A pdb=" N ASP O 393 " --> pdb=" O LYS O 389 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N MET O 394 " --> pdb=" O GLU O 390 " (cutoff:3.500A) Processing helix chain 'O' and resid 428 through 455 removed outlier: 3.622A pdb=" N LEU O 435 " --> pdb=" O ALA O 431 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA O 444 " --> pdb=" O TYR O 440 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ARG O 449 " --> pdb=" O ASN O 445 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N THR O 454 " --> pdb=" O ARG O 450 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N LYS O 455 " --> pdb=" O GLN O 451 " (cutoff:3.500A) Processing helix chain 'O' and resid 457 through 464 removed outlier: 3.738A pdb=" N LEU O 461 " --> pdb=" O LYS O 458 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLU O 462 " --> pdb=" O ARG O 459 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS O 463 " --> pdb=" O LEU O 460 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N SER O 464 " --> pdb=" O LEU O 461 " (cutoff:3.500A) Processing helix chain 'O' and resid 493 through 515 removed outlier: 3.653A pdb=" N LEU O 499 " --> pdb=" O GLU O 495 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ILE O 514 " --> pdb=" O ASP O 510 " (cutoff:3.500A) Processing helix chain 'O' and resid 517 through 530 removed outlier: 3.987A pdb=" N TYR O 526 " --> pdb=" O LEU O 522 " (cutoff:3.500A) Processing helix chain 'Q' and resid 46 through 61 removed outlier: 3.780A pdb=" N THR Q 50 " --> pdb=" O PRO Q 47 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLY Q 51 " --> pdb=" O LEU Q 48 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLU Q 52 " --> pdb=" O LYS Q 49 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU Q 54 " --> pdb=" O GLY Q 51 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N MET Q 57 " --> pdb=" O GLU Q 54 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU Q 58 " --> pdb=" O GLU Q 55 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N LYS Q 61 " --> pdb=" O LEU Q 58 " (cutoff:3.500A) Processing helix chain 'Q' and resid 71 through 76 Processing helix chain 'D' and resid 13 through 30 removed outlier: 3.525A pdb=" N LYS D 28 " --> pdb=" O LYS D 24 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLU D 29 " --> pdb=" O GLU D 25 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N SER D 30 " --> pdb=" O GLN D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 37 No H-bonds generated for 'chain 'D' and resid 35 through 37' Processing helix chain 'D' and resid 41 through 55 removed outlier: 3.664A pdb=" N LYS D 51 " --> pdb=" O TYR D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 76 removed outlier: 3.522A pdb=" N ALA D 72 " --> pdb=" O GLU D 68 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N SER D 75 " --> pdb=" O THR D 71 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N HIS D 76 " --> pdb=" O ALA D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 89 Processing helix chain 'D' and resid 94 through 98 Processing helix chain 'D' and resid 112 through 121 Processing helix chain 'M' and resid 70 through 76 Processing helix chain 'M' and resid 141 through 151 Processing helix chain 'N' and resid 253 through 260 Processing helix chain 'N' and resid 342 through 344 No H-bonds generated for 'chain 'N' and resid 342 through 344' Processing sheet with id= A, first strand: chain 'A' and resid 17 through 19 Processing sheet with id= B, first strand: chain 'A' and resid 84 through 87 removed outlier: 3.887A pdb=" N GLY A 84 " --> pdb=" O VAL A 257 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 364 through 368 removed outlier: 4.092A pdb=" N THR A 367 " --> pdb=" O MET A 505 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASP A 458 " --> pdb=" O ALA A 478 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 369 through 371 removed outlier: 5.889A pdb=" N PHE A 486 " --> pdb=" O SER A 370 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'A' and resid 391 through 395 Processing sheet with id= F, first strand: chain 'A' and resid 617 through 620 Processing sheet with id= G, first strand: chain 'A' and resid 1084 through 1088 Processing sheet with id= H, first strand: chain 'A' and resid 1118 through 1122 removed outlier: 3.639A pdb=" N LEU A1122 " --> pdb=" O ASP A1125 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 1166 through 1168 removed outlier: 3.828A pdb=" N VAL A1173 " --> pdb=" O HIS A1168 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 110 through 113 removed outlier: 3.526A pdb=" N GLY B 134 " --> pdb=" O ILE B 113 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 169 through 171 Processing sheet with id= L, first strand: chain 'B' and resid 181 through 184 Processing sheet with id= M, first strand: chain 'B' and resid 189 through 191 removed outlier: 4.094A pdb=" N ILE B 190 " --> pdb=" O GLY B 200 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ALA B 201 " --> pdb=" O THR B 214 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 538 through 541 Processing sheet with id= O, first strand: chain 'B' and resid 593 through 597 Processing sheet with id= P, first strand: chain 'B' and resid 709 through 712 Processing sheet with id= Q, first strand: chain 'B' and resid 739 through 741 Processing sheet with id= R, first strand: chain 'B' and resid 1075 through 1080 removed outlier: 3.631A pdb=" N ILE B1106 " --> pdb=" O PHE B1075 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL B1077 " --> pdb=" O LEU B1104 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'B' and resid 755 through 758 removed outlier: 7.275A pdb=" N LEU B 757 " --> pdb=" O GLY B 908 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ILE B 910 " --> pdb=" O LEU B 757 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'B' and resid 825 through 828 removed outlier: 4.064A pdb=" N GLN B 825 " --> pdb=" O TYR B 858 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ILE B 856 " --> pdb=" O LEU B 827 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'B' and resid 865 through 872 removed outlier: 6.705A pdb=" N LEU B 884 " --> pdb=" O GLU B 867 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N VAL B 869 " --> pdb=" O LYS B 882 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N LYS B 882 " --> pdb=" O VAL B 869 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ILE B 871 " --> pdb=" O LEU B 880 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LEU B 880 " --> pdb=" O ILE B 871 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'C' and resid 13 through 15 removed outlier: 3.534A pdb=" N ARG C 298 " --> pdb=" O THR C 240 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'C' and resid 173 through 176 removed outlier: 4.457A pdb=" N GLN C 139 " --> pdb=" O ILE C 176 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N CYS C 146 " --> pdb=" O GLN C 206 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLN C 206 " --> pdb=" O CYS C 146 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N VAL C 215 " --> pdb=" O VAL C 89 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N VAL C 89 " --> pdb=" O VAL C 215 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N GLY C 217 " --> pdb=" O MET C 87 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N MET C 87 " --> pdb=" O GLY C 217 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'C' and resid 233 through 235 Processing sheet with id= Y, first strand: chain 'C' and resid 167 through 169 removed outlier: 3.571A pdb=" N ALA C 200 " --> pdb=" O VAL C 168 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'G' and resid 3 through 13 Processing sheet with id= AA, first strand: chain 'G' and resid 37 through 39 removed outlier: 3.989A pdb=" N LYS G 37 " --> pdb=" O CYS G 45 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'G' and resid 83 through 87 removed outlier: 4.796A pdb=" N GLU G 83 " --> pdb=" O PHE G 150 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE G 150 " --> pdb=" O GLU G 83 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N SER G 189 " --> pdb=" O ARG G 151 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'K' and resid 39 through 45 Processing sheet with id= AD, first strand: chain 'E' and resid 103 through 105 removed outlier: 6.941A pdb=" N GLU E 128 " --> pdb=" O ILE E 104 " (cutoff:3.500A) No H-bonds generated for sheet with id= AD Processing sheet with id= AE, first strand: chain 'E' and resid 147 through 150 removed outlier: 3.820A pdb=" N GLU E 147 " --> pdb=" O ILE E 194 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'F' and resid 105 through 109 Processing sheet with id= AG, first strand: chain 'H' and resid 39 through 44 removed outlier: 3.649A pdb=" N LEU H 39 " --> pdb=" O CYS H 30 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N GLU H 31 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N VAL H 12 " --> pdb=" O GLU H 31 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ILE H 60 " --> pdb=" O LEU H 5 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N GLU H 7 " --> pdb=" O LEU H 58 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N LEU H 58 " --> pdb=" O GLU H 7 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N ILE H 9 " --> pdb=" O PHE H 56 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N PHE H 56 " --> pdb=" O ILE H 9 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'H' and resid 139 through 142 removed outlier: 4.220A pdb=" N SER H 139 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N TYR H 115 " --> pdb=" O TYR H 97 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU H 125 " --> pdb=" O ALA H 114 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU H 121 " --> pdb=" O TYR H 118 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'O' and resid 63 through 66 removed outlier: 3.674A pdb=" N GLN O 66 " --> pdb=" O GLU O 74 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU O 74 " --> pdb=" O GLN O 66 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'M' and resid 14 through 16 Processing sheet with id= AK, first strand: chain 'N' and resid 268 through 270 Processing sheet with id= AL, first strand: chain 'N' and resid 328 through 331 removed outlier: 3.685A pdb=" N LYS N 328 " --> pdb=" O LEU N 340 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N VAL N 337 " --> pdb=" O THR N 349 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR N 349 " --> pdb=" O VAL N 337 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'N' and resid 362 through 365 removed outlier: 6.063A pdb=" N GLY N 364 " --> pdb=" O VAL N 375 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N VAL N 375 " --> pdb=" O GLY N 364 " (cutoff:3.500A) 857 hydrogen bonds defined for protein. 2415 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 12.99 Time building geometry restraints manager: 15.