Starting phenix.real_space_refine on Fri Feb 23 04:33:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mk9_23887/02_2024/7mk9_23887.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mk9_23887/02_2024/7mk9_23887.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mk9_23887/02_2024/7mk9_23887.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mk9_23887/02_2024/7mk9_23887.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mk9_23887/02_2024/7mk9_23887.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mk9_23887/02_2024/7mk9_23887.pdb" } resolution = 3.54 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 582 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 8 6.06 5 P 95 5.49 5 Mg 2 5.21 5 S 193 5.16 5 C 22459 2.51 5 N 6324 2.21 5 O 7041 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 16": "OE1" <-> "OE2" Residue "A GLU 39": "OE1" <-> "OE2" Residue "A ASP 85": "OD1" <-> "OD2" Residue "A ASP 195": "OD1" <-> "OD2" Residue "A PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 257": "NH1" <-> "NH2" Residue "A GLU 293": "OE1" <-> "OE2" Residue "A ASP 356": "OD1" <-> "OD2" Residue "A ARG 416": "NH1" <-> "NH2" Residue "A TYR 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 433": "OE1" <-> "OE2" Residue "A ASP 438": "OD1" <-> "OD2" Residue "A TYR 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 486": "OE1" <-> "OE2" Residue "A TYR 551": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 591": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 602": "OD1" <-> "OD2" Residue "A ASP 609": "OD1" <-> "OD2" Residue "A PHE 646": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 662": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 755": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 777": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 792": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 826": "OD1" <-> "OD2" Residue "A TYR 868": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 874": "OD1" <-> "OD2" Residue "A TYR 933": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 942": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 947": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1018": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1042": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1135": "NH1" <-> "NH2" Residue "A ARG 1159": "NH1" <-> "NH2" Residue "A PHE 1332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1426": "OE1" <-> "OE2" Residue "B PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 106": "OD1" <-> "OD2" Residue "B PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 186": "OE1" <-> "OE2" Residue "B TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 209": "OE1" <-> "OE2" Residue "B GLU 216": "OE1" <-> "OE2" Residue "B ARG 241": "NH1" <-> "NH2" Residue "B TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 319": "OE1" <-> "OE2" Residue "B ASP 320": "OD1" <-> "OD2" Residue "B PHE 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 336": "NH1" <-> "NH2" Residue "B GLU 371": "OE1" <-> "OE2" Residue "B ARG 398": "NH1" <-> "NH2" Residue "B ARG 430": "NH1" <-> "NH2" Residue "B TYR 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 476": "NH1" <-> "NH2" Residue "B PHE 557": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 758": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 814": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 833": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 874": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1004": "OE1" <-> "OE2" Residue "B GLU 1053": "OE1" <-> "OE2" Residue "B TYR 1064": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1091": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1101": "OD1" <-> "OD2" Residue "B GLU 1120": "OE1" <-> "OE2" Residue "B PHE 1130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1186": "OD1" <-> "OD2" Residue "B ASP 1190": "OD1" <-> "OD2" Residue "B TYR 1198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 181": "OD1" <-> "OD2" Residue "C TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 210": "OE1" <-> "OE2" Residue "C TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 21": "OE1" <-> "OE2" Residue "D GLU 45": "OE1" <-> "OE2" Residue "D GLU 120": "OE1" <-> "OE2" Residue "D GLU 124": "OE1" <-> "OE2" Residue "D TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 190": "OE1" <-> "OE2" Residue "E GLU 21": "OE1" <-> "OE2" Residue "E GLU 81": "OE1" <-> "OE2" Residue "E TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 182": "OD1" <-> "OD2" Residue "E GLU 194": "OE1" <-> "OE2" Residue "F ASP 77": "OD1" <-> "OD2" Residue "F TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 145": "OD1" <-> "OD2" Residue "F GLU 150": "OE1" <-> "OE2" Residue "G PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 35": "OE1" <-> "OE2" Residue "G ARG 58": "NH1" <-> "NH2" Residue "G ARG 60": "NH1" <-> "NH2" Residue "G PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 165": "OE1" <-> "OE2" Residue "H PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 16": "OD1" <-> "OD2" Residue "H GLU 45": "OE1" <-> "OE2" Residue "H GLU 126": "OE1" <-> "OE2" Residue "I ARG 8": "NH1" <-> "NH2" Residue "I ARG 24": "NH1" <-> "NH2" Residue "I TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 47": "OE1" <-> "OE2" Residue "I ARG 92": "NH1" <-> "NH2" Residue "I ASP 94": "OD1" <-> "OD2" Residue "J TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 58": "OE1" <-> "OE2" Residue "J ARG 62": "NH1" <-> "NH2" Residue "K PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 108": "OE1" <-> "OE2" Residue "L ARG 47": "NH1" <-> "NH2" Residue "Q GLU 109": "OE1" <-> "OE2" Residue "Q ASP 132": "OD1" <-> "OD2" Residue "Q PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 54": "OE1" <-> "OE2" Residue "M ASP 58": "OD1" <-> "OD2" Residue "M PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 100": "OD1" <-> "OD2" Residue "M TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 230": "OD1" <-> "OD2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 36122 Number of models: 1 Model: "" Number of chains: 24 Chain: "N" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 822 Classifications: {'DNA': 40} Link IDs: {'rna3p': 39} Chain: "O" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 827 Classifications: {'DNA': 40} Link IDs: {'rna3p': 39} Chain: "A" Number of atoms: 11167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1425, 11167 Classifications: {'peptide': 1425} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'CIS': 4, 'PCIS': 1, 'PTRANS': 65, 'TRANS': 1354} Chain breaks: 3 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 27 Chain: "B" Number of atoms: 9227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1166, 9227 Classifications: {'peptide': 1166} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 8} Link IDs: {'CIS': 11, 'PCIS': 1, 'PTRANS': 50, 'TRANS': 1103} Chain breaks: 7 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 2, 'PHE:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "C" Number of atoms: 2086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2086 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 11, 'TRANS': 253} Chain: "D" Number of atoms: 1331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1331 Classifications: {'peptide': 168} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 3, 'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 165} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "E" Number of atoms: 1752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1752 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 201} Chain: "F" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 705 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 80} Chain: "G" Number of atoms: 1335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1335 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 162} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 1080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1080 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 130} Chain breaks: 2 Chain: "I" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 927 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "J" Number of atoms: 540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 540 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "K" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 924 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 5, 'TRANS': 109} Chain: "L" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 352 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'TRANS': 43} Chain: "R" Number of atoms: 312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 312 Classifications: {'RNA': 15} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 6, 'rna3p_pyr': 8} Link IDs: {'rna2p': 1, 'rna3p': 13} Chain: "Q" Number of atoms: 1619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1619 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 204} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 197 Unresolved non-hydrogen angles: 247 Unresolved non-hydrogen dihedrals: 162 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 110 Chain: "M" Number of atoms: 1106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1106 Classifications: {'peptide': 135} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 128} Chain breaks: 1 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 20 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2465 SG CYS A 107 76.884 39.694 80.229 1.00250.70 S ATOM 2489 SG CYS A 110 74.935 39.636 79.670 1.00242.09 S ATOM 2794 SG CYS A 148 76.353 38.327 83.403 1.00294.76 S ATOM 2932 SG CYS A 167 75.584 