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.37: 13606 1.37 - 1.56: 23285 1.56 - 1.76: 74 1.76 - 1.95: 378 1.95 - 2.14: 12 Bond restraints: 37355 Sorted by residual: bond pdb=" C PRO I 29 " pdb=" O PRO I 29 " ideal model delta sigma weight residual 1.235 1.184 0.051 7.90e-03 1.60e+04 4.12e+01 bond pdb=" CA GLN B 692 " pdb=" C GLN B 692 " ideal model delta sigma weight residual 1.523 1.445 0.078 1.41e-02 5.03e+03 3.04e+01 bond pdb=" N LEU M 45 " pdb=" CA LEU M 45 " ideal model delta sigma weight residual 1.458 1.492 -0.034 6.30e-03 2.52e+04 2.90e+01 bond pdb=" CA TYR B 357 " pdb=" C TYR B 357 " ideal model delta sigma weight residual 1.523 1.447 0.076 1.56e-02 4.11e+03 2.40e+01 bond pdb=" S1 SF4 P 401 " pdb="FE4 SF4 P 401 " ideal model delta sigma weight residual 2.280 2.134 0.146 3.00e-02 1.11e+03 2.38e+01 ... (remaining 37350 not shown) Histogram of bond angle deviations from ideal: 89.46 - 98.59: 35 98.59 - 107.73: 2350 107.73 - 116.87: 24204 116.87 - 126.01: 23389 126.01 - 135.15: 581 Bond angle restraints: 50559 Sorted by residual: angle pdb="FE3 SF4 P 401 " pdb=" S1 SF4 P 401 " pdb="FE4 SF4 P 401 " ideal model delta sigma weight residual 73.70 90.51 -16.81 1.50e+00 4.44e-01 1.26e+02 angle pdb="FE3 SF4 P 401 " pdb=" S2 SF4 P 401 " pdb="FE4 SF4 P 401 " ideal model delta sigma weight residual 73.70 90.51 -16.81 1.50e+00 4.44e-01 1.26e+02 angle pdb="FE2 SF4 P 401 " pdb=" S3 SF4 P 401 " pdb="FE4 SF4 P 401 " ideal model delta sigma weight residual 73.70 90.48 -16.78 1.50e+00 4.44e-01 1.25e+02 angle pdb="FE2 SF4 P 401 " pdb=" S1 SF4 P 401 " pdb="FE4 SF4 P 401 " ideal model delta sigma weight residual 73.70 90.48 -16.78 1.50e+00 4.44e-01 1.25e+02 angle pdb=" N ARG A 59 " pdb=" CA ARG A 59 " pdb=" C ARG A 59 " ideal model delta sigma weight residual 113.38 99.66 13.72 1.23e+00 6.61e-01 1.24e+02 ... (remaining 50554 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.71: 22037 35.71 - 71.42: 767 71.42 - 107.13: 31 107.13 - 142.84: 1 142.84 - 178.55: 1 Dihedral angle restraints: 22837 sinusoidal: 9723 harmonic: 13114 Sorted by residual: dihedral pdb=" C LEU B 809 " pdb=" N LEU B 809 " pdb=" CA LEU B 809 " pdb=" CB LEU B 809 " ideal model delta harmonic sigma weight residual -122.60 -145.73 23.13 0 2.50e+00 1.60e-01 8.56e+01 dihedral pdb=" N LEU B 809 " pdb=" C LEU B 809 " pdb=" CA LEU B 809 " pdb=" CB LEU B 809 " ideal model delta harmonic sigma weight residual 122.80 145.47 -22.67 0 2.50e+00 1.60e-01 8.22e+01 dihedral pdb=" C ILE M 77 " pdb=" N ILE M 77 " pdb=" CA ILE M 77 " pdb=" CB ILE M 77 " ideal model delta harmonic sigma weight residual -122.00 -141.38 19.38 0 2.50e+00 1.60e-01 6.01e+01 ... (remaining 22834 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.195: 5467 0.195 - 0.389: 220 0.389 - 0.584: 20 0.584 - 0.778: 1 0.778 - 0.973: 5 Chirality restraints: 5713 Sorted by residual: chirality pdb=" CA LEU B 809 " pdb=" N LEU B 809 " pdb=" C LEU B 809 " pdb=" CB LEU B 809 " both_signs ideal model delta sigma weight residual False 2.51 1.54 0.97 2.00e-01 2.50e+01 2.37e+01 chirality pdb="FE4 SF4 P 401 " pdb=" S1 SF4 P 401 " pdb=" S2 SF4 P 401 " pdb=" S3 SF4 P 401 " both_signs ideal model delta sigma weight residual False 10.55 9.72 0.83 2.00e-01 2.50e+01 1.73e+01 chirality pdb="FE1 SF4 P 401 " pdb=" S2 SF4 P 401 " pdb=" S3 SF4 P 401 " pdb=" S4 SF4 P 401 " both_signs ideal model delta sigma weight residual False -10.55 -9.73 -0.83 2.00e-01 2.50e+01 1.71e+01 ... (remaining 5710 not shown) Planarity restraints: 6357 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU C 162 " -0.024 2.00e-02 2.50e+03 4.81e-02 2.32e+01 pdb=" C LEU C 162 " 0.083 2.00e-02 2.50e+03 pdb=" O LEU C 162 " -0.031 2.00e-02 2.50e+03 pdb=" N TYR C 163 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A1111 " 0.023 2.00e-02 2.50e+03 4.71e-02 2.22e+01 pdb=" C GLY A1111 " -0.081 2.00e-02 2.50e+03 pdb=" O GLY A1111 " 0.030 2.00e-02 2.50e+03 pdb=" N GLU A1112 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 617 " -0.022 2.00e-02 2.50e+03 4.61e-02 2.13e+01 pdb=" C GLY B 617 " 0.080 2.00e-02 2.50e+03 pdb=" O GLY B 617 " -0.031 2.00e-02 2.50e+03 pdb=" N TYR B 618 " -0.027 2.00e-02 2.50e+03 ... (remaining 6354 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 1035 2.64 - 3.20: 33566 3.20 - 3.77: 59089 3.77 - 4.33: 79666 4.33 - 4.90: 127672 Nonbonded interactions: 301028 Sorted by model distance: nonbonded pdb=" N ASP C 183 " pdb=" OD1 ASP C 183 " model vdw 2.073 2.520 nonbonded pdb=" O ALA A 161 " pdb="ZN ZN A1903 " model vdw 2.102 2.230 nonbonded pdb=" O THR M 107 " pdb=" OG1 THR M 107 " model vdw 2.132 2.440 nonbonded pdb=" CD2 LEU N 357 " pdb=" NE2 GLN N 358 " model vdw 2.145 3.540 nonbonded pdb=" OD1 ASP A 499 " pdb="MG MG A1901 " model vdw 2.156 2.170 ... (remaining 301023 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 9.010 Check model and map are aligned: 0.600 Set scattering table: 0.370 Process input model: 107.600 Find NCS groups from input model: 0.980 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 123.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6868 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 : 0.012 0.146 37355 Z= 0.794 Angle : 1.420 16.812 50559 Z= 0.905 Chirality : 0.091 0.973 5713 Planarity : 0.008 0.080 6357 Dihedral : 17.067 178.552 14351 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 20.60 Ramachandran Plot: Outliers : 0.66 % Allowed : 9.85 % Favored : 89.49 % Rotamer: Outliers : 4.73 % Allowed : 13.33 % Favored : 81.94 % Cbeta Deviations : 0.73 % Peptide Plane: Cis-proline : 0.00 % 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: -4.76 (0.10), residues: 4426 helix: -3.86 (0.08), residues: 1495 sheet: -2.92 (0.20), residues: 506 loop : -2.76 (0.11), residues: 2425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP P 217 HIS 0.013 0.002 HIS A 82 PHE 0.037 0.003 PHE B 662 TYR 0.043 0.003 TYR M 114 ARG 0.013 0.001 ARG C 78 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8852 Ramachandran restraints generated. 4426 Oldfield, 0 Emsley, 4426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8852 Ramachandran restraints generated. 4426 Oldfield, 0 Emsley, 4426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1205 residues out of total 3987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 1017 time to evaluate : 4.141 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: A 97 TYR cc_start: 0.7564 (m-80) cc_final: 0.6979 (m-80) REVERT: A 429 LYS cc_start: 0.8470 (mmtt) cc_final: 0.8209 (mmtm) REVERT: A 440 MET cc_start: 0.7691 (mtt) cc_final: 0.7324 (mtt) REVERT: A 514 GLU cc_start: 0.7437 (mt-10) cc_final: 0.7215 (mt-10) REVERT: A 908 ASP cc_start: 0.8093 (m-30) cc_final: 0.7878 (m-30) REVERT: A 1115 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7483 (mp0) REVERT: A 1255 GLU cc_start: 0.7902 (tm-30) cc_final: 0.7639 (tm-30) REVERT: A 1321 PHE cc_start: 0.8889 (t80) cc_final: 0.8688 (t80) REVERT: B 190 ILE cc_start: 0.7856 (tp) cc_final: 0.7606 (pt) REVERT: B 236 ILE cc_start: 0.8303 (pt) cc_final: 0.8091 (mm) REVERT: B 243 MET cc_start: 0.7476 (tpp) cc_final: 0.7124 (mmp) REVERT: B 354 ARG cc_start: 0.6687 (ptm160) cc_final: 0.5866 (ptm160) REVERT: B 520 VAL cc_start: 0.7812 (m) cc_final: 0.7540 (m) REVERT: B 527 CYS cc_start: 0.6999 (m) cc_final: 0.6790 (m) REVERT: C 275 VAL cc_start: 0.6910 (OUTLIER) cc_final: 0.6569 (p) REVERT: G 9 ASP cc_start: 0.6870 (t0) cc_final: 0.6652 (t0) REVERT: G 45 CYS cc_start: 0.7508 (m) cc_final: 0.6871 (m) REVERT: G 129 TRP cc_start: 0.6468 (m-10) cc_final: 0.6219 (m100) REVERT: P 203 MET cc_start: 0.7935 (mpp) cc_final: 0.7473 (mmm) REVERT: E 128 GLU cc_start: 0.7197 (mt-10) cc_final: 0.6959 (mm-30) REVERT: F 80 MET cc_start: 0.7769 (mmt) cc_final: 0.7504 (mmt) REVERT: H 56 PHE cc_start: 0.8341 (p90) cc_final: 0.7899 (p90) REVERT: O 50 VAL cc_start: 0.9067 (t) cc_final: 0.8823 (p) REVERT: O 385 MET cc_start: 0.5563 (mmm) cc_final: 0.4667 (tpt) REVERT: O 398 MET cc_start: 0.7602 (mmp) cc_final: 0.7134 (mmt) REVERT: O 448 GLU cc_start: 0.7968 (tp30) cc_final: 0.7760 (pp20) REVERT: O 461 LEU cc_start: 0.7679 (pp) cc_final: 0.7452 (mp) REVERT: D 43 ASN cc_start: 0.5377 (OUTLIER) cc_final: 0.4242 (m110) REVERT: M 193 TYR cc_start: 0.2353 (OUTLIER) cc_final: 0.1318 (m-80) outliers start: 188 outliers final: 59 residues processed: 1125 average time/residue: 0.5178 time to fit residues: 918.0304 Evaluate side-chains 660 residues out of total 3987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 597 time to evaluate : 4.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 PHE Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 1110 LEU Chi-restraints excluded: chain A residue 1115 GLU Chi-restraints excluded: chain A residue 1140 LEU Chi-restraints excluded: chain A residue 1167 VAL Chi-restraints excluded: chain A residue 1173 VAL Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 572 VAL Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain B residue 660 GLU Chi-restraints excluded: chain B residue 743 VAL Chi-restraints excluded: chain B residue 771 VAL Chi-restraints excluded: chain B residue 815 CYS Chi-restraints excluded: chain B residue 907 CYS Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 23 ASN Chi-restraints excluded: chain C residue 166 HIS Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 43 ILE Chi-restraints excluded: chain O residue 408 GLU Chi-restraints excluded: chain O residue 409 ILE Chi-restraints excluded: chain O residue 414 ASP Chi-restraints excluded: chain O residue 423 LEU Chi-restraints excluded: chain Q residue 27 LEU Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain Q residue 86 ARG Chi-restraints excluded: chain Q residue 87 TYR Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 18 GLN Chi-restraints excluded: chain D residue 43 ASN Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain M residue 42 ILE Chi-restraints excluded: chain M residue 109 SER Chi-restraints excluded: chain M residue 114 TYR Chi-restraints excluded: chain M residue 121 GLN Chi-restraints excluded: chain M residue 136 ARG Chi-restraints excluded: chain M residue 193 TYR Chi-restraints excluded: chain M residue 195 PHE Chi-restraints excluded: chain N residue 328 LYS Chi-restraints excluded: chain N residue 329 LEU Chi-restraints excluded: chain N residue 330 LEU Chi-restraints excluded: chain N residue 358 GLN Chi-restraints excluded: chain N residue 373 MET Chi-restraints excluded: chain N residue 375 VAL Chi-restraints excluded: chain N residue 379 VAL Chi-restraints excluded: chain I residue 2 LEU Chi-restraints excluded: chain I residue 27 THR Chi-restraints excluded: chain I residue 36 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 377 optimal weight: 0.5980 chunk 338 optimal weight: 3.9990 chunk 187 optimal weight: 2.9990 chunk 115 optimal weight: 4.9990 chunk 228 optimal weight: 0.9980 chunk 181 optimal weight: 0.8980 chunk 350 optimal weight: 2.9990 chunk 135 optimal weight: 9.9990 chunk 213 optimal weight: 0.9980 chunk 260 optimal weight: 0.9980 chunk 405 optimal weight: 5.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 HIS A 94 HIS A 374 ASN A 422 GLN A 511 GLN A 543 GLN ** A 662 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 693 ASN A 738 GLN A 943 ASN A1364 HIS B 129 ASN B 227 HIS B 413 ASN B 417 ASN B 434 GLN B 472 GLN B 608 ASN B 639 ASN ** B 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 806 HIS B 825 GLN ** B 887 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1014 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1100 HIS C 42 GLN C 59 ASN C 127 GLN ** G 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 38 HIS ** K 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 85 GLN ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 274 ASN E 35 GLN ** E 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 14 GLN O 49 GLN O 113 ASN O 337 ASN O 379 GLN O 437 HIS ** O 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 457 ASN O 465 GLN O 507 ASN D 13 ASN D 26 GLN D 40 GLN D 43 ASN D 61 GLN D 88 ASN D 112 GLN ** M 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 66 ASN ** M 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 106 GLN M 125 HIS ** N 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 32 HIS Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6963 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.101 37355 Z= 0.250 Angle : 0.792 17.315 50559 Z= 0.402 Chirality : 0.047 0.305 5713 Planarity : 0.006 0.087 6357 Dihedral : 12.115 177.001 5418 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 16.49 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.65 % Favored : 91.05 % Rotamer: Outliers : 4.10 % Allowed : 19.32 % Favored : 76.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.86 (0.11), residues: 4426 helix: -2.47 (0.10), residues: 1555 sheet: -2.79 (0.20), residues: 487 loop : -2.59 (0.11), residues: 2384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP G 201 HIS 0.011 0.001 HIS A1364 PHE 0.025 0.002 PHE K 96 TYR 0.034 0.002 TYR D 47 ARG 0.010 0.001 ARG M 33 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8852 Ramachandran restraints generated. 4426 Oldfield, 0 Emsley, 4426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8852 Ramachandran restraints generated. 4426 Oldfield, 0 Emsley, 4426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 845 residues out of total 3987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 682 time to evaluate : 4.034 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: A 53 TYR cc_start: 0.5593 (t80) cc_final: 0.5234 (t80) REVERT: A 65 LYS cc_start: 0.8404 (tptp) cc_final: 0.8168 (tttt) REVERT: A 294 LYS cc_start: 0.8417 (tttt) cc_final: 0.8170 (ttmt) REVERT: A 429 LYS cc_start: 0.7940 (mmtt) cc_final: 0.7588 (mmtm) REVERT: A 440 MET cc_start: 0.7733 (mtt) cc_final: 0.7368 (mtt) REVERT: A 623 GLN cc_start: 0.8392 (OUTLIER) cc_final: 0.8176 (pp30) REVERT: A 881 ASP cc_start: 0.8796 (p0) cc_final: 0.8479 (p0) REVERT: A 1115 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7443 (mp0) REVERT: A 1178 ARG cc_start: 0.6893 (OUTLIER) cc_final: 0.6179 (tmt170) REVERT: A 1255 GLU cc_start: 0.7931 (tm-30) cc_final: 0.7687 (tm-30) REVERT: A 1317 MET cc_start: 0.7894 (tpt) cc_final: 0.7657 (tpt) REVERT: B 72 MET cc_start: 0.7430 (mmm) cc_final: 0.7189 (mmm) REVERT: B 73 TRP cc_start: 0.6043 (p-90) cc_final: 0.4251 (t-100) REVERT: B 236 ILE cc_start: 0.8106 (pt) cc_final: 0.7864 (pt) REVERT: B 243 MET cc_start: 0.7433 (tpp) cc_final: 0.7105 (mmp) REVERT: B 254 MET cc_start: 0.8202 (mmt) cc_final: 0.7750 (mmt) REVERT: B 409 ASP cc_start: 0.7931 (t0) cc_final: 0.7288 (t0) REVERT: B 530 GLU cc_start: 0.8068 (pp20) cc_final: 0.7836 (pp20) REVERT: B 580 ASP cc_start: 0.7351 (t70) cc_final: 0.7054 (t0) REVERT: B 870 MET cc_start: 0.7146 (tmm) cc_final: 0.6752 (tmm) REVERT: G 34 LEU cc_start: 0.8792 (mt) cc_final: 0.8199 (tp) REVERT: G 45 CYS cc_start: 0.7206 (m) cc_final: 0.6783 (m) REVERT: K 53 ASN cc_start: 0.8381 (t0) cc_final: 0.8180 (t0) REVERT: L 27 GLU cc_start: 0.6738 (tp30) cc_final: 0.6418 (tp30) REVERT: L 28 ILE cc_start: 0.8622 (OUTLIER) cc_final: 0.8323 (pt) REVERT: L 34 ILE cc_start: 0.8465 (OUTLIER) cc_final: 0.8033 (mp) REVERT: P 205 GLN cc_start: 0.4712 (OUTLIER) cc_final: 0.3488 (pt0) REVERT: P 266 HIS cc_start: 0.7800 (m-70) cc_final: 0.7355 (p90) REVERT: E 121 MET cc_start: 0.7590 (tmm) cc_final: 0.6748 (tmm) REVERT: E 125 TYR cc_start: 0.6564 (m-80) cc_final: 0.6030 (m-10) REVERT: H 87 GLN cc_start: 0.7705 (mm-40) cc_final: 0.7369 (mp10) REVERT: O 385 MET cc_start: 0.5812 (mmm) cc_final: 0.4750 (tpp) REVERT: O 398 MET cc_start: 0.7850 (mmp) cc_final: 0.7509 (mmt) REVERT: O 448 GLU cc_start: 0.7760 (tp30) cc_final: 0.7508 (pp20) REVERT: O 498 GLN cc_start: 0.7951 (tp40) cc_final: 0.7591 (tp40) REVERT: Q 68 MET cc_start: 0.6563 (ppp) cc_final: 0.6327 (ppp) REVERT: Q 71 MET cc_start: 0.6307 (mmp) cc_final: 0.5991 (mmt) REVERT: I 37 LYS cc_start: 0.6344 (OUTLIER) cc_final: 0.6047 (tptp) outliers start: 163 outliers final: 89 residues processed: 779 average time/residue: 0.4769 time to fit residues: 609.4325 Evaluate side-chains 631 residues out of total 3987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 535 time to evaluate : 4.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 156 CYS Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 623 GLN Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 799 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1110 LEU Chi-restraints excluded: chain A residue 1115 GLU Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1144 VAL Chi-restraints excluded: chain A residue 1173 VAL Chi-restraints excluded: chain A residue 1176 THR Chi-restraints excluded: chain A residue 1178 ARG Chi-restraints excluded: chain A residue 1185 MET Chi-restraints excluded: chain B residue 27 TRP Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 248 ASP Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 572 VAL Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 601 LYS Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain B residue 707 THR Chi-restraints excluded: chain B residue 708 LEU Chi-restraints excluded: chain B residue 771 VAL Chi-restraints excluded: chain B residue 869 VAL Chi-restraints excluded: chain B residue 919 CYS Chi-restraints excluded: chain B residue 971 ASP Chi-restraints excluded: chain B residue 989 VAL Chi-restraints excluded: chain B residue 1015 MET Chi-restraints excluded: chain B residue 1073 ASP Chi-restraints excluded: chain B residue 1077 VAL Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 23 ASN Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 127 GLN Chi-restraints excluded: chain C residue 166 HIS Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 183 ASP Chi-restraints excluded: chain C residue 212 MET Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain K residue 111 LEU Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 43 ILE Chi-restraints excluded: chain P residue 201 ASN Chi-restraints excluded: chain P residue 205 GLN Chi-restraints excluded: chain P residue 206 ARG Chi-restraints excluded: chain P residue 273 VAL Chi-restraints excluded: chain P residue 294 ASP Chi-restraints excluded: chain P residue 307 CYS Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain O residue 13 LEU Chi-restraints excluded: chain O residue 24 ILE Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 235 TRP Chi-restraints excluded: chain O residue 313 THR Chi-restraints excluded: chain O residue 408 GLU Chi-restraints excluded: chain O residue 409 ILE Chi-restraints excluded: chain O residue 414 ASP Chi-restraints excluded: chain Q residue 26 LYS Chi-restraints excluded: chain Q residue 27 LEU Chi-restraints excluded: chain Q residue 70 ARG Chi-restraints excluded: chain Q residue 87 TYR Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain M residue 42 ILE Chi-restraints excluded: chain M residue 114 TYR Chi-restraints excluded: chain M residue 195 PHE Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain N residue 330 LEU Chi-restraints excluded: chain N residue 361 VAL Chi-restraints excluded: chain N residue 375 VAL Chi-restraints excluded: chain I residue 27 THR Chi-restraints excluded: chain I residue 36 ARG Chi-restraints excluded: chain I residue 37 LYS Chi-restraints excluded: chain I residue 39 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 225 optimal weight: 1.9990 chunk 125 optimal weight: 8.9990 chunk 337 optimal weight: 10.0000 chunk 276 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 406 optimal weight: 8.9990 chunk 439 optimal weight: 10.0000 chunk 362 optimal weight: 5.9990 chunk 403 optimal weight: 4.9990 chunk 138 optimal weight: 4.9990 chunk 326 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 158 HIS A 662 ASN A 802 GLN A 872 GLN B 92 ASN ** B 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 GLN B 413 ASN B 472 GLN B 542 ASN ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 648 HIS B 692 GLN B 703 ASN B 850 GLN B 887 GLN B1093 HIS ** C 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 38 HIS ** K 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 16 HIS O 244 GLN ** M 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 197 GLN ** N 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 21 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.4441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.144 37355 Z= 0.395 Angle : 0.805 13.682 50559 Z= 0.415 Chirality : 0.049 0.285 5713 Planarity : 0.006 0.090 6357 Dihedral : 11.521 177.792 5356 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 16.56 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.60 % Favored : 90.15 % Rotamer: Outliers : 5.71 % Allowed : 21.00 % Favored : 73.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.14 (0.11), residues: 4426 helix: -1.45 (0.12), residues: 1512 sheet: -2.68 (0.21), residues: 502 loop : -2.40 (0.12), residues: 2412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP G 201 HIS 0.008 0.001 HIS B 552 PHE 0.025 0.002 PHE B 537 TYR 0.032 0.002 TYR D 14 ARG 0.009 0.001 ARG O 90 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8852 Ramachandran restraints generated. 4426 Oldfield, 0 Emsley, 4426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8852 Ramachandran restraints generated. 4426 Oldfield, 0 Emsley, 4426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 797 residues out of total 3987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 227 poor density : 570 time to evaluate : 4.347 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: A 53 TYR cc_start: 0.6464 (t80) cc_final: 0.5892 (t80) REVERT: A 128 TYR cc_start: 0.8451 (t80) cc_final: 0.8145 (t80) REVERT: A 305 MET cc_start: 0.7736 (ppp) cc_final: 0.7256 (ppp) REVERT: A 440 MET cc_start: 0.8352 (mtt) cc_final: 0.7981 (mtt) REVERT: A 461 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8686 (pp) REVERT: A 1115 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7661 (mp0) REVERT: A 1178 ARG cc_start: 0.6794 (OUTLIER) cc_final: 0.6172 (tmt170) REVERT: A 1198 LYS cc_start: 0.8680 (ptpt) cc_final: 0.8319 (mtmt) REVERT: A 1255 GLU cc_start: 0.8488 (tm-30) cc_final: 0.8171 (tm-30) REVERT: A 1317 MET cc_start: 0.8212 (tpt) cc_final: 0.7939 (tpt) REVERT: B 73 TRP cc_start: 0.6521 (p-90) cc_final: 0.4098 (t-100) REVERT: B 243 MET cc_start: 0.7821 (tpp) cc_final: 0.7495 (mmp) REVERT: B 530 GLU cc_start: 0.8181 (pp20) cc_final: 0.7831 (pp20) REVERT: B 580 ASP cc_start: 0.7717 (t70) cc_final: 0.7454 (t70) REVERT: B 794 MET cc_start: 0.7976 (tpp) cc_final: 0.7680 (mpp) REVERT: B 801 LYS cc_start: 0.8723 (mmmt) cc_final: 0.8420 (mmmt) REVERT: B 1003 TYR cc_start: 0.9015 (OUTLIER) cc_final: 0.8560 (t80) REVERT: B 1004 PHE cc_start: 0.8891 (OUTLIER) cc_final: 0.8631 (t80) REVERT: C 36 TYR cc_start: 0.8383 (m-10) cc_final: 0.8116 (m-80) REVERT: L 25 GLU cc_start: 0.7904 (mt-10) cc_final: 0.7699 (mt-10) REVERT: L 28 ILE cc_start: 0.8597 (pt) cc_final: 0.8340 (pt) REVERT: L 29 LYS cc_start: 0.7363 (ptpp) cc_final: 0.7033 (ptpp) REVERT: L 34 ILE cc_start: 0.8808 (OUTLIER) cc_final: 0.8370 (mp) REVERT: P 205 GLN cc_start: 0.5257 (OUTLIER) cc_final: 0.3908 (pt0) REVERT: P 266 HIS cc_start: 0.7846 (m-70) cc_final: 0.7402 (p90) REVERT: E 90 TYR cc_start: 0.7852 (OUTLIER) cc_final: 0.6920 (p90) REVERT: E 121 MET cc_start: 0.7661 (tmm) cc_final: 0.7157 (tmm) REVERT: E 125 TYR cc_start: 0.6934 (m-80) cc_final: 0.6643 (m-10) REVERT: E 131 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.9009 (tp) REVERT: F 91 LEU cc_start: 0.9183 (tp) cc_final: 0.8831 (mp) REVERT: O 139 MET cc_start: 0.3493 (ttp) cc_final: 0.3141 (tmm) REVERT: O 158 GLN cc_start: 0.5961 (pm20) cc_final: 0.5479 (pm20) REVERT: O 236 GLN cc_start: 0.7600 (pt0) cc_final: 0.7267 (pm20) REVERT: O 385 MET cc_start: 0.6088 (mmm) cc_final: 0.5129 (tpt) REVERT: O 398 MET cc_start: 0.8177 (mmp) cc_final: 0.7729 (mmt) REVERT: O 448 GLU cc_start: 0.7999 (tp30) cc_final: 0.7642 (pp20) REVERT: O 526 TYR cc_start: 0.7825 (t80) cc_final: 0.7607 (t80) REVERT: Q 68 MET cc_start: 0.6767 (ppp) cc_final: 0.5321 (ppp) REVERT: M 189 ARG cc_start: 0.5094 (tmt170) cc_final: 0.4858 (tmt170) REVERT: I 13 ILE cc_start: 0.7288 (OUTLIER) cc_final: 0.7003 (pt) outliers start: 227 outliers final: 136 residues processed: 730 average time/residue: 0.4704 time to fit residues: 563.3116 Evaluate side-chains 653 residues out of total 3987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 507 time to evaluate : 4.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ASP Chi-restraints excluded: chain A residue 22 MET Chi-restraints excluded: chain A residue 46 ASN Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 156 CYS Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 493 CYS Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 623 GLN Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 843 THR Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain A residue 1115 GLU Chi-restraints excluded: chain A residue 1119 GLU Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1144 VAL Chi-restraints excluded: chain A residue 1164 ASP Chi-restraints excluded: chain A residue 1173 VAL Chi-restraints excluded: chain A residue 1176 THR Chi-restraints excluded: chain A residue 1178 ARG Chi-restraints excluded: chain A residue 1185 MET Chi-restraints excluded: chain A residue 1200 VAL Chi-restraints excluded: chain A residue 1227 VAL Chi-restraints excluded: chain A residue 1246 THR Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1304 THR Chi-restraints excluded: chain A residue 1324 THR Chi-restraints excluded: chain A residue 1338 ASP Chi-restraints excluded: chain A residue 1349 MET Chi-restraints excluded: chain B residue 27 TRP Chi-restraints excluded: chain B residue 42 GLN Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 472 GLN Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 572 VAL Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 707 THR Chi-restraints excluded: chain B residue 708 LEU Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 771 VAL Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 863 ASP Chi-restraints excluded: chain B residue 869 VAL Chi-restraints excluded: chain B residue 898 SER Chi-restraints excluded: chain B residue 919 CYS Chi-restraints excluded: chain B residue 971 ASP Chi-restraints excluded: chain B residue 989 VAL Chi-restraints excluded: chain B residue 1003 TYR Chi-restraints excluded: chain B residue 1004 PHE Chi-restraints excluded: chain B residue 1015 MET Chi-restraints excluded: chain B residue 1045 LEU Chi-restraints excluded: chain B residue 1073 ASP Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 23 ASN Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 166 HIS Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 183 ASP Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 306 