36.362 79.575 1.00293.62 S ATOM 2160 SG CYS A 67 64.923 77.009 46.485 1.00231.64 S ATOM 2182 SG CYS A 70 62.738 76.249 48.734 1.00224.65 S ATOM 2235 SG CYS A 77 66.537 76.222 49.624 1.00202.98 S ATOM 21568 SG CYS B1163 57.581 70.370 62.684 1.00222.04 S ATOM 21586 SG CYS B1166 59.891 67.574 62.298 1.00229.02 S ATOM 21711 SG CYS B1182 59.359 69.468 59.216 1.00232.64 S ATOM 22690 SG CYS C 86 88.477 139.918 34.090 1.00323.13 S ATOM 22707 SG CYS C 88 88.685 136.498 32.435 1.00317.15 S ATOM 22740 SG CYS C 92 90.601 139.272 31.060 1.00296.54 S ATOM 22763 SG CYS C 95 91.735 137.791 34.343 1.00293.39 S ATOM 30385 SG CYS I 7 147.110 41.292 92.248 1.00276.12 S ATOM 30410 SG CYS I 10 144.714 41.504 89.078 1.00275.03 S ATOM 30576 SG CYS I 29 143.248 41.153 92.419 1.00273.60 S ATOM 30600 SG CYS I 32 145.484 38.340 91.078 1.00262.01 S ATOM 30927 SG CYS I 75 157.577 86.318 98.966 1.00273.06 S ATOM 30949 SG CYS I 78 159.188 86.143 97.907 1.00266.82 S ATOM 31185 SG CYS I 106 157.186 83.547 97.750 1.00279.11 S ATOM 31313 SG CYS J 7 115.754 130.004 54.667 1.00192.03 S ATOM 31336 SG CYS J 10 114.768 133.523 54.764 1.00191.68 S ATOM 31616 SG CYS J 45 116.352 132.348 57.916 1.00197.06 S ATOM 31622 SG CYS J 46 117.806 133.548 54.637 1.00203.76 S ATOM 32766 SG CYS L 31 113.611 99.946 19.816 1.00302.20 S ATOM 32890 SG CYS L 48 115.345 96.769 19.764 1.00309.77 S ATOM 32913 SG CYS L 51 118.040 99.250 20.018 1.00 30.00 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb="ZN ZN A1801 " occ=0.95 Time building chain proxies: 19.58, per 1000 atoms: 0.54 Number of scatterers: 36122 At special positions: 0 Unit cell: (195.48, 172.8, 147.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 8 29.99 S 193 16.00 P 95 15.00 Mg 2 11.99 O 7041 8.00 N 6324 7.00 C 22459 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: 17.49 Conformation dependent library (CDL) restraints added in 6.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1801 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 110 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 167 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 107 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 148 " pdb=" ZN A1802 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 77 " pdb="ZN ZN A1802 " - pdb=" NE2 HIS A 80 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 67 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 70 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1166 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1163 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1182 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 92 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 86 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 95 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 32 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 29 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 7 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 10 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 75 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 106 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 78 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 46 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb=" ZN L 201 " pdb="ZN ZN L 201 " - pdb=" SG CYS L 48 " pdb="ZN ZN L 201 " - pdb=" SG CYS L 51 " pdb="ZN ZN L 201 " - pdb=" SG CYS L 31 " Number of angles added : 27 8518 Ramachandran restraints generated. 4259 Oldfield, 0 Emsley, 4259 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8126 Finding SS restraints... Secondary structure from input PDB file: 145 helices and 40 sheets defined 36.7% alpha, 16.3% beta 36 base pairs and 66 stacking pairs defined. Time for finding SS restraints: 13.32 Creating SS restraints... Processing helix chain 'A' and resid 23 through 31 Processing helix chain 'A' and resid 92 through 94 No H-bonds generated for 'chain 'A' and resid 92 through 94' Processing helix chain 'A' and resid 95 through 105 Processing helix chain 'A' and resid 119 through 128 Processing helix chain 'A' and resid 132 through 142 Processing helix chain 'A' and resid 203 through 213 removed outlier: 3.593A pdb=" N ILE A 207 " --> pdb=" O SER A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 222 removed outlier: 3.541A pdb=" N PHE A 219 " --> pdb=" O SER A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 235 Processing helix chain 'A' and resid 243 through 247 Processing helix chain 'A' and resid 260 through 282 Processing helix chain 'A' and resid 287 through 305 removed outlier: 4.034A pdb=" N GLU A 291 " --> pdb=" O HIS A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 330 Processing helix chain 'A' and resid 368 through 374 Processing helix chain 'A' and resid 384 through 395 removed outlier: 3.657A pdb=" N GLY A 395 " --> pdb=" O LEU A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 479 removed outlier: 3.775A pdb=" N TYR A 478 " --> pdb=" O VAL A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 505 removed outlier: 3.919A pdb=" N ARG A 498 " --> pdb=" O SER A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 511 removed outlier: 3.630A pdb=" N LEU A 509 " --> pdb=" O ALA A 506 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ILE A 511 " --> pdb=" O PRO A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 535 Processing helix chain 'A' and resid 542 through 553 removed outlier: 3.712A pdb=" N ASN A 548 " --> pdb=" O ASP A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 582 removed outlier: 4.073A pdb=" N VAL A 580 " --> pdb=" O GLN A 576 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ALA A 581 " --> pdb=" O ILE A 577 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE A 582 " --> pdb=" O LEU A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 623 Processing helix chain 'A' and resid 628 through 637 Processing helix chain 'A' and resid 640 through 661 removed outlier: 3.660A pdb=" N LYS A 644 " --> pdb=" O GLN A 640 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N HIS A 659 " --> pdb=" O PHE A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 670 removed outlier: 4.016A pdb=" N THR A 669 " --> pdb=" O GLY A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 699 Processing helix chain 'A' and resid 709 through 737 Processing helix chain 'A' and resid 741 through 749 removed outlier: 3.557A pdb=" N GLN A 745 " --> pdb=" O ASN A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 754 through 763 Processing helix chain 'A' and resid 809 through 845 removed outlier: 4.637A pdb=" N ALA A 832 " --> pdb=" O ALA A 828 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU A 845 " --> pdb=" O LEU A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 871 Processing helix chain 'A' and resid 889 through 898 Processing helix chain 'A' and resid 913 through 917 removed outlier: 4.613A pdb=" N SER A 917 " --> pdb=" O GLU A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 947 Processing helix chain 'A' and resid 960 through 972 Processing helix chain 'A' and resid 982 through 997 removed outlier: 3.919A pdb=" N LYS A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1015 removed outlier: 3.508A pdb=" N GLN A1008 " --> pdb=" O ASN A1004 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL A1015 " --> pdb=" O GLN A1011 " (cutoff:3.500A) Processing helix chain 'A' and resid 1015 through 1026 Processing helix chain 'A' and resid 1027 through 1035 Processing helix chain 'A' and resid 1038 through 1056 Processing helix chain 'A' and resid 1063 through 1074 Processing helix chain 'A' and resid 1075 through 1077 No H-bonds generated for 'chain 'A' and resid 1075 through 1077' Processing helix chain 'A' and resid 1096 through 1106 removed outlier: 3.526A pdb=" N ARG A1100 " --> pdb=" O SER A1096 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1139 Processing helix chain 'A' and resid 1142 through 1146 removed outlier: 3.734A pdb=" N VAL A1146 " --> pdb=" O THR A1142 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1142 through 1146' Processing helix chain 'A' and resid 1163 through 1166 Processing helix chain 'A' and resid 1167 through 1174 removed outlier: 3.610A pdb=" N GLN A1171 " --> pdb=" O GLU A1167 " (cutoff:3.500A) Processing helix chain 'A' and resid 1198 through 1205 removed outlier: 3.599A pdb=" N LYS A1205 " --> pdb=" O ALA A1201 " (cutoff:3.500A) Processing helix chain 'A' and resid 1208 through 1221 removed outlier: 3.644A pdb=" N VAL A1212 " --> pdb=" O THR A1208 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N PHE A1220 " --> pdb=" O ILE A1216 " (cutoff:3.500A) Processing helix chain 'A' and resid 1255 through 1271 removed outlier: 4.168A pdb=" N MET A1259 " --> pdb=" O GLU A1255 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE A1271 " --> pdb=" O MET A1267 " (cutoff:3.500A) Processing helix chain 'A' and resid 1331 through 1339 removed outlier: 3.865A pdb=" N ILE A1335 " --> pdb=" O SER A1331 " (cutoff:3.500A) Processing helix chain 'A' and resid 1340 through 1358 Processing helix chain 'A' and resid 1364 through 1377 removed outlier: 4.069A pdb=" N MET A1368 " --> pdb=" O ASN A1364 " (cutoff:3.500A) Processing helix chain 'A' and resid 1395 through 1401 Processing helix chain 'A' and resid 1404 through 1416 Processing helix chain 'A' and resid 1423 through 1431 Processing helix chain 'A' and resid 1436 through 1439 Processing helix chain 'A' and resid 1446 through 1453 removed outlier: 3.526A pdb=" N LEU A1450 " --> pdb=" O ASP A1446 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 28 No H-bonds generated for 'chain 'B' and resid 26 through 28' Processing helix chain 'B' and resid 29 through 42 