TYR Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 36 ASN Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 199 SER Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 111 LEU Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 43 ILE Chi-restraints excluded: chain P residue 201 ASN Chi-restraints excluded: chain P residue 205 GLN Chi-restraints excluded: chain P residue 206 ARG Chi-restraints excluded: chain P residue 277 ILE Chi-restraints excluded: chain P residue 294 ASP Chi-restraints excluded: chain P residue 303 SER Chi-restraints excluded: chain P residue 307 CYS Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 90 TYR Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain O residue 13 LEU Chi-restraints excluded: chain O residue 24 ILE Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 154 THR Chi-restraints excluded: chain O residue 168 ASN Chi-restraints excluded: chain O residue 235 TRP Chi-restraints excluded: chain O residue 313 THR Chi-restraints excluded: chain O residue 408 GLU Chi-restraints excluded: chain O residue 414 ASP Chi-restraints excluded: chain O residue 506 VAL Chi-restraints excluded: chain Q residue 26 LYS Chi-restraints excluded: chain Q residue 60 LEU Chi-restraints excluded: chain Q residue 84 ILE Chi-restraints excluded: chain Q residue 87 TYR Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 98 GLN Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 42 ILE Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain M residue 114 TYR Chi-restraints excluded: chain M residue 123 GLU Chi-restraints excluded: chain M residue 195 PHE Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain N residue 331 ILE Chi-restraints excluded: chain N residue 361 VAL Chi-restraints excluded: chain N residue 362 SER Chi-restraints excluded: chain N residue 379 VAL Chi-restraints excluded: chain I residue 13 ILE Chi-restraints excluded: chain I residue 18 GLN Chi-restraints excluded: chain I residue 27 THR Chi-restraints excluded: chain I residue 36 ARG Chi-restraints excluded: chain I residue 39 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 401 optimal weight: 9.9990 chunk 305 optimal weight: 7.9990 chunk 211 optimal weight: 0.7980 chunk 45 optimal weight: 5.9990 chunk 194 optimal weight: 0.7980 chunk 273 optimal weight: 0.9980 chunk 408 optimal weight: 8.9990 chunk 432 optimal weight: 9.9990 chunk 213 optimal weight: 1.9990 chunk 386 optimal weight: 0.8980 chunk 116 optimal weight: 5.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 HIS ** A 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 289 ASN ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 26 ASN ** P 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 451 GLN ** D 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 85 GLN ** M 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 44 HIS ** M 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.4852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.133 37355 Z= 0.217 Angle : 0.681 12.213 50559 Z= 0.343 Chirality : 0.044 0.228 5713 Planarity : 0.005 0.080 6357 Dihedral : 11.243 177.413 5346 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.27 % Favored : 91.50 % Rotamer: Outliers : 4.70 % Allowed : 22.64 % Favored : 72.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.70 (0.12), residues: 4426 helix: -0.92 (0.13), residues: 1525 sheet: -2.62 (0.20), residues: 523 loop : -2.21 (0.12), residues: 2378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 40 HIS 0.008 0.001 HIS C 194 PHE 0.034 0.001 PHE B 278 TYR 0.051 0.001 TYR D 47 ARG 0.014 0.000 ARG C 125 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8852 Ramachandran restraints generated. 4426 Oldfield, 0 Emsley, 4426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8852 Ramachandran restraints generated. 4426 Oldfield, 0 Emsley, 4426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 754 residues out of total 3987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 567 time to evaluate : 4.494 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: A 53 TYR cc_start: 0.6350 (t80) cc_final: 0.5671 (t80) REVERT: A 126 LEU cc_start: 0.8747 (mp) cc_final: 0.8291 (tt) REVERT: A 128 TYR cc_start: 0.8413 (t80) cc_final: 0.8196 (t80) REVERT: A 440 MET cc_start: 0.8360 (mtt) cc_final: 0.7948 (mtt) REVERT: A 461 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8657 (pp) REVERT: A 1119 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7745 (pm20) REVERT: A 1178 ARG cc_start: 0.6914 (OUTLIER) cc_final: 0.6265 (tmt170) REVERT: A 1198 LYS cc_start: 0.8614 (ptpt) cc_final: 0.8145 (mtmt) REVERT: A 1255 GLU cc_start: 0.8429 (tm-30) cc_final: 0.8129 (tm-30) REVERT: A 1261 GLU cc_start: 0.7321 (mm-30) cc_final: 0.7060 (mm-30) REVERT: A 1317 MET cc_start: 0.8155 (tpt) cc_final: 0.7883 (tpt) REVERT: B 73 TRP cc_start: 0.6657 (p-90) cc_final: 0.4283 (t-100) REVERT: B 243 MET cc_start: 0.7658 (tpp) cc_final: 0.7398 (mmp) REVERT: B 530 GLU cc_start: 0.8170 (pp20) cc_final: 0.7475 (pp20) REVERT: B 580 ASP cc_start: 0.7756 (t70) cc_final: 0.7504 (t0) REVERT: B 794 MET cc_start: 0.7921 (tpp) cc_final: 0.7657 (mpp) REVERT: B 1003 TYR cc_start: 0.8974 (OUTLIER) cc_final: 0.8476 (t80) REVERT: B 1004 PHE cc_start: 0.8883 (OUTLIER) cc_final: 0.8623 (t80) REVERT: B 1042 ASP cc_start: 0.8356 (t0) cc_final: 0.8152 (t0) REVERT: B 1112 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8467 (tp) REVERT: C 178 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8235 (tp) REVERT: G 131 TYR cc_start: 0.3949 (m-10) cc_final: 0.3595 (m-80) REVERT: G 201 TRP cc_start: 0.6189 (p-90) cc_final: 0.5235 (p-90) REVERT: K 59 ILE cc_start: 0.8557 (OUTLIER) cc_final: 0.8349 (tt) REVERT: K 60 MET cc_start: 0.8312 (tpp) cc_final: 0.8062 (mmp) REVERT: L 28 ILE cc_start: 0.8509 (pt) cc_final: 0.8092 (pt) REVERT: L 34 ILE cc_start: 0.8672 (OUTLIER) cc_final: 0.8348 (mp) REVERT: P 205 GLN cc_start: 0.5013 (OUTLIER) cc_final: 0.3446 (pt0) REVERT: P 266 HIS cc_start: 0.7785 (m-70) cc_final: 0.7365 (p-80) REVERT: P 309 TYR cc_start: 0.5510 (m-80) cc_final: 0.5217 (m-10) REVERT: E 121 MET cc_start: 0.7537 (tmm) cc_final: 0.7179 (tmm) REVERT: E 125 TYR cc_start: 0.6890 (m-80) cc_final: 0.6677 (m-10) REVERT: E 131 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8925 (tp) REVERT: F 91 LEU cc_start: 0.9102 (tp) cc_final: 0.8794 (mp) REVERT: H 8 ASP cc_start: 0.6642 (OUTLIER) cc_final: 0.6411 (m-30) REVERT: O 85 MET cc_start: 0.7720 (mpp) cc_final: 0.7453 (mpp) REVERT: O 106 ILE cc_start: 0.7747 (mt) cc_final: 0.7430 (mm) REVERT: O 236 GLN cc_start: 0.7576 (pt0) cc_final: 0.7375 (pm20) REVERT: O 385 MET cc_start: 0.5981 (mmm) cc_final: 0.4991 (tpp) REVERT: O 398 MET cc_start: 0.8093 (mmp) cc_final: 0.7593 (mmt) REVERT: O 448 GLU cc_start: 0.7794 (tp30) cc_final: 0.7479 (pp20) REVERT: Q 68 MET cc_start: 0.7110 (ppp) cc_final: 0.5530 (ppp) REVERT: Q 81 ARG cc_start: 0.4969 (tmm-80) cc_final: 0.4268 (tmm-80) REVERT: D 74 LYS cc_start: 0.0846 (mmtt) cc_final: -0.0157 (mmtt) REVERT: M 189 ARG cc_start: 0.5115 (tmt170) cc_final: 0.4853 (tmt170) REVERT: I 13 ILE cc_start: 0.7310 (OUTLIER) cc_final: 0.7082 (pt) outliers start: 187 outliers final: 122 residues processed: 698 average time/residue: 0.4815 time to fit residues: 556.9268 Evaluate side-chains 655 residues out of total 3987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 520 time to evaluate : 4.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 MET Chi-restraints excluded: chain A residue 46 ASN Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 156 CYS Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 385 HIS Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 623 GLN Chi-restraints excluded: chain A residue 834 VAL Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1007 THR Chi-restraints excluded: chain A residue 1119 GLU Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1173 VAL Chi-restraints excluded: chain A residue 1176 THR Chi-restraints excluded: chain A residue 1178 ARG Chi-restraints excluded: chain A residue 1200 VAL Chi-restraints excluded: chain A residue 1201 VAL Chi-restraints excluded: chain A residue 1246 THR Chi-restraints excluded: chain A residue 1349 MET Chi-restraints excluded: chain B residue 27 TRP Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 42 GLN Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 572 VAL Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 707 THR Chi-restraints excluded: chain B residue 708 LEU Chi-restraints excluded: chain B residue 771 VAL Chi-restraints excluded: chain B residue 869 VAL Chi-restraints excluded: chain B residue 898 SER Chi-restraints excluded: chain B residue 971 ASP Chi-restraints excluded: chain B residue 1003 TYR Chi-restraints excluded: chain B residue 1004 PHE Chi-restraints excluded: chain B residue 1073 ASP Chi-restraints excluded: chain B residue 1077 VAL Chi-restraints excluded: chain B residue 1112 LEU Chi-restraints excluded: chain B residue 1115 GLN Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 23 ASN Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 166 HIS Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 306 TYR Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 154 ASP Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 111 LEU Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 43 ILE Chi-restraints excluded: chain P residue 201 ASN Chi-restraints excluded: chain P residue 205 GLN Chi-restraints excluded: chain P residue 273 VAL Chi-restraints excluded: chain P residue 277 ILE Chi-restraints excluded: chain P residue 294 ASP Chi-restraints excluded: chain P residue 307 CYS Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain H residue 8 ASP Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain J residue 57 GLU Chi-restraints excluded: chain O residue 13 LEU Chi-restraints excluded: chain O residue 24 ILE Chi-restraints excluded: chain O residue 28 LEU Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 154 THR Chi-restraints excluded: chain O residue 168 ASN Chi-restraints excluded: chain O residue 235 TRP Chi-restraints excluded: chain O residue 313 THR Chi-restraints excluded: chain O residue 414 ASP Chi-restraints excluded: chain Q residue 26 LYS Chi-restraints excluded: chain Q residue 41 THR Chi-restraints excluded: chain Q residue 60 LEU Chi-restraints excluded: chain Q residue 87 TYR Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 32 LYS Chi-restraints excluded: chain D residue 89 HIS Chi-restraints excluded: chain D residue 98 GLN Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain M residue 42 ILE Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain M residue 114 TYR Chi-restraints excluded: chain M residue 118 LEU Chi-restraints excluded: chain M residue 123 GLU Chi-restraints excluded: chain M residue 136 ARG Chi-restraints excluded: chain M residue 195 PHE Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain N residue 331 ILE Chi-restraints excluded: chain N residue 361 VAL Chi-restraints excluded: chain N residue 362 SER Chi-restraints excluded: chain N residue 379 VAL Chi-restraints excluded: chain I residue 13 ILE Chi-restraints excluded: chain I residue 18 GLN Chi-restraints excluded: chain I residue 27 THR Chi-restraints excluded: chain I residue 36 ARG Chi-restraints excluded: chain I residue 39 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 359 optimal weight: 0.7980 chunk 245 optimal weight: 0.0050 chunk 6 optimal weight: 0.0670 chunk 321 optimal weight: 6.9990 chunk 178 optimal weight: 0.0870 chunk 368 optimal weight: 9.9990 chunk 298 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 220 optimal weight: 0.6980 chunk 387 optimal weight: 20.0000 chunk 109 optimal weight: 7.9990 overall best weight: 0.3310 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 HIS ** A 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1371 ASN B 472 GLN B 544 ASN B 979 HIS ** K 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 26 ASN ** P 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 286 GLN ** D 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 54 GLN ** M 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7229 moved from start: 0.5149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 37355 Z= 0.171 Angle : 0.651 11.140 50559 Z= 0.325 Chirality : 0.044 0.472 5713 Planarity : 0.004 0.077 6357 Dihedral : 10.909 177.763 5337 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.16 % Favored : 91.66 % Rotamer: Outliers : 4.12 % Allowed : 23.84 % Favored : 72.