removed outlier: 4.294A pdb=" N VAL B 33 " --> pdb=" O ASP B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 57 Processing helix chain 'B' and resid 59 through 66 removed outlier: 4.017A pdb=" N ASP B 66 " --> pdb=" O ILE B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 121 Processing helix chain 'B' and resid 179 through 184 removed outlier: 3.676A pdb=" N GLU B 183 " --> pdb=" O TYR B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 192 Processing helix chain 'B' and resid 282 through 290 Processing helix chain 'B' and resid 293 through 302 removed outlier: 3.561A pdb=" N ILE B 297 " --> pdb=" O PRO B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 Proline residue: B 316 - end of helix Processing helix chain 'B' and resid 326 through 332 Processing helix chain 'B' and resid 348 through 359 Processing helix chain 'B' and resid 370 through 390 removed outlier: 3.588A pdb=" N CYS B 388 " --> pdb=" O ARG B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 430 Processing helix chain 'B' and resid 444 through 464 removed outlier: 3.853A pdb=" N ILE B 448 " --> pdb=" O MET B 444 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY B 464 " --> pdb=" O ALA B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 496 removed outlier: 3.503A pdb=" N LEU B 495 " --> pdb=" O THR B 491 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ARG B 496 " --> pdb=" O LEU B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 519 Processing helix chain 'B' and resid 551 through 561 Processing helix chain 'B' and resid 567 through 569 No H-bonds generated for 'chain 'B' and resid 567 through 569' Processing helix chain 'B' and resid 592 through 606 removed outlier: 4.165A pdb=" N LEU B 596 " --> pdb=" O ASN B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 667 removed outlier: 3.673A pdb=" N ILE B 658 " --> pdb=" O ARG B 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 687 removed outlier: 4.561A pdb=" N GLU B 687 " --> pdb=" O SER B 683 " (cutoff:3.500A) Processing helix chain 'B' and resid 696 through 701 removed outlier: 3.664A pdb=" N GLU B 699 " --> pdb=" O GLU B 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 744 through 749 removed outlier: 3.940A pdb=" N LEU B 749 " --> pdb=" O SER B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 750 through 755 removed outlier: 3.592A pdb=" N SER B 754 " --> pdb=" O GLY B 750 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ILE B 755 " --> pdb=" O VAL B 751 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 750 through 755' Processing helix chain 'B' and resid 758 through 762 removed outlier: 3.713A pdb=" N ASN B 762 " --> pdb=" O PRO B 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 763 through 775 removed outlier: 4.332A pdb=" N LYS B 775 " --> pdb=" O SER B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 783 through 787 removed outlier: 4.308A pdb=" N ASN B 786 " --> pdb=" O THR B 783 " (cutoff:3.500A) Processing helix chain 'B' and resid 807 through 812 removed outlier: 4.342A pdb=" N TYR B 811 " --> pdb=" O ARG B 807 " (cutoff:3.500A) Processing helix chain 'B' and resid 843 through 849 Processing helix chain 'B' and resid 889 through 893 Processing helix chain 'B' and resid 995 through 999 Processing helix chain 'B' and resid 1015 through 1021 removed outlier: 4.404A pdb=" N SER B1019 " --> pdb=" O HIS B1015 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ARG B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) Processing helix chain 'B' and resid 1023 through 1039 Processing helix chain 'B' and resid 1051 through 1062 removed outlier: 3.758A pdb=" N ILE B1055 " --> pdb=" O THR B1051 " (cutoff:3.500A) Processing helix chain 'B' and resid 1098 through 1103 removed outlier: 3.752A pdb=" N LYS B1102 " --> pdb=" O MET B1098 " (cutoff:3.500A) Processing helix chain 'B' and resid 1131 through 1142 Processing helix chain 'B' and resid 1143 through 1153 Processing helix chain 'B' and resid 1174 through 1178 Processing helix chain 'B' and resid 1197 through 1210 Processing helix chain 'C' and resid 26 through 40 Processing helix chain 'C' and resid 59 through 68 Processing helix chain 'C' and resid 92 through 96 removed outlier: 3.741A pdb=" N SER C 96 " --> pdb=" O ASP C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 118 No H-bonds generated for 'chain 'C' and resid 116 through 118' Processing helix chain 'C' and resid 167 through 171 Processing helix chain 'C' and resid 239 through 266 Processing helix chain 'D' and resid 51 through 76 removed outlier: 3.870A pdb=" N LYS D 60 " --> pdb=" O ARG D 56 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLU D 61 " --> pdb=" O LEU D 57 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA D 62 " --> pdb=" O VAL D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 134 removed outlier: 3.850A pdb=" N GLU D 124 " --> pdb=" O GLU D 120 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ASP D 127 " --> pdb=" O LEU D 123 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N THR D 133 " --> pdb=" O LEU D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 152 removed outlier: 3.593A pdb=" N PHE D 151 " --> pdb=" O TYR D 147 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER D 152 " --> pdb=" O LEU D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 171 removed outlier: 3.672A pdb=" N VAL D 160 " --> pdb=" O ASP D 156 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER D 169 " --> pdb=" O GLN D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 183 Processing helix chain 'D' and resid 187 through 195 Processing helix chain 'D' and resid 195 through 202 removed outlier: 3.575A pdb=" N ILE D 202 " --> pdb=" O LEU D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 216 removed outlier: 4.184A pdb=" N GLU D 213 " --> pdb=" O ARG D 209 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 26 removed outlier: 4.413A pdb=" N ARG E 7 " --> pdb=" O GLN E 3 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 36 removed outlier: 3.877A pdb=" N VAL E 35 " --> pdb=" O THR E 31 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLU E 36 " --> pdb=" O GLN E 32 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 31 through 36' Processing helix chain 'E' and resid 38 through 46 Processing helix chain 'E' and resid 54 through 59 removed outlier: 3.549A pdb=" N MET E 58 " --> pdb=" O GLN E 54 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N SER E 59 " --> pdb=" O ARG E 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 54 through 59' Processing helix chain 'E' and resid 65 through 72 removed outlier: 3.553A pdb=" N ILE E 69 " --> pdb=" O THR E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 103 Processing helix chain 'E' and resid 117 through 121 Processing helix chain 'E' and resid 138 through 141 Processing helix chain 'E' and resid 143 through 147 Processing helix chain 'E' and resid 157 through 169 Processing helix chain 'E' and resid 182 through 189 Processing helix chain 'F' and resid 86 through 103 Processing helix chain 'F' and resid 116 through 128 Processing helix chain 'G' and resid 22 through 35 Processing helix chain 'I' and resid 61 through 65 Processing helix chain 'J' and resid 17 through 25 removed outlier: 3.522A pdb=" N LEU J 25 " --> pdb=" O TYR J 21 " (cutoff:3.500A) Processing helix chain 'J' and resid 31 through 40 Processing helix chain 'J' and resid 44 through 53 removed outlier: 4.208A pdb=" N MET J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ILE J 50 " --> pdb=" O CYS J 46 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 62 removed outlier: 3.738A pdb=" N ARG J 62 " --> pdb=" O GLU J 58 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 9 removed outlier: 3.597A pdb=" N GLU K 8 " --> pdb=" O ASP K 5 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 53 removed outlier: 4.819A pdb=" N LEU K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASP K 53 " --> pdb=" O GLU K 49 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 112 Processing helix chain 'Q' and resid 23 through 35 removed outlier: 3.657A pdb=" N MET Q 27 " --> pdb=" O LYS Q 23 " (cutoff:3.500A) Processing helix chain 'Q' and resid 107 through 112 removed outlier: 3.748A pdb=" N GLU Q 112 " --> pdb=" O LYS Q 108 " (cutoff:3.500A) Processing helix chain 'Q' and resid 128 through 133 Processing helix chain 'Q' and resid 152 through 164 Processing helix chain 'Q' and resid 336 through 347 Processing helix chain 'Q' and resid 405 through 414 Processing helix chain 'Q' and resid 423 through 432 Processing helix chain 'Q' and resid 436 through 447 Processing helix chain 'M' and resid 61 through 65 removed outlier: 3.796A pdb=" N SER M 64 " --> pdb=" O LEU M 61 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ASN M 65 " --> pdb=" O GLU M 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 61 through 65' Processing helix chain 'M' and resid 74 through 82 removed outlier: 3.503A pdb=" N LYS M 80 " --> pdb=" O PHE M 76 " (cutoff:3.500A) Processing helix chain 'M' and resid 110 through 113 Processing helix chain 'M' and resid 234 through 243 removed outlier: 3.503A pdb=" N GLU M 238 " --> pdb=" O HIS M 234 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1418 through 1419 removed outlier: 3.606A pdb=" N VAL A 17 " --> pdb=" O ASP A1419 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 83 through 90 removed outlier: 10.202A pdb=" N LEU A 86 " --> pdb=" O PRO A 240 " (cutoff:3.500A) removed outlier: 11.266A pdb=" N LYS A 88 " --> pdb=" O CYS A 238 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N CYS A 238 " --> pdb=" O LYS A 88 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 106 through 107 Processing