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.12), residues: 4426 helix: -0.52 (0.13), residues: 1525 sheet: -2.43 (0.21), residues: 513 loop : -2.11 (0.12), residues: 2388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP O 235 HIS 0.008 0.001 HIS M 207 PHE 0.023 0.001 PHE A 288 TYR 0.023 0.001 TYR D 47 ARG 0.009 0.000 ARG K 37 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8852 Ramachandran restraints generated. 4426 Oldfield, 0 Emsley, 4426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8852 Ramachandran restraints generated. 4426 Oldfield, 0 Emsley, 4426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 721 residues out of total 3987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 557 time to evaluate : 4.034 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: A 53 TYR cc_start: 0.6240 (t80) cc_final: 0.5556 (t80) REVERT: A 126 LEU cc_start: 0.8707 (mp) cc_final: 0.8235 (tt) REVERT: A 281 MET cc_start: 0.7967 (mmm) cc_final: 0.7736 (mmm) REVERT: A 440 MET cc_start: 0.8406 (mtt) cc_final: 0.8020 (mtt) REVERT: A 461 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8593 (pp) REVERT: A 1119 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7018 (pm20) REVERT: A 1159 ARG cc_start: 0.8555 (mtt180) cc_final: 0.8179 (tpt90) REVERT: A 1178 ARG cc_start: 0.6923 (OUTLIER) cc_final: 0.6265 (tmt170) REVERT: A 1198 LYS cc_start: 0.8584 (ptpt) cc_final: 0.8106 (mtmt) REVERT: A 1255 GLU cc_start: 0.8488 (tm-30) cc_final: 0.8165 (tm-30) REVERT: B 73 TRP cc_start: 0.6326 (p-90) cc_final: 0.4358 (t-100) REVERT: B 243 MET cc_start: 0.7614 (tpp) cc_final: 0.7339 (mmp) REVERT: B 530 GLU cc_start: 0.8112 (pp20) cc_final: 0.7510 (pp20) REVERT: B 588 ASP cc_start: 0.7919 (t0) cc_final: 0.7701 (t0) REVERT: B 1004 PHE cc_start: 0.8743 (OUTLIER) cc_final: 0.8465 (t80) REVERT: B 1045 LEU cc_start: 0.7046 (OUTLIER) cc_final: 0.6808 (pp) REVERT: B 1120 MET cc_start: 0.7406 (mtm) cc_final: 0.7147 (ptp) REVERT: C 68 ILE cc_start: 0.8931 (OUTLIER) cc_final: 0.8617 (pt) REVERT: G 34 LEU cc_start: 0.8620 (mt) cc_final: 0.8416 (tt) REVERT: G 131 TYR cc_start: 0.3764 (m-10) cc_final: 0.3535 (m-80) REVERT: G 184 TYR cc_start: 0.5574 (OUTLIER) cc_final: 0.4225 (m-80) REVERT: G 201 TRP cc_start: 0.6362 (p-90) cc_final: 0.5430 (p-90) REVERT: K 102 GLU cc_start: 0.8053 (mm-30) cc_final: 0.7652 (mt-10) REVERT: K 104 MET cc_start: 0.7767 (ttm) cc_final: 0.7542 (ttm) REVERT: P 205 GLN cc_start: 0.5084 (OUTLIER) cc_final: 0.3488 (pt0) REVERT: P 266 HIS cc_start: 0.7820 (m-70) cc_final: 0.7433 (p-80) REVERT: E 90 TYR cc_start: 0.7610 (p90) cc_final: 0.6769 (p90) REVERT: E 121 MET cc_start: 0.7468 (tmm) cc_final: 0.7182 (tmm) REVERT: E 125 TYR cc_start: 0.6974 (m-80) cc_final: 0.6713 (m-10) REVERT: E 131 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8880 (tp) REVERT: F 91 LEU cc_start: 0.9028 (tp) cc_final: 0.8707 (mp) REVERT: O 139 MET cc_start: 0.3109 (tmm) cc_final: 0.2886 (tmm) REVERT: O 385 MET cc_start: 0.6113 (mmm) cc_final: 0.4894 (tpp) REVERT: O 448 GLU cc_start: 0.7853 (tp30) cc_final: 0.7637 (pp20) REVERT: Q 68 MET cc_start: 0.7281 (ppp) cc_final: 0.6644 (ppp) REVERT: Q 79 GLU cc_start: 0.7691 (pm20) cc_final: 0.7475 (pm20) REVERT: Q 115 LYS cc_start: 0.3700 (mttt) cc_final: 0.2700 (mttp) REVERT: D 74 LYS cc_start: 0.0580 (mmtt) cc_final: -0.0150 (mmtt) REVERT: M 189 ARG cc_start: 0.4871 (tmt170) cc_final: 0.4641 (tmt170) outliers start: 164 outliers final: 104 residues processed: 669 average time/residue: 0.4675 time to fit residues: 517.8267 Evaluate side-chains 622 residues out of total 3987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 509 time to evaluate : 4.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 MET Chi-restraints excluded: chain A residue 46 ASN Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 156 CYS Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 385 HIS Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 623 GLN Chi-restraints excluded: chain A residue 843 THR Chi-restraints excluded: chain A residue 908 ASP Chi-restraints excluded: chain A residue 949 THR Chi-restraints excluded: chain A residue 1007 THR Chi-restraints excluded: chain A residue 1119 GLU Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1173 VAL Chi-restraints excluded: chain A residue 1176 THR Chi-restraints excluded: chain A residue 1178 ARG Chi-restraints excluded: chain A residue 1185 MET Chi-restraints excluded: chain A residue 1200 VAL Chi-restraints excluded: chain A residue 1201 VAL Chi-restraints excluded: chain A residue 1227 VAL Chi-restraints excluded: chain A residue 1246 THR Chi-restraints excluded: chain A residue 1251 THR Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1324 THR Chi-restraints excluded: chain A residue 1349 MET Chi-restraints excluded: chain B residue 27 TRP Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 42 GLN Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 281 MET Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 572 VAL Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 678 ASN Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 863 ASP Chi-restraints excluded: chain B residue 869 VAL Chi-restraints excluded: chain B residue 880 LEU Chi-restraints excluded: chain B residue 898 SER Chi-restraints excluded: chain B residue 971 ASP Chi-restraints excluded: chain B residue 989 VAL Chi-restraints excluded: chain B residue 1004 PHE Chi-restraints excluded: chain B residue 1045 LEU Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 23 ASN Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 183 ASP Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 306 TYR Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 154 ASP Chi-restraints excluded: chain G residue 184 TYR Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain L residue 43 ILE Chi-restraints excluded: chain P residue 201 ASN Chi-restraints excluded: chain P residue 205 GLN Chi-restraints excluded: chain P residue 277 ILE Chi-restraints excluded: chain P residue 307 CYS Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain H residue 8 ASP Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain O residue 13 LEU Chi-restraints excluded: chain O residue 24 ILE Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain O residue 98 LEU Chi-restraints excluded: chain O residue 235 TRP Chi-restraints excluded: chain O residue 414 ASP Chi-restraints excluded: chain Q residue 26 LYS Chi-restraints excluded: chain Q residue 41 THR Chi-restraints excluded: chain Q residue 60 LEU Chi-restraints excluded: chain Q residue 87 TYR Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 32 LYS Chi-restraints excluded: chain D residue 89 HIS Chi-restraints excluded: chain D residue 98 GLN Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain M residue 42 ILE Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain M residue 114 TYR Chi-restraints excluded: chain M residue 118 LEU Chi-restraints excluded: chain M residue 129 LEU Chi-restraints excluded: chain M residue 136 ARG Chi-restraints excluded: chain M residue 195 PHE Chi-restraints excluded: chain N residue 361 VAL Chi-restraints excluded: chain N residue 379 VAL Chi-restraints excluded: chain I residue 27 THR Chi-restraints excluded: chain I residue 36 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 145 optimal weight: 30.0000 chunk 389 optimal weight: 9.9990 chunk 85 optimal weight: 2.9990 chunk 253 optimal weight: 5.9990 chunk 106 optimal weight: 7.9990 chunk 432 optimal weight: 20.0000 chunk 359 optimal weight: 10.0000 chunk 200 optimal weight: 10.0000 chunk 35 optimal weight: 0.9980 chunk 143 optimal weight: 6.9990 chunk 227 optimal weight: 5.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 HIS ** A 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 693 ASN A 836 ASN A1239 HIS B 472 GLN B 535 ASN ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1115 GLN ** C 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 38 HIS ** K 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 402 ASN ** D 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 53 GLN M 100 GLN ** M 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.6184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.088 37355 Z= 0.498 Angle : 0.832 13.765 50559 Z= 0.424 Chirality : 0.050 0.303 5713 Planarity : 0.006 0.077 6357 Dihedral : 11.083 177.860 5330 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 18.33 Ramachandran Plot: Outliers : 0.20 % Allowed : 10.66 % Favored : 89.13 % Rotamer: Outliers : 5.33 % Allowed : 24.27 % Favored : 70.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.58 (0.12), residues: 4426 helix: -0.74 (0.13), residues: 1542 sheet: -2.60 (0.20), residues: 522 loop : -2.20 (0.12), residues: 2362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP G 200 HIS 0.023 0.002 HIS K 45 PHE 0.023 0.002 PHE B 662 TYR 0.048 0.002 TYR D 47 ARG 0.024 0.001 ARG A 351 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8852 Ramachandran restraints generated. 4426 Oldfield, 0 Emsley, 4426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8852 Ramachandran restraints generated. 4426 Oldfield, 0 Emsley, 4426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 709 residues out of total 3987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 497 time to evaluate : 4.006 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: A 126 LEU cc_start: 0.8862 (mp) cc_final: 0.8371 (tt) REVERT: A 281 MET cc_start: 0.7941 (mmm) cc_final: 0.7732 (mmm) REVERT: A 440 MET cc_start: 0.8691 (mtt) cc_final: 0.8358 (mtt) REVERT: A 461 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8774 (pp) REVERT: A 471 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8535 (mm) REVERT: A 1159 ARG cc_start: 0.8682 (mtt180) cc_final: 0.8142 (tpt90) REVERT: A 1178 ARG cc_start: 0.6922 (OUTLIER) cc_final: 0.6275 (tmt170) REVERT: A 1255 GLU cc_start: 0.8624 (tm-30) cc_final: 0.8179 (tt0) REVERT: B 73 TRP cc_start: 0.6488 (p-90) cc_final: 0.4064 (t-100) REVERT: B 236 ILE cc_start: 0.8043 (pt) cc_final: 0.7656 (mm) REVERT: B 292 ARG cc_start: 0.7726 (tmt170) cc_final: 0.7489 (tmt170) REVERT: B 424 TRP cc_start: 0.7141 (m100) cc_final: 0.6530 (m100) REVERT: B 530 GLU cc_start: 0.8123 (pp20) cc_final: 0.7632 (pp20) REVERT: B 809 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7697 (mp) REVERT: B 814 ILE cc_start: 0.9253 (mm) cc_final: 0.9037 (mm) REVERT: B 1003 TYR cc_start: 0.9069 (OUTLIER) cc_final: 0.8570 (t80) REVERT: B 1004 PHE cc_start: 0.8924 (OUTLIER) cc_final: 0.8708 (t80) REVERT: B 1045 LEU cc_start: 0.7361 (OUTLIER) cc_final: 0.6734 (pp) REVERT: B 1115 GLN cc_start: 0.8891 (OUTLIER) cc_final: 0.8449 (mt0) REVERT: C 28 ASP cc_start: 0.7657 (t0) cc_final: 0.7396 (t0) REVERT: C 212 MET cc_start: 0.7907 (OUTLIER) cc_final: 0.7602 (mtp) REVERT: G 131 TYR cc_start: 0.3991 (m-10) cc_final: 0.3713 (m-80) REVERT: G 201 TRP cc_start: 0.7162 (p-90) cc_final: 0.6082 (p-90) REVERT: K 102 GLU cc_start: 0.8037 (mm-30) cc_final: 0.7815 (mt-10) REVERT: L 31 ARG cc_start: 0.8145 (tpp-160) cc_final: 0.7852 (mmm160) REVERT: P 205 GLN cc_start: 0.5662 (OUTLIER) cc_final: 0.4269 (pt0) REVERT: P 266 HIS cc_start: 0.7745 (m-70) cc_final: 0.7467 (p-80) REVERT: P 303 SER cc_start: 0.8173 (OUTLIER) cc_final: 0.7940 (t) REVERT: E 131 LEU cc_start: 0.9257 (OUTLIER) cc_final: 0.8960 (tp) REVERT: F 91 LEU cc_start: 0.9156 (tp) cc_final: 0.8839 (mp) REVERT: O 68 HIS cc_start: 0.4792 (p90) cc_final: 0.4424 (p90) REVERT: O 385 MET cc_start: 0.5939 (mmm) cc_final: 0.5082 (tpp) REVERT: O 448 GLU cc_start: 0.8298 (tp30) cc_final: 0.7868 (tp30) outliers start: 212 outliers final: 140 residues processed: 659 average time/residue: 0.4758 time to fit residues: 521.1997 Evaluate side-chains 620 residues out of total 3987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 468 time to evaluate : 4.