sheet with id=AA4, first strand: chain 'A' and resid 173 through 177 removed outlier: 3.757A pdb=" N THR A 173 " --> pdb=" O SER A 184 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 343 through 345 removed outlier: 4.100A pdb=" N LEU B1128 " --> pdb=" O VAL A 345 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1104 through 1106 removed outlier: 3.553A pdb=" N ALA A 349 " --> pdb=" O LEU A 489 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N MET A 456 " --> pdb=" O PHE A 444 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N VAL A 364 " --> pdb=" O LYS A 461 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ILE A 463 " --> pdb=" O VAL A 364 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N VAL A 366 " --> pdb=" O ILE A 463 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N PHE A 468 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N VAL A 352 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N LEU A 470 " --> pdb=" O VAL A 352 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N SER A 354 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 376 through 379 Processing sheet with id=AA8, first strand: chain 'A' and resid 588 through 589 removed outlier: 7.087A pdb=" N LEU A 606 " --> pdb=" O ILE A 613 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 849 through 850 removed outlier: 6.574A pdb=" N THR A 856 " --> pdb=" O ILE A 864 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 879 through 882 removed outlier: 3.610A pdb=" N GLN A 881 " --> pdb=" O TRP A 954 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1283 through 1292 removed outlier: 3.548A pdb=" N TYR A1328 " --> pdb=" O THR A1117 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1224 through 1228 removed outlier: 4.356A pdb=" N LEU A1236 " --> pdb=" O LEU A1197 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N VAL A1242 " --> pdb=" O TRP A1191 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N TRP A1191 " --> pdb=" O VAL A1242 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N SER A1150 " --> pdb=" O ARG I 45 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N ARG I 45 " --> pdb=" O SER A1150 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N ILE A1152 " --> pdb=" O VAL I 43 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 48 through 49 removed outlier: 3.974A pdb=" N ILE D 48 " --> pdb=" O ILE G 4 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLY G 59 " --> pdb=" O ILE A1445 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N VAL A1443 " --> pdb=" O ILE G 61 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 48 through 49 removed outlier: 3.974A pdb=" N ILE D 48 " --> pdb=" O ILE G 4 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N ARG G 75 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N VAL G 48 " --> pdb=" O ARG G 75 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N VAL G 77 " --> pdb=" O LEU G 46 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N SER G 37 " --> pdb=" O ILE G 45 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 68 through 70 removed outlier: 5.512A pdb=" N ASP B 131 " --> pdb=" O GLY B 93 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N ILE B 95 " --> pdb=" O PHE B 129 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N PHE B 129 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N VAL B 97 " --> pdb=" O GLY B 127 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N GLY B 127 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLY B 168 " --> pdb=" O LEU B 128 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N VAL B 130 " --> pdb=" O PHE B 166 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N PHE B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 101 through 103 Processing sheet with id=AB8, first strand: chain 'B' and resid 203 through 204 Processing sheet with id=AB9, first strand: chain 'B' and resid 404 through 407 Processing sheet with id=AC1, first strand: chain 'B' and resid 224 through 226 removed outlier: 3.523A pdb=" N GLN B 224 " --> pdb=" O GLU B 239 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N HIS B 236 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLN B 255 " --> pdb=" O THR B 272 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR B 268 " --> pdb=" O TYR B 259 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 544 through 547 removed outlier: 6.538A pdb=" N CYS B 544 " --> pdb=" O VAL B 633 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N VAL B 633 " --> pdb=" O CYS B 544 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N SER B 546 " --> pdb=" O GLY B 631 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 564 through 565 removed outlier: 5.328A pdb=" N TRP B 586 " --> pdb=" O VAL B 582 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL B 582 " --> pdb=" O TRP B 586 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLY B 588 " --> pdb=" O VAL B 580 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 650 through 651 Processing sheet with id=AC5, first strand: chain 'B' and resid 792 through 796 removed outlier: 3.518A pdb=" N ALA B 793 " --> pdb=" O PHE B 856 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE B 795 " --> pdb=" O LEU B 854 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N PHE B 963 " --> pdb=" O VAL B 954 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N VAL B 954 " --> pdb=" O PHE B 963 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N LYS B 965 " --> pdb=" O VAL B 952 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N VAL B 952 " --> pdb=" O LYS B 965 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 1069 through 1070 removed outlier: 4.466A pdb=" N PHE B1086 " --> pdb=" O ILE B 827 " (cutoff:3.500A) removed outlier: 9.006A pdb=" N LEU B1010 " --> pdb=" O ASN B 822 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ILE B 824 " --> pdb=" O LEU B1010 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N ILE B1012 " --> pdb=" O ILE B 824 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ALA B 826 " --> pdb=" O ILE B1012 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N MET B 839 " --> pdb=" O GLY B 991 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N THR B 993 " --> pdb=" O MET B 839 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N MET B 841 " --> pdb=" O THR B 993 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA B 981 " --> pdb=" O GLN B1093 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 1158 through 1162 Processing sheet with id=AC8, first strand: chain 'C' and resid 8 through 13 removed outlier: 6.800A pdb=" N ASP C 19 " --> pdb=" O ARG C 11 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ALA C 13 " --> pdb=" O ASN C 17 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ASN C 17 " --> pdb=" O ALA C 13 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ASN C 231 " --> pdb=" O GLU C 177 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 119 through 120 removed outlier: 6.144A pdb=" N GLU C 152 " --> pdb=" O ASN C 54 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ASN C 54 " --> pdb=" O GLU C 152 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N LYS C 154 " --> pdb=" O GLU C 52 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N LYS C 160 " --> pdb=" O ILE C 46 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N ILE C 46 " --> pdb=" O LYS C 160 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N VAL L 65 " --> pdb=" O VAL C 51 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 72 through 74 removed outlier: 4.856A pdb=" N GLN C 73 " --> pdb=" O GLY C 130 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 111 through 114 removed outlier: 3.986A pdb=" N CYS C 145 " --> pdb=" O VAL C 113 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 36 through 38 Processing sheet with id=AD4, first strand: chain 'E' and resid 78 through 80 removed outlier: 6.358A pdb=" N TRP E 79 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N VAL E 111 " --> pdb=" O TRP E 79 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 152 through 155 removed outlier: 3.503A pdb=" N ARG E 200 " --> pdb=" O TYR E 208 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 86 through 93 removed outlier: 5.430A pdb=" N VAL G 91 " --> pdb=" O GLN G 102 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N GLN G 102 " --> pdb=" O VAL G 91 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER G 93 " --> pdb=" O GLU G 100 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N LYS G 107 " --> pdb=" O ALA G 159 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N GLY G 161 " --> pdb=" O LYS G 107 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N PHE G 109 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N SER G 162 " --> pdb=" O ILE G 147 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N ILE G 147 " --> pdb=" O SER G 162 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 121 through 122 removed outlier: 3.895A pdb=" N SER G 129 " --> pdb=" O ASN G 122 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 54 through 58 removed outlier: 3.782A pdb=" N ASP H 8 " --> pdb=" O VAL H 57 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N GLU H 27 " --> pdb=" O SER H 13 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N LEU H 111 " --> pdb=" O GLU H 106 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N GLU H 106 " --> pdb=" O LEU H 111 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ALA H 113 " --> pdb=" O PHE H 104 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N PHE H 104 " --> pdb=" O ALA H 113 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N TYR H 115 " --> pdb=" O TYR H 102 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 14 through 18 Processing sheet with id=AE1, first strand: chain 'I' and resid 84 through 87 Processing sheet with id=AE2, first strand: chain 'K' and resid 19 through 23 Processing sheet with id=AE3, first strand: chain 'Q' and resid 102 through 104 removed outlier: 4.148A pdb=" N GLY M 93 " --> pdb=" O LEU Q 103 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ILE M 104 " --> pdb=" O LEU M 122 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N GLU M 221 " --> pdb=" O THR M 125 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N VAL M 68 " --> pdb=" O CYS M 219 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N GLU M 221 " --> pdb=" O VAL M 68 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LEU M 70 " --> pdb=" O GLU M 221 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N GLN M 223 " --> pdb=" O LEU M 70 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ARG M 72 " --> pdb=" O GLN M 223 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N MET M 225 " --> pdb=" O ARG M 72 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N GLN M 67 " --> pdb=" O VAL Q 378 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N VAL Q 378 " --> pdb=" O GLN M 67 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'Q' and resid 102 through 104 removed outlier: 4.148A pdb=" N GLY M 93 " --> pdb=" O LEU Q 103 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ILE M 104 " --> pdb=" O LEU M 122 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N GLU M 221 " --> pdb=" O THR M 125 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL M 134 " --> pdb=" O VAL M 215 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N THR M 217 " --> pdb=" O GLU M 132 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N GLU M 132 " --> pdb=" O THR M 217 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N THR Q 116 " --> pdb=" O LYS Q 391 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N TYR Q 393 " --> pdb=" O THR Q 116 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N LEU Q 118 " --> pdb=" O TYR Q 393 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N PHE Q 395 " --> pdb=" O LEU Q 118 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N LYS Q 120 " --> pdb=" O PHE Q 395 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N ALA Q 397 " --> pdb=" O LYS Q 120 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N GLN Q 122 " --> pdb=" O ALA Q 397 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N THR Q 360 " --> pdb=" O ARG Q 398 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N TRP Q 350 " --> pdb=" O GLY Q 363 " (cutoff:3.500A) 1341 hydrogen bonds defined for protein. 3753 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 85 hydrogen bonds 170 hydrogen bond angles 0 basepair planarities 36 basepair parallelities 66 stacking parallelities Total time for adding SS restraints: 20.88 Time building geometry restraints manager: 18.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 11531 1.34 - 1.46: 8046 1.46 - 1.58: 16884 1.58 - 1.71: 185 1.71 - 1.83: 312 Bond restraints: 36958 Sorted by residual: bond pdb=" O3' C R 15 " pdb=" P C R 16 " ideal model delta sigma weight residual 1.607 1.666 -0.059 1.50e-02 4.44e+03 1.56e+01 bond pdb=" O3' U R 13 " pdb=" P C R 14 " ideal model delta sigma weight residual 1.607 1.655 -0.048 1.50e-02 4.44e+03 1.03e+01 bond pdb=" N ASP A 188 " pdb=" CA ASP A 188 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.29e-02 6.01e+03 9.41e+00 bond pdb=" N ASP B1186 " pdb=" CA ASP B1186 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.15e-02 7.56e+03 8.54e+00 bond pdb=" N CYS B1182 " pdb=" CA CYS B1182 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.18e-02 7.18e+03 8.53e+00 ... (remaining 36953 not shown) Histogram of bond angle deviations from ideal: 96.07 - 103.69: 720 103.69 - 111.31: 16029 111.31 - 118.93: 14211 118.93 - 126.55: 18664 126.55 - 134.17: 702 Bond angle restraints: 50326 Sorted by residual: angle pdb=" N PRO Q 421 " pdb=" CA PRO Q 421 " pdb=" CB PRO Q 421 " ideal model delta sigma weight residual 103.27 110.16 -6.89 9.00e-01 1.23e+00 5.87e+01 angle pdb=" C THR B 79 " pdb=" N GLU B 80 " pdb=" CA GLU B 80 " ideal model delta sigma weight residual 121.70 133.32 -11.62 1.80e+00 3.09e-01 4.17e+01 angle pdb=" C ILE B 918 " pdb=" N SER B 919 " pdb=" CA SER B 919 " ideal model delta sigma weight residual 121.70 131.16 -9.46 1.80e+00 3.09e-01 2.76e+01 angle pdb=" C VAL A1107 " pdb=" N ALA A1108 " pdb=" CA ALA A1108 " ideal model delta sigma weight residual 121.70 130.85 -9.15 1.80e+00 3.09e-01 2.58e+01 angle pdb=" C4' A R 12 " pdb=" C3' A R 12 " pdb=" O3' A R 12 " ideal model delta sigma weight residual 113.00 105.70 7.30 1.50e+00 4.44e-01 2.37e+01 ... (remaining 50321 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.82: 21641 35.82 - 71.63: 738 71.63 - 107.45: 51 107.45 - 143.27: 3 143.27 - 179.08: 1 Dihedral angle restraints: 22434 sinusoidal: 9894 harmonic: 12540 Sorted by residual: dihedral pdb=" CA HIS B 363 " pdb=" C HIS B 363 " pdb=" N ILE B 364 " pdb=" CA ILE B 364 " ideal model delta harmonic sigma weight residual -180.00 -133.31 -46.69 0 5.00e+00 4.00e-02 8.72e+01 dihedral pdb=" CA LYS B 510 " pdb=" C LYS B 510 " pdb=" N PRO B 511 " pdb=" CA PRO B 511 " ideal model delta harmonic sigma weight residual -180.00 -134.49 -45.51 0 5.00e+00 4.00e-02 8.28e+01 dihedral pdb=" CA PHE A 252 " pdb=" C PHE A 252 " pdb=" N ASN A 253 " pdb=" CA ASN A 253 " ideal model delta harmonic sigma weight residual 180.00 138.65 41.35 0 5.00e+00 4.00e-02 6.84e+01 ... (remaining 22431 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 4653 0.059 - 0.118: 903 0.118 - 0.177: 98 0.177 - 0.236: 10 0.236 - 0.295: 2 Chirality restraints: 5666 Sorted by residual: chirality pdb=" C3' DG O -7 " pdb=" C4' DG O -7 " pdb=" O3' DG O -7 " pdb=" C2' DG O -7 " both_signs ideal model delta sigma weight residual False -2.66 -2.36 -0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" CB VAL C 243 " pdb=" CA VAL C 243 " pdb=" CG1 VAL C 243 " pdb=" CG2 VAL C 243 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CB VAL A 474 " pdb=" CA VAL A 474 " pdb=" CG1 VAL A 474 " pdb=" CG2 VAL A 474 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.20e+00 ... (remaining 5663 not shown) Planarity restraints: 6198 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 510 " 0.065 5.00e-02 4.00e+02 9.72e-02 1.51e+01 pdb=" N PRO B 511 " -0.168 5.00e-02 4.00e+02 pdb=" CA PRO B 511 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO B 511 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DA O -3 " -0.005 2.00e-02 2.50e+03 1.59e-02 6.98e+00 pdb=" N9 DA O -3 " 0.034 2.00e-02 2.50e+03 pdb=" C8 DA O -3 " -0.031 2.00e-02 2.50e+03 pdb=" N7 DA O -3 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DA O -3 " 0.003 2.00e-02 2.50e+03 pdb=" C6 DA O -3 " 0.004 2.00e-02 2.50e+03 pdb=" N6 DA O -3 " 0.003 2.00e-02 2.50e+03 pdb=" N1 DA O -3 " 0.004 2.00e-02 2.50e+03 pdb=" C2 DA O -3 " -0.023 2.00e-02 2.50e+03 pdb=" N3 DA O -3 " 0.005 2.00e-02 2.50e+03 pdb=" C4 DA O -3 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR F 82 " -0.043 5.00e-02 4.00e+02 6.59e-02 6.94e+00 pdb=" N PRO F 83 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO F 83 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO F 83 " -0.036 5.00e-02 4.00e+02 ... (remaining 6195 not shown) Histogram of nonbonded interaction distances: 1.24 - 1.97: 2 1.97 - 2.71: 1923 2.71 - 3.44: 57123 3.44 - 4.17: 87417 4.17 - 4.90: 146697 Nonbonded interactions: 293162 Sorted by model distance: nonbonded pdb=" OP1 U R 13 " pdb="MG MG R 101 " model vdw 1.243 2.170 nonbonded pdb=" SG CYS B1185 " pdb=" NZ LYS D 16 " model vdw 1.793 2.880 nonbonded pdb=" O CYS A 67 " pdb="ZN ZN A1802 " model vdw 2.000 2.230 nonbonded pdb=" N GLY A1395 " pdb="MG MG A1803 " model vdw 2.011 2.250 nonbonded pdb=" O2' C R 14 " pdb=" O2 C R 14 " model vdw 2.025 2.440 ... (remaining 293157 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=0.95 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 0.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.220 Construct map_model_manager: 0.030 Extract box with map and model: 4.570 Check model and map are aligned: 0.560 Set scattering table: 0.310 Process input model: 118.200 Find NCS groups from input model: 1.110 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 128.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6924 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 36958 Z= 0.332 Angle : 0.800 12.213 50326 Z= 0.468 Chirality : 0.046 0.295 5666 Planarity : 0.004 0.097 6198 Dihedral : 16.824 179.082 14308 Min Nonbonded Distance : 1.243 Molprobity Statistics. All-atom Clashscore : 19.59 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.33 % Favored : 89.55 % Rotamer: Outliers : 0.19 % Allowed : 0.48 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.69 % Cis-general : 0.37 % Twisted Proline : 1.08 % Twisted General : 0.12 % 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: -1.38 (0.13), residues: 4259 helix: 0.55 (0.14), residues: 1359 sheet: -0.68 (0.20), residues: 685 loop : -2.01 (0.13), residues: 2215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 954 HIS 0.011 0.002 HIS A 399 PHE 0.022 0.002 PHE A 81 TYR 0.016 0.002 TYR B 679 ARG 0.009 0.001 ARG F 135 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8518 Ramachandran restraints generated. 4259 Oldfield, 0 Emsley, 4259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8518 Ramachandran restraints generated. 