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ASP Chi-restraints excluded: chain A residue 46 ASN Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 156 CYS Chi-restraints excluded: chain A residue 225 ASN Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 385 HIS Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 493 CYS Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 623 GLN Chi-restraints excluded: chain A residue 834 VAL Chi-restraints excluded: chain A residue 843 THR Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain A residue 1007 THR Chi-restraints excluded: chain A residue 1073 ILE Chi-restraints excluded: chain A residue 1106 GLU Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1160 VAL Chi-restraints excluded: chain A residue 1167 VAL Chi-restraints excluded: chain A residue 1173 VAL Chi-restraints excluded: chain A residue 1176 THR Chi-restraints excluded: chain A residue 1178 ARG Chi-restraints excluded: chain A residue 1200 VAL Chi-restraints excluded: chain A residue 1201 VAL Chi-restraints excluded: chain A residue 1227 VAL Chi-restraints excluded: chain A residue 1246 THR Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1304 THR Chi-restraints excluded: chain A residue 1324 THR Chi-restraints excluded: chain A residue 1338 ASP Chi-restraints excluded: chain A residue 1349 MET Chi-restraints excluded: chain A residue 1355 ILE Chi-restraints excluded: chain B residue 27 TRP Chi-restraints excluded: chain B residue 42 GLN Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 545 ILE Chi-restraints excluded: chain B residue 572 VAL Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 707 THR Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 809 LEU Chi-restraints excluded: chain B residue 863 ASP Chi-restraints excluded: chain B residue 869 VAL Chi-restraints excluded: chain B residue 880 LEU Chi-restraints excluded: chain B residue 898 SER Chi-restraints excluded: chain B residue 919 CYS Chi-restraints excluded: chain B residue 946 LEU Chi-restraints excluded: chain B residue 989 VAL Chi-restraints excluded: chain B residue 1003 TYR Chi-restraints excluded: chain B residue 1004 PHE Chi-restraints excluded: chain B residue 1045 LEU Chi-restraints excluded: chain B residue 1073 ASP Chi-restraints excluded: chain B residue 1115 GLN Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 23 ASN Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 183 ASP Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 212 MET Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 306 TYR Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 154 ASP Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 111 LEU Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 41 TYR Chi-restraints excluded: chain L residue 43 ILE Chi-restraints excluded: chain P residue 201 ASN Chi-restraints excluded: chain P residue 205 GLN Chi-restraints excluded: chain P residue 219 TYR Chi-restraints excluded: chain P residue 303 SER Chi-restraints excluded: chain P residue 307 CYS Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 21 CYS Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain H residue 38 ASP Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 57 GLU Chi-restraints excluded: chain O residue 24 ILE Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 154 THR Chi-restraints excluded: chain O residue 168 ASN Chi-restraints excluded: chain O residue 313 THR Chi-restraints excluded: chain O residue 414 ASP Chi-restraints excluded: chain O residue 454 THR Chi-restraints excluded: chain O residue 522 LEU Chi-restraints excluded: chain O residue 523 LEU Chi-restraints excluded: chain Q residue 41 THR Chi-restraints excluded: chain Q residue 48 LEU Chi-restraints excluded: chain Q residue 60 LEU Chi-restraints excluded: chain Q residue 87 TYR Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 32 LYS Chi-restraints excluded: chain D residue 89 HIS Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 98 GLN Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain M residue 38 THR Chi-restraints excluded: chain M residue 39 TYR Chi-restraints excluded: chain M residue 46 SER Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain M residue 114 TYR Chi-restraints excluded: chain M residue 118 LEU Chi-restraints excluded: chain M residue 123 GLU Chi-restraints excluded: chain M residue 129 LEU Chi-restraints excluded: chain M residue 151 GLU Chi-restraints excluded: chain M residue 195 PHE Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain N residue 331 ILE Chi-restraints excluded: chain N residue 361 VAL Chi-restraints excluded: chain N residue 375 VAL Chi-restraints excluded: chain N residue 379 VAL Chi-restraints excluded: chain I residue 27 THR Chi-restraints excluded: chain I residue 36 ARG Chi-restraints excluded: chain I residue 39 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 416 optimal weight: 20.0000 chunk 48 optimal weight: 0.9990 chunk 246 optimal weight: 3.9990 chunk 315 optimal weight: 7.9990 chunk 244 optimal weight: 3.9990 chunk 364 optimal weight: 10.0000 chunk 241 optimal weight: 2.9990 chunk 430 optimal weight: 7.9990 chunk 269 optimal weight: 0.7980 chunk 262 optimal weight: 0.9990 chunk 198 optimal weight: 0.9980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 HIS A 422 GLN ** A 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1190 GLN B 472 GLN B 806 HIS B1010 GLN B1115 GLN B1118 GLN ** G 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 26 ASN ** P 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.6410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 37355 Z= 0.215 Angle : 0.685 12.474 50559 Z= 0.343 Chirality : 0.044 0.249 5713 Planarity : 0.004 0.076 6357 Dihedral : 10.845 178.016 5328 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.38 % Favored : 91.44 % Rotamer: Outliers : 3.85 % Allowed : 25.93 % Favored : 70.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.26 (0.12), residues: 4426 helix: -0.37 (0.13), residues: 1521 sheet: -2.49 (0.21), residues: 516 loop : -2.06 (0.13), residues: 2389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP G 200 HIS 0.008 0.001 HIS B 552 PHE 0.028 0.001 PHE G 157 TYR 0.022 0.001 TYR D 52 ARG 0.014 0.000 ARG C 255 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8852 Ramachandran restraints generated. 4426 Oldfield, 0 Emsley, 4426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8852 Ramachandran restraints generated. 4426 Oldfield, 0 Emsley, 4426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 687 residues out of total 3987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 534 time to evaluate : 4.262 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: A 126 LEU cc_start: 0.8763 (mp) cc_final: 0.8258 (tt) REVERT: A 440 MET cc_start: 0.8717 (mtt) cc_final: 0.8349 (mtt) REVERT: A 461 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8748 (pp) REVERT: A 650 MET cc_start: 0.9077 (mmm) cc_final: 0.8874 (mmp) REVERT: A 1159 ARG cc_start: 0.8660 (mtt180) cc_final: 0.7931 (tpt90) REVERT: A 1178 ARG cc_start: 0.7023 (OUTLIER) cc_final: 0.6342 (tmt170) REVERT: A 1255 GLU cc_start: 0.8607 (tm-30) cc_final: 0.8252 (tm-30) REVERT: B 73 TRP cc_start: 0.6441 (p-90) cc_final: 0.4271 (t-100) REVERT: B 236 ILE cc_start: 0.7766 (pt) cc_final: 0.7447 (mm) REVERT: B 292 ARG cc_start: 0.7656 (tmt170) cc_final: 0.7443 (tmt170) REVERT: B 530 GLU cc_start: 0.8118 (pp20) cc_final: 0.7576 (pp20) REVERT: B 1003 TYR cc_start: 0.8993 (OUTLIER) cc_final: 0.8447 (t80) REVERT: B 1045 LEU cc_start: 0.7147 (OUTLIER) cc_final: 0.6818 (pp) REVERT: C 96 ASN cc_start: 0.7947 (p0) cc_final: 0.7251 (t0) REVERT: C 215 VAL cc_start: 0.8603 (t) cc_final: 0.8374 (m) REVERT: G 9 ASP cc_start: 0.7397 (OUTLIER) cc_final: 0.7168 (m-30) REVERT: G 34 LEU cc_start: 0.8574 (mt) cc_final: 0.8346 (tt) REVERT: G 116 GLN cc_start: 0.0350 (OUTLIER) cc_final: -0.0191 (pp30) REVERT: G 184 TYR cc_start: 0.5653 (OUTLIER) cc_final: 0.4406 (m-80) REVERT: G 201 TRP cc_start: 0.7243 (p-90) cc_final: 0.6257 (p-90) REVERT: P 205 GLN cc_start: 0.5283 (OUTLIER) cc_final: 0.3868 (pt0) REVERT: P 303 SER cc_start: 0.8286 (OUTLIER) cc_final: 0.7998 (t) REVERT: E 131 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.8927 (tp) REVERT: F 91 LEU cc_start: 0.9089 (tp) cc_final: 0.8816 (mp) REVERT: J 41 LYS cc_start: 0.8406 (mmmm) cc_final: 0.8162 (mmtt) REVERT: J 57 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7845 (mt-10) REVERT: O 85 MET cc_start: 0.8036 (mpp) cc_final: 0.7790 (mpp) REVERT: O 106 ILE cc_start: 0.7842 (mt) cc_final: 0.7539 (mm) REVERT: O 385 MET cc_start: 0.5739 (mmm) cc_final: 0.5106 (tpp) REVERT: O 398 MET cc_start: 0.8427 (tpp) cc_final: 0.8189 (mmt) REVERT: O 448 GLU cc_start: 0.8148 (tp30) cc_final: 0.7814 (tp30) REVERT: Q 115 LYS cc_start: 0.4182 (mttt) cc_final: 0.3213 (mttp) REVERT: D 74 LYS cc_start: 0.1167 (mttt) cc_final: 0.0657 (mmtt) outliers start: 153 outliers final: 107 residues processed: 643 average time/residue: 0.4722 time to fit residues: 503.4392 Evaluate side-chains 604 residues out of total 3987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 486 time to evaluate : 4.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASN Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 156 CYS Chi-restraints excluded: chain A residue 225 ASN Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 385 HIS Chi-restraints excluded: chain A residue 428 MET Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 493 CYS Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 623 GLN Chi-restraints excluded: chain A residue 834 VAL Chi-restraints excluded: chain A residue 843 THR Chi-restraints excluded: chain A residue 897 ILE Chi-restraints excluded: chain A residue 946 ILE Chi-restraints excluded: chain A residue 1007 THR Chi-restraints excluded: chain A residue 1073 ILE Chi-restraints excluded: chain A residue 1106 GLU Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1144 VAL Chi-restraints excluded: chain A residue 1160 VAL Chi-restraints excluded: chain A residue 1167 VAL Chi-restraints excluded: chain A residue 1173 VAL Chi-restraints excluded: chain A residue 1176 THR Chi-restraints excluded: chain A residue 1178 ARG Chi-restraints excluded: chain A residue 1200 VAL Chi-restraints excluded: chain A residue 1201 VAL Chi-restraints excluded: chain A residue 1227 VAL Chi-restraints excluded: chain A residue 1246 THR Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1324 THR Chi-restraints excluded: chain A residue 1349 MET Chi-restraints excluded: chain B residue 27 TRP Chi-restraints excluded: chain B residue 42 GLN Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 572 VAL Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 678 ASN Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 863 ASP Chi-restraints excluded: chain B residue 869 VAL Chi-restraints excluded: chain B residue 880 LEU Chi-restraints excluded: chain B residue 940 VAL Chi-restraints excluded: chain B residue 1003 TYR Chi-restraints excluded: chain B residue 1045 LEU Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 23 ASN Chi-restraints excluded: chain C residue 183 ASP Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 306 TYR Chi-restraints excluded: chain G residue 9 ASP Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 116 GLN Chi-restraints excluded: chain G residue 154 ASP Chi-restraints excluded: chain G residue 160 THR Chi-restraints excluded: chain G residue 184 TYR Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain P residue 201 ASN Chi-restraints excluded: chain P residue 205 GLN Chi-restraints excluded: chain P residue 303 SER Chi-restraints excluded: chain P residue 307 CYS Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain H residue 8 ASP Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain J residue 57 GLU Chi-restraints excluded: chain O residue 24 ILE Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 55 CYS Chi-restraints excluded: chain O residue 154 THR Chi-restraints excluded: chain O residue 235 TRP Chi-restraints excluded: chain O residue 414 ASP Chi-restraints excluded: chain Q residue 41 THR Chi-restraints excluded: chain Q residue 48 LEU Chi-restraints excluded: chain Q residue 60 LEU Chi-restraints excluded: chain Q residue 71 MET Chi-restraints excluded: chain Q residue 87 TYR Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 32 LYS Chi-restraints excluded: chain D residue 98 GLN Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain M residue 14 ASP Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain M residue 114 TYR Chi-restraints excluded: chain M residue 118 LEU Chi-restraints excluded: chain M residue 123 GLU Chi-restraints excluded: chain M residue 136 ARG Chi-restraints excluded: chain M residue 195 PHE Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain M residue 207 HIS Chi-restraints excluded: chain N residue 258 LEU Chi-restraints excluded: chain N residue 344 VAL Chi-restraints excluded: chain N residue 361 VAL Chi-restraints excluded: chain N residue 379 VAL Chi-restraints excluded: chain I residue 36 ARG Chi-restraints excluded: chain I residue 39 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 266 optimal weight: 9.9990 chunk 172 optimal weight: 2.9990 chunk 257 optimal weight: 5.9990 chunk 129 optimal weight: 0.0050 chunk 84 optimal weight: 0.0870 chunk 83 optimal weight: 0.9980 chunk 273 optimal weight: 4.9990 chunk 293 optimal weight: 8.9990 chunk 213 optimal weight: 4.9990 chunk 40 optimal weight: 0.0570 chunk 338 optimal weight: 9.9990 overall best weight: 0.8292 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 HIS A 528 ASN ** A1371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN ** K 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 26 ASN ** P 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 266 HIS P 306 ASN ** O 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 61 GLN ** D 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 29 GLN M 100 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.6596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 37355 Z= 0.189 Angle : 0.670 11.256 50559 Z= 0.335 Chirality : 0.044 0.219 5713 Planarity : 0.004 0.085 6357 Dihedral : 10.648 178.403 5325 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 14.50 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.81 % Favored : 90.99 % Rotamer: Outliers : 3.62 % Allowed : 26.41 % Favored : 69.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.12), residues: 4426 helix: -0.15 (0.13), residues: 1513 sheet: -2.32 (0.21), residues: 517 loop : -2.01 (0.13), residues: 2396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP G 200 HIS 0.007 0.001 HIS B 260 PHE 0.029 0.001 PHE A 288 TYR 0.024 0.001 TYR M 141 ARG 0.011 0.000 ARG L 35 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8852 Ramachandran restraints generated. 4426 Oldfield, 0 Emsley, 4426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8852 Ramachandran restraints generated. 4426 Oldfield, 0 Emsley, 4426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 674 residues out of total 3987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 530 time to evaluate : 4.219 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: A 126 LEU cc_start: 0.8717 (mp) cc_final: 0.8210 (tt) REVERT: A 128 TYR cc_start: 0.8424 (t80) cc_final: 0.8166 (t80) REVERT: A 440 MET cc_start: 0.8736 (mtt) cc_final: 0.8374 (mtt) REVERT: A 650 MET cc_start: 0.9084 (mmm) cc_final: 0.8871 (mmp) REVERT: A 790 ILE cc_start: 0.8909 (mm) cc_final: 0.8704 (mt) REVERT: A 1159 ARG cc_start: 0.8653 (mtt180) cc_final: 0.7934 (tpt90) REVERT: A 1178 ARG cc_start: 0.7040 (OUTLIER) cc_final: 0.6416 (tmt170) REVERT: A 1209 ARG cc_start: 0.8002 (tmm-80) cc_final: 0.7411 (tmm-80) REVERT: A 1255 GLU cc_start: 0.8598 (tm-30) cc_final: 0.8233 (tm-30) REVERT: A 1270 GLU cc_start: 0.7887 (mm-30) cc_final: 0.7656 (mm-30) REVERT: B 73 TRP cc_start: 0.6387 (p-90) cc_final: 0.4270 (t-100) REVERT: B 236 ILE cc_start: 0.7807 (pt) cc_final: 0.7373 (mm) REVERT: B 338 MET cc_start: 0.8583 (ttm) cc_final: 0.8370 (ttp) REVERT: B 530 GLU cc_start: 0.8055 (pp20) cc_final: 0.7526 (pp20) REVERT: B 1003 TYR cc_start: 0.8984 (OUTLIER) cc_final: 0.8463 (t80) REVERT: B 1045 LEU cc_start: 0.7165 (OUTLIER) cc_final: 0.6843 (pp) REVERT: C 33 TYR cc_start: 0.8508 (m-80) cc_final: 0.8299 (m-80) REVERT: C 96 ASN cc_start: 0.7946 (p0) cc_final: 0.7192 (t0) REVERT: C 306 TYR cc_start: 0.6422 (OUTLIER) cc_final: 0.5863 (p90) REVERT: G 34 LEU cc_start: 0.8576 (mt) cc_final: 0.8296 (tt) REVERT: G 131 TYR cc_start: 0.4375 (m-80) cc_final: 0.4030 (m-80) REVERT: G 184 TYR cc_start: 0.5664 (OUTLIER) cc_final: 0.4334 (m-80) REVERT: G 201 TRP cc_start: 0.6921 (p-90) cc_final: 0.6599 (p-90) REVERT: K 104 MET cc_start: 0.7955 (tpp) cc_final: 0.7733 (ttm) REVERT: P 205 GLN cc_start: 0.5333 (OUTLIER) cc_final: 0.3742 (pm20) REVERT: P 218 LYS cc_start: 0.8371 (ptpp) cc_final: 0.7816 (pttt) REVERT: P 222 GLU cc_start: 0.7862 (tp30) cc_final: 0.7030 (tt0) REVERT: P 303 SER cc_start: 0.8390 (OUTLIER) cc_final: 0.8125 (t) REVERT: E 131 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8889 (tp) REVERT: O 85 MET cc_start: 0.7978 (mpp) cc_final: 0.7762 (mpp) REVERT: O 355 GLN cc_start: 0.8788 (OUTLIER) cc_final: 0.8287 (tp-100) REVERT: O 385 MET cc_start: 0.5818 (mmm) cc_final: 0.5107 (tpp) REVERT: O 448 GLU cc_start: 0.8114 (tp30) cc_final: 0.7830 (tp30) REVERT: M 60 MET cc_start: 0.3028 (mmm) cc_final: 0.2740 (mmm) outliers start: 144 outliers final: 103 residues processed: 631 average time/residue: 0.4616 time to fit residues: 482.8275 Evaluate side-chains 604 residues out of total 3987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 492 time to evaluate : 4.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASN Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 156 CYS Chi-restraints excluded: chain A residue 225 ASN Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 385 HIS Chi-restraints excluded: chain A residue 428 MET Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 493 CYS Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 623 GLN Chi-restraints excluded: chain A residue 834 VAL Chi-restraints excluded: chain A residue 843 THR Chi-restraints excluded: chain A residue 1007 THR Chi-restraints excluded: chain A residue 1073 ILE Chi-restraints excluded: chain A residue 1106 GLU Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1160 VAL Chi-restraints excluded: chain A residue 1167 VAL Chi-restraints excluded: chain A residue 1173 VAL Chi-restraints excluded: chain A residue 1176 THR Chi-restraints excluded: chain A residue 1178 ARG Chi-restraints excluded: chain A residue 1200 VAL Chi-restraints excluded: chain A residue 1246 THR Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1324 THR Chi-restraints excluded: chain A residue 1349 MET Chi-restraints excluded: chain B residue 27 TRP Chi-restraints excluded: chain B residue 42 GLN Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 572 VAL Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 678 ASN Chi-restraints excluded: chain B residue 707 THR Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 863 ASP Chi-restraints excluded: chain B residue 869 VAL Chi-restraints excluded: chain B residue 880 LEU Chi-restraints excluded: chain B residue 940 VAL Chi-restraints excluded: chain B residue 1003 TYR Chi-restraints excluded: chain B residue 1045 LEU Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 23 ASN Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 306 TYR Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 116 GLN Chi-restraints excluded: chain G residue 154 ASP Chi-restraints excluded: chain G residue 184 TYR Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 111 LEU Chi-restraints excluded: chain P residue 201 ASN Chi-restraints excluded: chain P residue 205 GLN Chi-restraints excluded: chain P residue 303 SER Chi-restraints excluded: chain P residue 307 CYS Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain H residue 8 ASP Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain O residue 55 CYS Chi-restraints excluded: chain O residue 98 LEU Chi-restraints excluded: chain O residue 154 THR Chi-restraints excluded: chain O residue 168 ASN Chi-restraints excluded: chain O residue 235 TRP Chi-restraints excluded: chain O residue 355 GLN Chi-restraints excluded: chain O residue 414 ASP Chi-restraints excluded: chain O residue 522 LEU Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain Q residue 41 THR Chi-restraints excluded: chain Q residue 48 LEU Chi-restraints excluded: chain Q residue 87 TYR Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 32 LYS Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 98 GLN Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain M residue 123 GLU Chi-restraints excluded: chain M residue 124 LEU Chi-restraints excluded: chain M residue 129 LEU Chi-restraints excluded: chain M residue 136 ARG Chi-restraints excluded: chain M residue 195 PHE Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain M residue 207 HIS Chi-restraints excluded: chain N residue 258 LEU Chi-restraints excluded: chain N residue 347 ASP Chi-restraints excluded: chain N residue 361 VAL Chi-restraints excluded: chain N residue 379 VAL Chi-restraints excluded: chain I residue 36 ARG Chi-restraints excluded: chain I residue 39 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 391 optimal weight: 0.7980 chunk 412 optimal weight: 10.0000 chunk 376 optimal weight: 20.0000 chunk 401 optimal weight: 0.1980 chunk 241 optimal weight: 7.9990 chunk 174 optimal weight: 6.9990 chunk 315 optimal weight: 9.9990 chunk 123 optimal weight: 6.9990 chunk 362 optimal weight: 9.9990 chunk 379 optimal weight: 20.0000 chunk 400 optimal weight: 3.9990 overall best weight: 3.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1118 GLN ** C 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 100 GLN ** M 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.6897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 37355 Z= 0.409 Angle : 0.767 13.666 50559 Z= 0.387 Chirality : 0.047 0.219 5713 Planarity : 0.005 0.088 6357 Dihedral : 10.747 178.627 5323 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 17.35 Ramachandran Plot: Outliers : 0.20 % Allowed : 10.37 % Favored : 89.43 % Rotamer: Outliers : 3.52 % Allowed : 26.89 % Favored : 69.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.12), residues: 4426 helix: -0.21 (0.13), residues: 1509 sheet: -2.49 (0.20), residues: 535 loop : -2.02 (0.13), residues: 2382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP G 200 HIS 0.009 0.001 HIS A 483 PHE 0.026 0.002 PHE B 537 TYR 0.045 0.002 TYR P 219 ARG 0.008 0.001 ARG A 351 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8852 Ramachandran restraints generated. 4426 Oldfield, 0 Emsley, 4426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8852 Ramachandran restraints generated. 4426 Oldfield, 0 Emsley, 4426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 636 residues out of total 3987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 496 time to evaluate : 4.197 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: A 126 LEU cc_start: 0.8808 (mp) cc_final: 0.8279 (tt) REVERT: A 440 MET cc_start: 0.8749 (mtt) cc_final: 0.8440 (mtt) REVERT: A 471 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8490 (mm) REVERT: A 790 ILE cc_start: 0.8975 (mm) cc_final: 0.8759 (mt) REVERT: A 1178 ARG cc_start: 0.6976 (OUTLIER) cc_final: 0.6325 (tmt170) REVERT: A 1255 GLU cc_start: 0.8600 (tm-30) cc_final: 0.8255 (tm-30) REVERT: B 73 TRP cc_start: 0.6437 (p-90) cc_final: 0.3990 (t-100) REVERT: B 236 ILE cc_start: 0.8194 (pt) cc_final: 0.7696 (mm) REVERT: B 292 ARG cc_start: 0.7641 (tmt170) cc_final: 0.7182 (tmm160) REVERT: B 530 GLU cc_start: 0.8146 (pp20) cc_final: 0.7866 (pp20) REVERT: B 1003 TYR cc_start: 0.9088 (OUTLIER) cc_final: 0.8615 (t80) REVERT: B 1045 LEU cc_start: 0.7288 (OUTLIER) cc_final: 0.6778 (pp) REVERT: C 96 ASN cc_start: 0.8062 (p0) cc_final: 0.7364 (t0) REVERT: G 25 SER cc_start: 0.8529 (m) cc_final: 0.8324 (t) REVERT: G 201 TRP cc_start: 0.7161 (p-90) cc_final: 0.6728 (p-90) REVERT: P 205 GLN cc_start: 0.5461 (OUTLIER) cc_final: 0.3993 (pt0) REVERT: P 218 LYS cc_start: 0.8128 (ptpp) cc_final: 0.7586 (pttt) REVERT: P 266 HIS cc_start: 0.7884 (m-70) cc_final: 0.7649 (p90) REVERT: E 131 LEU cc_start: 0.9254 (OUTLIER) cc_final: 0.8949 (tp) REVERT: O 355 GLN cc_start: 0.8864 (OUTLIER) cc_final: 0.8346 (tp-100) REVERT: O 385 MET cc_start: 0.5962 (mmm) cc_final: 0.5301 (tpp) REVERT: O 448 GLU cc_start: 0.8250 (tp30) cc_final: 0.7941 (tp30) REVERT: Q 115 LYS cc_start: 0.4982 (mttp) cc_final: 0.4074 (mttp) REVERT: D 53 ILE cc_start: 0.6231 (tp) cc_final: 0.6001 (tp) outliers start: 140 outliers final: 118 residues processed: 599 average time/residue: 0.4674 time to fit residues: 464.1289 Evaluate side-chains 594 residues out of total 3987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 469 time to evaluate : 4.