4259 Oldfield, 0 Emsley, 4259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1000 residues out of total 3815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 993 time to evaluate : 4.213 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: A 92 HIS cc_start: 0.8136 (t-90) cc_final: 0.6797 (t-90) REVERT: A 95 PHE cc_start: 0.9282 (m-80) cc_final: 0.8559 (m-80) REVERT: A 117 GLU cc_start: 0.9604 (tt0) cc_final: 0.9375 (tm-30) REVERT: A 225 ASN cc_start: 0.8861 (t0) cc_final: 0.8515 (t0) REVERT: A 234 MET cc_start: 0.9210 (ttm) cc_final: 0.8826 (ttm) REVERT: A 247 ARG cc_start: 0.8725 (ptt90) cc_final: 0.8202 (ptt-90) REVERT: A 445 ASN cc_start: 0.8527 (t0) cc_final: 0.8112 (t0) REVERT: A 450 LEU cc_start: 0.9151 (mm) cc_final: 0.8810 (tp) REVERT: A 456 MET cc_start: 0.8661 (mpp) cc_final: 0.7988 (mpp) REVERT: A 463 ILE cc_start: 0.9227 (mm) cc_final: 0.8897 (mm) REVERT: A 478 TYR cc_start: 0.7872 (m-80) cc_final: 0.6907 (m-80) REVERT: A 505 CYS cc_start: 0.9166 (m) cc_final: 0.8693 (m) REVERT: A 521 MET cc_start: 0.8737 (mmm) cc_final: 0.8170 (mmm) REVERT: A 535 THR cc_start: 0.8666 (m) cc_final: 0.8453 (t) REVERT: A 549 MET cc_start: 0.9141 (ptp) cc_final: 0.8874 (ptm) REVERT: A 662 PHE cc_start: 0.8432 (t80) cc_final: 0.7939 (t80) REVERT: A 696 GLU cc_start: 0.9163 (tt0) cc_final: 0.8887 (tp30) REVERT: A 741 ASN cc_start: 0.8541 (t0) cc_final: 0.8325 (t0) REVERT: A 786 HIS cc_start: 0.8452 (m-70) cc_final: 0.7735 (m-70) REVERT: A 846 GLU cc_start: 0.8753 (mt-10) cc_final: 0.8450 (mt-10) REVERT: A 847 ASP cc_start: 0.8112 (p0) cc_final: 0.7624 (p0) REVERT: A 1063 MET cc_start: 0.8329 (mmp) cc_final: 0.8099 (mmm) REVERT: A 1120 LEU cc_start: 0.9641 (mt) cc_final: 0.9234 (tp) REVERT: A 1147 THR cc_start: 0.9381 (m) cc_final: 0.9144 (p) REVERT: A 1309 ASP cc_start: 0.9069 (t70) cc_final: 0.8292 (p0) REVERT: A 1364 ASN cc_start: 0.8584 (t0) cc_final: 0.8317 (t0) REVERT: B 239 GLU cc_start: 0.8068 (tt0) cc_final: 0.7405 (tm-30) REVERT: B 258 LEU cc_start: 0.9133 (tp) cc_final: 0.8924 (tp) REVERT: B 292 ILE cc_start: 0.9092 (mt) cc_final: 0.8852 (mm) REVERT: B 296 GLU cc_start: 0.9348 (mm-30) cc_final: 0.8971 (mp0) REVERT: B 361 LEU cc_start: 0.9026 (tp) cc_final: 0.8649 (tt) REVERT: B 396 ASP cc_start: 0.7756 (m-30) cc_final: 0.7373 (m-30) REVERT: B 404 LYS cc_start: 0.9228 (mttt) cc_final: 0.8828 (mttt) REVERT: B 566 LEU cc_start: 0.9364 (mt) cc_final: 0.9090 (mt) REVERT: B 576 ASP cc_start: 0.9197 (p0) cc_final: 0.8888 (t70) REVERT: B 610 ASN cc_start: 0.8715 (t0) cc_final: 0.8468 (t0) REVERT: B 705 MET cc_start: 0.7655 (mmm) cc_final: 0.6798 (mmm) REVERT: B 767 ASN cc_start: 0.8107 (m110) cc_final: 0.7859 (m110) REVERT: B 809 MET cc_start: 0.8155 (pmm) cc_final: 0.7839 (pmm) REVERT: B 834 ASN cc_start: 0.8727 (p0) cc_final: 0.8114 (p0) REVERT: B 846 ILE cc_start: 0.9647 (mm) cc_final: 0.9338 (tt) REVERT: B 847 ASP cc_start: 0.8844 (m-30) cc_final: 0.8525 (m-30) REVERT: B 860 MET cc_start: 0.8554 (ppp) cc_final: 0.7799 (ppp) REVERT: B 963 PHE cc_start: 0.8588 (t80) cc_final: 0.7822 (t80) REVERT: B 980 PHE cc_start: 0.8527 (m-10) cc_final: 0.8274 (m-10) REVERT: B 1069 PHE cc_start: 0.8782 (m-10) cc_final: 0.8444 (m-10) REVERT: B 1082 MET cc_start: 0.9052 (tpt) cc_final: 0.8691 (tpt) REVERT: B 1133 MET cc_start: 0.9181 (mtp) cc_final: 0.8759 (mtm) REVERT: B 1152 MET cc_start: 0.8178 (mmm) cc_final: 0.7549 (mmm) REVERT: B 1168 LEU cc_start: 0.8802 (mm) cc_final: 0.8588 (mm) REVERT: B 1183 LYS cc_start: 0.6857 (OUTLIER) cc_final: 0.6548 (mmmt) REVERT: B 1206 GLU cc_start: 0.9245 (mp0) cc_final: 0.9011 (mp0) REVERT: C 15 LYS cc_start: 0.9151 (tttm) cc_final: 0.8907 (tmtt) REVERT: C 16 ASP cc_start: 0.9122 (p0) cc_final: 0.8633 (p0) REVERT: C 46 ILE cc_start: 0.9253 (mt) cc_final: 0.8688 (tp) REVERT: C 52 GLU cc_start: 0.8992 (tm-30) cc_final: 0.8752 (tm-30) REVERT: C 77 ILE cc_start: 0.9256 (tp) cc_final: 0.9048 (mm) REVERT: C 157 CYS cc_start: 0.9349 (m) cc_final: 0.9111 (m) REVERT: C 165 LYS cc_start: 0.9045 (tttt) cc_final: 0.8688 (tttt) REVERT: C 228 PHE cc_start: 0.8622 (m-10) cc_final: 0.8149 (m-10) REVERT: C 233 GLU cc_start: 0.8888 (tt0) cc_final: 0.8023 (tt0) REVERT: E 7 ARG cc_start: 0.9075 (ptm-80) cc_final: 0.8657 (ttp80) REVERT: E 18 THR cc_start: 0.8663 (p) cc_final: 0.8427 (p) REVERT: E 75 MET cc_start: 0.7567 (mpp) cc_final: 0.7352 (mpp) REVERT: E 140 LEU cc_start: 0.9530 (tp) cc_final: 0.9299 (tp) REVERT: F 81 THR cc_start: 0.9032 (m) cc_final: 0.8529 (p) REVERT: F 88 TYR cc_start: 0.7871 (m-10) cc_final: 0.7577 (m-10) REVERT: F 109 VAL cc_start: 0.8708 (p) cc_final: 0.8494 (p) REVERT: G 32 GLU cc_start: 0.8758 (mp0) cc_final: 0.8495 (mp0) REVERT: G 42 PHE cc_start: 0.8656 (m-80) cc_final: 0.8454 (m-80) REVERT: G 44 TYR cc_start: 0.8361 (t80) cc_final: 0.7910 (t80) REVERT: G 55 ASP cc_start: 0.7876 (m-30) cc_final: 0.7636 (m-30) REVERT: H 1 MET cc_start: 0.0921 (pmm) cc_final: -0.0576 (tpt) REVERT: H 10 PHE cc_start: 0.8814 (m-80) cc_final: 0.7796 (m-10) REVERT: H 97 MET cc_start: 0.7280 (ppp) cc_final: 0.6948 (ppp) REVERT: H 102 TYR cc_start: 0.8635 (p90) cc_final: 0.8230 (p90) REVERT: H 116 TYR cc_start: 0.7773 (m-80) cc_final: 0.7538 (m-80) REVERT: H 123 MET cc_start: 0.9248 (ppp) cc_final: 0.9038 (ppp) REVERT: H 133 ASN cc_start: 0.9055 (t0) cc_final: 0.8833 (t0) REVERT: I 65 ASP cc_start: 0.9471 (t70) cc_final: 0.9105 (t70) REVERT: I 68 LEU cc_start: 0.9378 (mp) cc_final: 0.9019 (mp) REVERT: J 13 VAL cc_start: 0.9448 (m) cc_final: 0.9199 (m) REVERT: K 18 LYS cc_start: 0.8324 (mmmm) cc_final: 0.8068 (mtmt) REVERT: K 37 LYS cc_start: 0.8630 (mmtt) cc_final: 0.8386 (mmmt) REVERT: K 38 GLU cc_start: 0.9403 (mp0) cc_final: 0.9082 (mp0) REVERT: K 53 ASP cc_start: 0.8339 (t0) cc_final: 0.7852 (t70) REVERT: K 91 CYS cc_start: 0.9498 (m) cc_final: 0.9256 (m) REVERT: K 92 ASN cc_start: 0.9385 (m110) cc_final: 0.9030 (m-40) REVERT: K 106 GLU cc_start: 0.8638 (mp0) cc_final: 0.8374 (mp0) REVERT: Q 393 TYR cc_start: 0.7403 (m-80) cc_final: 0.6946 (m-10) REVERT: M 129 VAL cc_start: 0.7556 (t) cc_final: 0.5907 (t) outliers start: 7 outliers final: 0 residues processed: 999 average time/residue: 0.4984 time to fit residues: 802.1464 Evaluate side-chains 607 residues out of total 3815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 606 time to evaluate : 3.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1183 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 366 optimal weight: 8.9990 chunk 328 optimal weight: 10.0000 chunk 182 optimal weight: 7.9990 chunk 112 optimal weight: 10.0000 chunk 221 optimal weight: 8.9990 chunk 175 optimal weight: 3.9990 chunk 340 optimal weight: 30.0000 chunk 131 optimal weight: 20.0000 chunk 206 optimal weight: 4.9990 chunk 253 optimal weight: 3.9990 chunk 394 optimal weight: 2.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 ASN A 363 GLN A 399 HIS ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 510 GLN A 654 ASN A 742 ASN ** A 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN ** A1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1427 ASN B 538 ASN ** B 834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 842 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 881 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 74 GLN ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7045 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 36958 Z= 0.293 Angle : 0.773 11.942 50326 Z= 0.404 Chirality : 0.047 0.304 5666 Planarity : 0.005 0.072 6198 Dihedral : 16.089 172.173 5807 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 21.43 Ramachandran Plot: Outliers : 0.05 % Allowed : 11.04 % Favored : 88.92 % Rotamer: Outliers : 2.54 % Allowed : 13.44 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.69 % Cis-general : 0.37 % Twisted Proline : 1.08 % Twisted General : 0.15 % 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: -1.37 (0.13), residues: 4259 helix: 0.57 (0.14), residues: 1401 sheet: -0.58 (0.21), residues: 643 loop : -2.07 (0.13), residues: 2215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 954 HIS 0.011 0.002 HIS A1387 PHE 0.034 0.002 PHE G 121 TYR 0.022 0.002 TYR B 830 ARG 0.008 0.001 ARG F 97 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8518 Ramachandran restraints generated. 4259 Oldfield, 0 Emsley, 4259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8518 Ramachandran restraints generated. 4259 Oldfield, 0 Emsley, 4259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 721 residues out of total 3815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 626 time to evaluate : 4.294 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: A 41 MET cc_start: 0.7273 (tpt) cc_final: 0.7060 (tpt) REVERT: A 92 HIS cc_start: 0.8143 (t-90) cc_final: 0.6970 (t-90) REVERT: A 117 GLU cc_start: 0.9652 (tt0) cc_final: 0.9452 (tm-30) REVERT: A 122 MET cc_start: 0.9298 (tmm) cc_final: 0.8930 (ppp) REVERT: A 225 ASN cc_start: 0.8938 (t0) cc_final: 0.8540 (t0) REVERT: A 304 MET cc_start: 0.9129 (tpt) cc_final: 0.8864 (tpt) REVERT: A 437 MET cc_start: 0.7549 (mtt) cc_final: 0.7296 (ptp) REVERT: A 445 ASN cc_start: 0.9014 (t0) cc_final: 0.8474 (t0) REVERT: A 450 LEU cc_start: 0.9128 (mm) cc_final: 0.8808 (tp) REVERT: A 456 MET cc_start: 0.8765 (mpp) cc_final: 0.8384 (mpp) REVERT: A 478 TYR cc_start: 0.8221 (m-80) cc_final: 0.7954 (m-80) REVERT: A 487 MET cc_start: 0.7384 (mmm) cc_final: 0.6669 (mmm) REVERT: A 505 CYS cc_start: 0.9064 (m) cc_final: 0.8654 (m) REVERT: A 521 MET cc_start: 0.8818 (mmm) cc_final: 0.8205 (mmm) REVERT: A 662 PHE cc_start: 0.8637 (t80) cc_final: 0.8295 (t80) REVERT: A 696 GLU cc_start: 0.9138 (tt0) cc_final: 0.8903 (tp30) REVERT: A 741 ASN cc_start: 0.8762 (t0) cc_final: 0.8436 (t0) REVERT: A 761 MET cc_start: 0.9041 (mtm) cc_final: 0.8506 (mmp) REVERT: A 786 HIS cc_start: 0.8627 (m-70) cc_final: 0.7732 (m-70) REVERT: A 847 ASP cc_start: 0.8107 (p0) cc_final: 0.7599 (p0) REVERT: A 1120 LEU cc_start: 0.9671 (mt) cc_final: 0.9232 (tp) REVERT: A 1277 GLU cc_start: 0.9541 (pm20) cc_final: 0.9277 (pm20) REVERT: A 1285 MET cc_start: 0.8602 (mmm) cc_final: 0.8343 (mmm) REVERT: A 1315 GLU cc_start: 0.8703 (mp0) cc_final: 0.8491 (mp0) REVERT: A 1317 MET cc_start: 0.9359 (mmm) cc_final: 0.8948 (mmm) REVERT: A 1364 ASN cc_start: 0.8788 (t0) cc_final: 0.8533 (t0) REVERT: A 1427 ASN cc_start: 0.8487 (m-40) cc_final: 0.8234 (t0) REVERT: B 173 MET cc_start: 0.5994 (tpt) cc_final: 0.5619 (tpt) REVERT: B 239 GLU cc_start: 0.8049 (tt0) cc_final: 0.7630 (tm-30) REVERT: B 292 ILE cc_start: 0.9160 (mt) cc_final: 0.8901 (mm) REVERT: B 296 GLU cc_start: 0.9370 (mm-30) cc_final: 0.8996 (mp0) REVERT: B 313 MET cc_start: 0.9507 (mmp) cc_final: 0.9298 (tpp) REVERT: B 361 LEU cc_start: 0.9101 (tp) cc_final: 0.8548 (tt) REVERT: B 381 MET cc_start: 0.9441 (OUTLIER) cc_final: 0.9173 (tpt) REVERT: B 396 ASP cc_start: 0.7788 (m-30) cc_final: 0.7473 (m-30) REVERT: B 404 LYS cc_start: 0.9204 (mttt) cc_final: 0.8871 (mttt) REVERT: B 481 GLN cc_start: 0.8409 (mt0) cc_final: 0.8183 (mt0) REVERT: B 610 ASN cc_start: 0.8731 (t0) cc_final: 0.8489 (t0) REVERT: B 698 GLU cc_start: 0.8494 (mp0) cc_final: 0.8239 (mp0) REVERT: B 705 MET cc_start: 0.7967 (mmm) cc_final: 0.7012 (mmm) REVERT: B 767 ASN cc_start: 0.8204 (m110) cc_final: 0.7887 (m110) REVERT: B 773 MET cc_start: 0.8686 (ttm) cc_final: 0.8465 (ttm) REVERT: B 790 ASP cc_start: 0.8037 (t70) cc_final: 0.7780 (t70) REVERT: B 809 MET cc_start: 0.8244 (pmm) cc_final: 0.7793 (pmm) REVERT: B 834 ASN cc_start: 0.8564 (p0) cc_final: 0.7890 (p0) REVERT: B 846 ILE cc_start: 0.9659 (mm) cc_final: 0.9440 (tt) REVERT: B 860 MET cc_start: 0.8416 (ppp) cc_final: 0.7867 (ppp) REVERT: B 963 PHE cc_start: 0.8605 (t80) cc_final: 0.8068 (t80) REVERT: B 967 ARG cc_start: 0.8705 (ttp-170) cc_final: 0.8179 (mtp-110) REVERT: B 999 MET cc_start: 0.8968 (tpp) cc_final: 0.8361 (mmt) REVERT: B 1082 MET cc_start: 0.9043 (tpt) cc_final: 0.8722 (tpt) REVERT: B 1095 LEU cc_start: 0.9172 (mm) cc_final: 0.8836 (mm) REVERT: B 1133 MET cc_start: 0.9159 (mtp) cc_final: 0.8660 (mtm) REVERT: B 1168 LEU cc_start: 0.8929 (mm) cc_final: 0.8699 (mm) REVERT: C 16 ASP cc_start: 0.9171 (p0) cc_final: 0.8773 (p0) REVERT: C 37 MET cc_start: 0.9331 (tpp) cc_final: 0.9065 (tpp) REVERT: C 46 ILE cc_start: 0.9226 (mt) cc_final: 0.8726 (tp) REVERT: C 52 GLU cc_start: 0.8785 (tm-30) cc_final: 0.8515 (tm-30) REVERT: C 157 CYS cc_start: 0.9289 (m) cc_final: 0.8932 (m) REVERT: C 165 LYS cc_start: 0.9036 (tttt) cc_final: 0.8719 (tttm) REVERT: C 169 LYS cc_start: 0.9348 (mtpt) cc_final: 0.9131 (ptpp) REVERT: E 7 ARG cc_start: 0.9072 (ptm-80) cc_final: 0.8663 (ttp80) REVERT: E 58 MET cc_start: 0.9341 (ttp) cc_final: 0.8978 (tmm) REVERT: E 110 PHE cc_start: 0.9231 (t80) cc_final: 0.9001 (t80) REVERT: E 115 ASN cc_start: 0.9201 (p0) cc_final: 0.8990 (p0) REVERT: E 121 MET cc_start: 0.9296 (ppp) cc_final: 0.9057 (ppp) REVERT: E 194 GLU cc_start: 0.8222 (mp0) cc_final: 0.8000 (mp0) REVERT: E 208 TYR cc_start: 0.7585 (t80) cc_final: 0.6949 (t80) REVERT: E 211 TYR cc_start: 0.8863 (m-80) cc_final: 0.8596 (m-80) REVERT: F 81 THR cc_start: 0.9042 (m) cc_final: 0.8439 (p) REVERT: F 88 TYR cc_start: 0.7801 (m-10) cc_final: 0.7541 (m-10) REVERT: F 103 MET cc_start: 0.9158 (tmm) cc_final: 0.8860 (tmm) REVERT: F 124 GLU cc_start: 0.9067 (tm-30) cc_final: 0.8707 (tm-30) REVERT: G 21 ARG cc_start: 0.7875 (ttp80) cc_final: 0.7574 (ttp80) REVERT: H 1 MET cc_start: 0.1013 (pmm) cc_final: -0.0364 (tpt) REVERT: H 10 PHE cc_start: 0.8594 (m-80) cc_final: 0.7525 (m-80) REVERT: H 97 MET cc_start: 0.8145 (ppp) cc_final: 0.7751 (ppp) REVERT: H 123 MET cc_start: 0.9073 (ppp) cc_final: 0.8722 (ppp) REVERT: H 133 ASN cc_start: 0.9103 (t0) cc_final: 0.8883 (t0) REVERT: I 65 ASP cc_start: 0.9351 (t70) cc_final: 0.8800 (t0) REVERT: I 68 LEU cc_start: 0.9460 (mp) cc_final: 0.8968 (mp) REVERT: J 52 THR cc_start: 0.9065 (t) cc_final: 0.8803 (t) REVERT: K 38 GLU cc_start: 0.9321 (mp0) cc_final: 0.9100 (mp0) REVERT: K 53 ASP cc_start: 0.8497 (t0) cc_final: 0.8013 (t70) REVERT: K 92 ASN cc_start: 0.9366 (m110) cc_final: 0.9018 (m-40) REVERT: Q 365 TYR cc_start: 0.7766 (t80) cc_final: 0.6899 (t80) REVERT: M 121 ASP cc_start: 0.8073 (OUTLIER) cc_final: 0.7703 (p0) outliers start: 95 outliers final: 67 residues processed: 681 average time/residue: 0.4468 time to fit residues: 503.8451 Evaluate side-chains 601 residues out of total 3815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 532 time to evaluate : 3.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 399 HIS Chi-restraints excluded: chain A residue 496 GLU Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain A residue 781 ASP Chi-restraints excluded: chain A residue 834 THR Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 894 GLU Chi-restraints excluded: chain A residue 953 ASN Chi-restraints excluded: chain A residue 1013 ASP Chi-restraints excluded: chain A residue 1111 MET Chi-restraints excluded: chain A residue 1356 ILE Chi-restraints excluded: chain A residue 1385 THR Chi-restraints excluded: chain A residue 1405 THR Chi-restraints excluded: chain A residue 1424 VAL Chi-restraints excluded: chain A residue 1450 LEU Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 310 MET Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 381 MET Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 432 MET Chi-restraints excluded: chain B residue 445 LYS Chi-restraints excluded: chain B residue 465 ASN Chi-restraints excluded: chain B residue 516 ASN Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 789 MET Chi-restraints excluded: chain B residue 854 LEU Chi-restraints excluded: chain B residue 1049 ASP Chi-restraints excluded: chain B residue 1066 SER Chi-restraints excluded: chain B residue 1103 ILE Chi-restraints excluded: chain B residue 1156 ASP Chi-restraints excluded: chain B residue 1175 LEU Chi-restraints excluded: chain B residue 1202 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 145 CYS Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain G residue 35 GLU Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 168 LEU Chi-restraints excluded: chain H residue 130 ARG Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 37 GLU Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain L residue 53 HIS Chi-restraints excluded: chain Q residue 106 ILE Chi-restraints excluded: chain Q residue 119 LEU Chi-restraints excluded: chain M residue 121 ASP Chi-restraints excluded: chain M residue 125 THR Chi-restraints excluded: chain M residue 214 ILE Chi-restraints excluded: chain M residue 236 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 219 optimal weight: 10.0000 chunk 122 optimal weight: 7.9990 chunk 328 optimal weight: 9.9990 chunk 268 optimal weight: 5.9990 chunk 108 optimal weight: 0.9990 chunk 394 optimal weight: 3.9990 chunk 426 optimal weight: 30.0000 chunk 351 optimal weight: 20.0000 chunk 391 optimal weight: 7.9990 chunk 134 optimal weight: 0.0670 chunk 316 optimal weight: 9.9990 overall best weight: 3.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 439 ASN ** A 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 451 HIS A 654 ASN A 767 GLN ** A 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1128 GLN ** B 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 842 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 881 ASN ** B1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 43 ASN ** H 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 36958 Z= 0.242 Angle : 0.705 11.991 50326 Z= 0.368 Chirality : 0.045 0.250 5666 Planarity : 0.005 0.066 6198 Dihedral : 16.010 169.050 5803 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 19.85 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.12 % Favored : 89.83 % Rotamer: Outliers : 3.21 % Allowed : 16.55 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.69 % Cis-general : 0.37 % Twisted Proline : 1.08 % Twisted General : 0.15 % 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: -1.25 (0.13), residues: 4259 helix: 0.74 (0.14), residues: 1403 sheet: -0.66 (0.20), residues: 675 loop : -2.01 (0.13), residues: 2181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP M 81 HIS 0.012 0.001 HIS A 399 PHE 0.031 0.002 PHE J 8 TYR 0.037 0.002 TYR Q 373 ARG 0.011 0.000 ARG M 72 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8518 Ramachandran restraints generated. 4259 Oldfield, 0 Emsley, 4259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8518 Ramachandran restraints generated. 