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ASP Chi-restraints excluded: chain A residue 46 ASN Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 156 CYS Chi-restraints excluded: chain A residue 225 ASN Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 385 HIS Chi-restraints excluded: chain A residue 428 MET Chi-restraints excluded: chain A residue 445 LYS Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 493 CYS Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 623 GLN Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 834 VAL Chi-restraints excluded: chain A residue 843 THR Chi-restraints excluded: chain A residue 897 ILE Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 946 ILE Chi-restraints excluded: chain A residue 1007 THR Chi-restraints excluded: chain A residue 1073 ILE Chi-restraints excluded: chain A residue 1106 GLU Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1144 VAL Chi-restraints excluded: chain A residue 1160 VAL Chi-restraints excluded: chain A residue 1167 VAL Chi-restraints excluded: chain A residue 1173 VAL Chi-restraints excluded: chain A residue 1176 THR Chi-restraints excluded: chain A residue 1178 ARG Chi-restraints excluded: chain A residue 1200 VAL Chi-restraints excluded: chain A residue 1227 VAL Chi-restraints excluded: chain A residue 1246 THR Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1324 THR Chi-restraints excluded: chain A residue 1349 MET Chi-restraints excluded: chain B residue 27 TRP Chi-restraints excluded: chain B residue 42 GLN Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 281 MET Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 572 VAL Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 678 ASN Chi-restraints excluded: chain B residue 707 THR Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 863 ASP Chi-restraints excluded: chain B residue 869 VAL Chi-restraints excluded: chain B residue 880 LEU Chi-restraints excluded: chain B residue 940 VAL Chi-restraints excluded: chain B residue 989 VAL Chi-restraints excluded: chain B residue 1003 TYR Chi-restraints excluded: chain B residue 1045 LEU Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 23 ASN Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 166 HIS Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 306 TYR Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 116 GLN Chi-restraints excluded: chain G residue 154 ASP Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain P residue 201 ASN Chi-restraints excluded: chain P residue 205 GLN Chi-restraints excluded: chain P residue 307 CYS Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain O residue 55 CYS Chi-restraints excluded: chain O residue 154 THR Chi-restraints excluded: chain O residue 168 ASN Chi-restraints excluded: chain O residue 235 TRP Chi-restraints excluded: chain O residue 355 GLN Chi-restraints excluded: chain O residue 414 ASP Chi-restraints excluded: chain O residue 522 LEU Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain Q residue 41 THR Chi-restraints excluded: chain Q residue 48 LEU Chi-restraints excluded: chain Q residue 87 TYR Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 32 LYS Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 98 GLN Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain M residue 118 LEU Chi-restraints excluded: chain M residue 123 GLU Chi-restraints excluded: chain M residue 124 LEU Chi-restraints excluded: chain M residue 126 LEU Chi-restraints excluded: chain M residue 136 ARG Chi-restraints excluded: chain M residue 195 PHE Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain N residue 258 LEU Chi-restraints excluded: chain N residue 331 ILE Chi-restraints excluded: chain N residue 344 VAL Chi-restraints excluded: chain N residue 347 ASP Chi-restraints excluded: chain N residue 361 VAL Chi-restraints excluded: chain N residue 379 VAL Chi-restraints excluded: chain I residue 36 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 263 optimal weight: 0.0980 chunk 424 optimal weight: 9.9990 chunk 259 optimal weight: 7.9990 chunk 201 optimal weight: 0.0870 chunk 295 optimal weight: 2.9990 chunk 445 optimal weight: 10.0000 chunk 409 optimal weight: 8.9990 chunk 354 optimal weight: 10.0000 chunk 36 optimal weight: 1.9990 chunk 273 optimal weight: 7.9990 chunk 217 optimal weight: 0.9980 overall best weight: 1.2362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 HIS ** A1371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1118 GLN ** K 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 26 ASN P 240 ASN ** E 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 100 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.7063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 37355 Z= 0.211 Angle : 0.699 13.844 50559 Z= 0.348 Chirality : 0.044 0.216 5713 Planarity : 0.004 0.088 6357 Dihedral : 10.643 178.589 5323 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.54 % Favored : 91.28 % Rotamer: Outliers : 3.02 % Allowed : 27.59 % Favored : 69.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.13), residues: 4426 helix: -0.01 (0.14), residues: 1502 sheet: -2.23 (0.22), residues: 505 loop : -1.93 (0.13), residues: 2419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP G 200 HIS 0.007 0.001 HIS B 260 PHE 0.020 0.001 PHE B 537 TYR 0.033 0.001 TYR M 141 ARG 0.009 0.000 ARG M 113 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8852 Ramachandran restraints generated. 4426 Oldfield, 0 Emsley, 4426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8852 Ramachandran restraints generated. 4426 Oldfield, 0 Emsley, 4426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 3987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 494 time to evaluate : 4.333 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: A 126 LEU cc_start: 0.8740 (mp) cc_final: 0.8238 (tt) REVERT: A 128 TYR cc_start: 0.8543 (t80) cc_final: 0.8284 (t80) REVERT: A 158 HIS cc_start: 0.6878 (m-70) cc_final: 0.6562 (m90) REVERT: A 440 MET cc_start: 0.8749 (mtt) cc_final: 0.8428 (mtt) REVERT: A 461 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8777 (pp) REVERT: A 650 MET cc_start: 0.9053 (mmm) cc_final: 0.8832 (mmp) REVERT: A 790 ILE cc_start: 0.8929 (mm) cc_final: 0.8726 (mt) REVERT: A 1112 GLU cc_start: 0.6851 (tp30) cc_final: 0.6539 (tp30) REVERT: A 1159 ARG cc_start: 0.8603 (mtt180) cc_final: 0.8012 (tpt90) REVERT: A 1178 ARG cc_start: 0.7137 (OUTLIER) cc_final: 0.6514 (tmt170) REVERT: A 1209 ARG cc_start: 0.8070 (tmm-80) cc_final: 0.7506 (tmm-80) REVERT: A 1255 GLU cc_start: 0.8632 (tm-30) cc_final: 0.8262 (tm-30) REVERT: A 1270 GLU cc_start: 0.7850 (mm-30) cc_final: 0.7579 (mm-30) REVERT: B 73 TRP cc_start: 0.6443 (p-90) cc_final: 0.4203 (t-100) REVERT: B 292 ARG cc_start: 0.7418 (tmt170) cc_final: 0.7138 (tmm160) REVERT: B 530 GLU cc_start: 0.8110 (pp20) cc_final: 0.7881 (pp20) REVERT: B 1003 TYR cc_start: 0.9026 (OUTLIER) cc_final: 0.8497 (t80) REVERT: B 1045 LEU cc_start: 0.7171 (OUTLIER) cc_final: 0.6860 (pp) REVERT: C 96 ASN cc_start: 0.7861 (p0) cc_final: 0.7280 (t0) REVERT: G 25 SER cc_start: 0.8459 (m) cc_final: 0.8248 (t) REVERT: G 201 TRP cc_start: 0.6697 (p-90) cc_final: 0.6293 (p-90) REVERT: P 205 GLN cc_start: 0.5183 (OUTLIER) cc_final: 0.3641 (pm20) REVERT: P 218 LYS cc_start: 0.8100 (ptpp) cc_final: 0.7616 (pttt) REVERT: P 266 HIS cc_start: 0.7894 (m-70) cc_final: 0.7683 (p-80) REVERT: E 131 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8871 (tp) REVERT: O 355 GLN cc_start: 0.8794 (OUTLIER) cc_final: 0.8294 (tp-100) REVERT: O 385 MET cc_start: 0.5900 (mmm) cc_final: 0.5308 (tpp) REVERT: O 448 GLU cc_start: 0.8221 (tp30) cc_final: 0.7943 (tp30) REVERT: Q 115 LYS cc_start: 0.4966 (mttp) cc_final: 0.4119 (mttp) REVERT: D 53 ILE cc_start: 0.6174 (tp) cc_final: 0.5882 (tp) outliers start: 120 outliers final: 103 residues processed: 583 average time/residue: 0.4786 time to fit residues: 462.5623 Evaluate side-chains 580 residues out of total 3987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 470 time to evaluate : 4.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASN Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 156 CYS Chi-restraints excluded: chain A residue 225 ASN Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 385 HIS Chi-restraints excluded: chain A residue 428 MET Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 493 CYS Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 834 VAL Chi-restraints excluded: chain A residue 843 THR Chi-restraints excluded: chain A residue 845 THR Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1007 THR Chi-restraints excluded: chain A residue 1073 ILE Chi-restraints excluded: chain A residue 1106 GLU Chi-restraints excluded: chain A residue 1144 VAL Chi-restraints excluded: chain A residue 1160 VAL Chi-restraints excluded: chain A residue 1167 VAL Chi-restraints excluded: chain A residue 1173 VAL Chi-restraints excluded: chain A residue 1176 THR Chi-restraints excluded: chain A residue 1178 ARG Chi-restraints excluded: chain A residue 1200 VAL Chi-restraints excluded: chain A residue 1227 VAL Chi-restraints excluded: chain A residue 1246 THR Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1324 THR Chi-restraints excluded: chain A residue 1349 MET Chi-restraints excluded: chain B residue 27 TRP Chi-restraints excluded: chain B residue 42 GLN Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 572 VAL Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 678 ASN Chi-restraints excluded: chain B residue 707 THR Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 863 ASP Chi-restraints excluded: chain B residue 869 VAL Chi-restraints excluded: chain B residue 880 LEU Chi-restraints excluded: chain B residue 940 VAL Chi-restraints excluded: chain B residue 1003 TYR Chi-restraints excluded: chain B residue 1045 LEU Chi-restraints excluded: chain B residue 1073 ASP Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 23 ASN Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 183 ASP Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 306 TYR Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 116 GLN Chi-restraints excluded: chain G residue 154 ASP Chi-restraints excluded: chain G residue 160 THR Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain P residue 201 ASN Chi-restraints excluded: chain P residue 205 GLN Chi-restraints excluded: chain P residue 307 CYS Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain H residue 8 ASP Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain O residue 55 CYS Chi-restraints excluded: chain O residue 98 LEU Chi-restraints excluded: chain O residue 154 THR Chi-restraints excluded: chain O residue 168 ASN Chi-restraints excluded: chain O residue 235 TRP Chi-restraints excluded: chain O residue 355 GLN Chi-restraints excluded: chain O residue 414 ASP Chi-restraints excluded: chain O residue 522 LEU Chi-restraints excluded: chain Q residue 41 THR Chi-restraints excluded: chain Q residue 48 LEU Chi-restraints excluded: chain Q residue 87 TYR Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 32 LYS Chi-restraints excluded: chain D residue 98 GLN Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain M residue 118 LEU Chi-restraints excluded: chain M residue 123 GLU Chi-restraints excluded: chain M residue 126 LEU Chi-restraints excluded: chain M residue 195 PHE Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain N residue 258 LEU Chi-restraints excluded: chain N residue 344 VAL Chi-restraints excluded: chain N residue 347 ASP Chi-restraints excluded: chain N residue 361 VAL Chi-restraints excluded: chain N residue 379 VAL Chi-restraints excluded: chain I residue 36 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 281 optimal weight: 0.0980 chunk 377 optimal weight: 3.9990 chunk 108 optimal weight: 9.9990 chunk 326 optimal weight: 5.9990 chunk 52 optimal weight: 0.0270 chunk 98 optimal weight: 0.9980 chunk 355 optimal weight: 6.9990 chunk 148 optimal weight: 9.9990 chunk 364 optimal weight: 10.0000 chunk 44 optimal weight: 5.9990 chunk 65 optimal weight: 6.9990 overall best weight: 2.2242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1118 GLN G 41 ASN ** K 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.105491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.077287 restraints weight = 89958.070| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 3.31 r_work: 0.3067 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.7219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 37355 Z= 0.276 Angle : 0.717 15.286 50559 Z= 0.356 Chirality : 0.045 0.212 5713 Planarity : 0.004 0.088 6357 Dihedral : 10.616 178.860 5323 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 15.63 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.67 % Favored : 90.15 % Rotamer: Outliers : 3.09 % Allowed : 27.72 % Favored : 69.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.13), residues: 4426 helix: 0.04 (0.14), residues: 1496 sheet: -2.33 (0.21), residues: 509 loop : -1.94 (0.13), residues: 2421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP G 200 HIS 0.009 0.001 HIS B 260 PHE 0.021 0.001 PHE B 537 TYR 0.030 0.002 TYR M 141 ARG 0.010 0.000 ARG M 113 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9955.01 seconds wall clock time: 180 minutes 18.89 seconds (10818.89 seconds total)