4259 Oldfield, 0 Emsley, 4259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 694 residues out of total 3815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 574 time to evaluate : 4.449 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: A 41 MET cc_start: 0.7217 (tpt) cc_final: 0.6639 (tpt) REVERT: A 43 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.8083 (mp0) REVERT: A 92 HIS cc_start: 0.8152 (t-90) cc_final: 0.6085 (t-90) REVERT: A 95 PHE cc_start: 0.9470 (m-80) cc_final: 0.8231 (m-80) REVERT: A 117 GLU cc_start: 0.9662 (tt0) cc_final: 0.9419 (tm-30) REVERT: A 122 MET cc_start: 0.9276 (tmm) cc_final: 0.9014 (ppp) REVERT: A 225 ASN cc_start: 0.8958 (t0) cc_final: 0.8565 (t0) REVERT: A 234 MET cc_start: 0.9349 (ttm) cc_final: 0.8824 (tpp) REVERT: A 444 PHE cc_start: 0.8948 (t80) cc_final: 0.8715 (t80) REVERT: A 450 LEU cc_start: 0.9149 (mm) cc_final: 0.8795 (tp) REVERT: A 456 MET cc_start: 0.8893 (mpp) cc_final: 0.7935 (mpp) REVERT: A 504 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.8132 (mm) REVERT: A 505 CYS cc_start: 0.9106 (m) cc_final: 0.8511 (m) REVERT: A 521 MET cc_start: 0.8820 (mmm) cc_final: 0.8284 (mmm) REVERT: A 605 MET cc_start: 0.8977 (ttm) cc_final: 0.8667 (mtt) REVERT: A 696 GLU cc_start: 0.9159 (tt0) cc_final: 0.8898 (tp30) REVERT: A 761 MET cc_start: 0.9070 (mtm) cc_final: 0.8509 (mmp) REVERT: A 786 HIS cc_start: 0.8621 (m-70) cc_final: 0.7744 (m-70) REVERT: A 818 MET cc_start: 0.9291 (tpp) cc_final: 0.8783 (mmt) REVERT: A 846 GLU cc_start: 0.8828 (mt-10) cc_final: 0.8333 (mt-10) REVERT: A 847 ASP cc_start: 0.8105 (p0) cc_final: 0.7572 (p0) REVERT: A 1120 LEU cc_start: 0.9678 (mt) cc_final: 0.9242 (tp) REVERT: A 1277 GLU cc_start: 0.9574 (pm20) cc_final: 0.9319 (pm20) REVERT: A 1315 GLU cc_start: 0.8663 (mp0) cc_final: 0.8440 (mp0) REVERT: A 1364 ASN cc_start: 0.8958 (t0) cc_final: 0.8607 (t0) REVERT: A 1427 ASN cc_start: 0.8626 (m-40) cc_final: 0.8320 (t0) REVERT: B 239 GLU cc_start: 0.8141 (tt0) cc_final: 0.7615 (tm-30) REVERT: B 258 LEU cc_start: 0.9325 (OUTLIER) cc_final: 0.9019 (tp) REVERT: B 296 GLU cc_start: 0.9395 (mm-30) cc_final: 0.8996 (mp0) REVERT: B 313 MET cc_start: 0.9600 (mmp) cc_final: 0.9340 (tpp) REVERT: B 361 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8496 (tp) REVERT: B 404 LYS cc_start: 0.9195 (mttt) cc_final: 0.8851 (mttt) REVERT: B 481 GLN cc_start: 0.8494 (mt0) cc_final: 0.8206 (mt0) REVERT: B 563 MET cc_start: 0.8481 (mtp) cc_final: 0.8245 (mtp) REVERT: B 610 ASN cc_start: 0.8722 (t0) cc_final: 0.8456 (t0) REVERT: B 698 GLU cc_start: 0.8429 (mp0) cc_final: 0.8181 (mp0) REVERT: B 705 MET cc_start: 0.7970 (mmm) cc_final: 0.7045 (mmm) REVERT: B 767 ASN cc_start: 0.8208 (m110) cc_final: 0.7886 (m110) REVERT: B 773 MET cc_start: 0.8620 (ttm) cc_final: 0.8419 (ttm) REVERT: B 790 ASP cc_start: 0.8098 (t70) cc_final: 0.7720 (t70) REVERT: B 809 MET cc_start: 0.8440 (pmm) cc_final: 0.7818 (pmm) REVERT: B 834 ASN cc_start: 0.8465 (p0) cc_final: 0.7723 (p0) REVERT: B 846 ILE cc_start: 0.9626 (mm) cc_final: 0.9424 (tt) REVERT: B 860 MET cc_start: 0.8299 (ppp) cc_final: 0.7819 (ppp) REVERT: B 963 PHE cc_start: 0.8563 (t80) cc_final: 0.7965 (t80) REVERT: B 1015 HIS cc_start: 0.8454 (m170) cc_final: 0.8121 (m170) REVERT: B 1072 MET cc_start: 0.7736 (tpt) cc_final: 0.7474 (tpt) REVERT: B 1082 MET cc_start: 0.9044 (tpt) cc_final: 0.8787 (tpt) REVERT: B 1095 LEU cc_start: 0.9159 (mm) cc_final: 0.8864 (mm) REVERT: B 1133 MET cc_start: 0.9091 (mtp) cc_final: 0.8607 (mtm) REVERT: B 1139 ILE cc_start: 0.9709 (mm) cc_final: 0.9488 (mt) REVERT: B 1208 MET cc_start: 0.9026 (ptt) cc_final: 0.8766 (ptt) REVERT: C 16 ASP cc_start: 0.9204 (p0) cc_final: 0.8736 (p0) REVERT: C 37 MET cc_start: 0.9332 (tpp) cc_final: 0.9120 (tpp) REVERT: C 46 ILE cc_start: 0.9214 (mt) cc_final: 0.8728 (tp) REVERT: C 52 GLU cc_start: 0.8745 (tm-30) cc_final: 0.8474 (tm-30) REVERT: C 157 CYS cc_start: 0.9259 (m) cc_final: 0.8893 (m) REVERT: C 165 LYS cc_start: 0.9058 (tttt) cc_final: 0.8703 (tttm) REVERT: D 35 LEU cc_start: 0.8488 (mt) cc_final: 0.8280 (pt) REVERT: D 131 GLU cc_start: 0.6328 (OUTLIER) cc_final: 0.6050 (pt0) REVERT: E 7 ARG cc_start: 0.9094 (ptm-80) cc_final: 0.8693 (ttp80) REVERT: E 58 MET cc_start: 0.9356 (ttp) cc_final: 0.8992 (tmm) REVERT: E 115 ASN cc_start: 0.9281 (p0) cc_final: 0.9061 (p0) REVERT: E 121 MET cc_start: 0.9261 (ppp) cc_final: 0.9011 (ppp) REVERT: E 211 TYR cc_start: 0.8887 (m-80) cc_final: 0.8603 (m-80) REVERT: F 81 THR cc_start: 0.9064 (m) cc_final: 0.8521 (p) REVERT: F 103 MET cc_start: 0.9127 (OUTLIER) cc_final: 0.8293 (tmt) REVERT: F 124 GLU cc_start: 0.9136 (tm-30) cc_final: 0.8713 (tm-30) REVERT: G 21 ARG cc_start: 0.7793 (ttp80) cc_final: 0.7511 (ttp80) REVERT: G 44 TYR cc_start: 0.7681 (t80) cc_final: 0.7217 (t80) REVERT: H 1 MET cc_start: 0.1709 (pmm) cc_final: 0.0160 (tpt) REVERT: H 10 PHE cc_start: 0.8445 (m-80) cc_final: 0.7413 (m-80) REVERT: H 123 MET cc_start: 0.9152 (ppp) cc_final: 0.8836 (ppp) REVERT: H 133 ASN cc_start: 0.9140 (t0) cc_final: 0.8917 (t0) REVERT: I 65 ASP cc_start: 0.9323 (t70) cc_final: 0.8791 (t0) REVERT: I 68 LEU cc_start: 0.9461 (mp) cc_final: 0.8936 (mp) REVERT: J 52 THR cc_start: 0.9081 (t) cc_final: 0.8829 (t) REVERT: K 92 ASN cc_start: 0.9356 (m110) cc_final: 0.8989 (m-40) REVERT: Q 365 TYR cc_start: 0.7784 (t80) cc_final: 0.7559 (t80) REVERT: M 72 ARG cc_start: 0.8167 (ttp80) cc_final: 0.7579 (ttp80) REVERT: M 121 ASP cc_start: 0.7949 (OUTLIER) cc_final: 0.7591 (p0) outliers start: 120 outliers final: 79 residues processed: 640 average time/residue: 0.4509 time to fit residues: 482.8654 Evaluate side-chains 594 residues out of total 3815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 508 time to evaluate : 4.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 496 GLU Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 757 ASN Chi-restraints excluded: chain A residue 767 GLN Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 953 ASN Chi-restraints excluded: chain A residue 1013 ASP Chi-restraints excluded: chain A residue 1105 LEU Chi-restraints excluded: chain A residue 1284 MET Chi-restraints excluded: chain A residue 1331 SER Chi-restraints excluded: chain A residue 1358 SER Chi-restraints excluded: chain A residue 1385 THR Chi-restraints excluded: chain A residue 1424 VAL Chi-restraints excluded: chain A residue 1450 LEU Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 178 ASN Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 310 MET Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 432 MET Chi-restraints excluded: chain B residue 445 LYS Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 465 ASN Chi-restraints excluded: chain B residue 516 ASN Chi-restraints excluded: chain B residue 639 ILE Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain B residue 737 THR Chi-restraints excluded: chain B residue 789 MET Chi-restraints excluded: chain B residue 854 LEU Chi-restraints excluded: chain B residue 1028 GLU Chi-restraints excluded: chain B residue 1034 VAL Chi-restraints excluded: chain B residue 1049 ASP Chi-restraints excluded: chain B residue 1066 SER Chi-restraints excluded: chain B residue 1103 ILE Chi-restraints excluded: chain B residue 1113 VAL Chi-restraints excluded: chain B residue 1147 LEU Chi-restraints excluded: chain B residue 1156 ASP Chi-restraints excluded: chain B residue 1162 ILE Chi-restraints excluded: chain B residue 1175 LEU Chi-restraints excluded: chain B residue 1202 LEU Chi-restraints excluded: chain B residue 1205 GLN Chi-restraints excluded: chain B residue 1206 GLU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 145 CYS Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 131 GLU Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 168 LEU Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain J residue 57 ILE Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain L residue 31 CYS Chi-restraints excluded: chain L residue 53 HIS Chi-restraints excluded: chain L residue 56 LEU Chi-restraints excluded: chain M residue 121 ASP Chi-restraints excluded: chain M residue 214 ILE Chi-restraints excluded: chain M residue 224 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 390 optimal weight: 10.0000 chunk 296 optimal weight: 8.9990 chunk 204 optimal weight: 6.9990 chunk 43 optimal weight: 5.9990 chunk 188 optimal weight: 0.9990 chunk 265 optimal weight: 9.9990 chunk 396 optimal weight: 30.0000 chunk 419 optimal weight: 20.0000 chunk 207 optimal weight: 10.0000 chunk 375 optimal weight: 6.9990 chunk 113 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 445 ASN A 510 GLN ** A 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 481 GLN ** B 834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 842 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 35 GLN I 22 ASN ** J 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 36958 Z= 0.292 Angle : 0.720 11.861 50326 Z= 0.376 Chirality : 0.045 0.337 5666 Planarity : 0.005 0.065 6198 Dihedral : 15.977 165.733 5803 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 21.65 Ramachandran Plot: Outliers : 0.05 % Allowed : 11.08 % Favored : 88.87 % Rotamer: Outliers : 3.80 % Allowed : 18.90 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.69 % Cis-general : 0.37 % Twisted Proline : 1.08 % Twisted General : 0.12 % 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: -1.29 (0.13), residues: 4259 helix: 0.71 (0.14), residues: 1408 sheet: -0.62 (0.20), residues: 672 loop : -2.07 (0.13), residues: 2179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 556 HIS 0.012 0.001 HIS B 363 PHE 0.029 0.002 PHE J 8 TYR 0.016 0.002 TYR B 486 ARG 0.005 0.000 ARG M 84 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8518 Ramachandran restraints generated. 4259 Oldfield, 0 Emsley, 4259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8518 Ramachandran restraints generated. 4259 Oldfield, 0 Emsley, 4259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 667 residues out of total 3815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 525 time to evaluate : 4.273 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: A 41 MET cc_start: 0.7184 (tpt) cc_final: 0.6818 (tpt) REVERT: A 43 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.8132 (mp0) REVERT: A 92 HIS cc_start: 0.8190 (t-90) cc_final: 0.6376 (t-90) REVERT: A 95 PHE cc_start: 0.9499 (m-80) cc_final: 0.8099 (m-80) REVERT: A 117 GLU cc_start: 0.9684 (tt0) cc_final: 0.9447 (tm-30) REVERT: A 122 MET cc_start: 0.9253 (tmm) cc_final: 0.8788 (ppp) REVERT: A 225 ASN cc_start: 0.8937 (t0) cc_final: 0.8605 (t0) REVERT: A 234 MET cc_start: 0.9358 (ttm) cc_final: 0.8899 (tpt) REVERT: A 450 LEU cc_start: 0.9117 (mm) cc_final: 0.8669 (tp) REVERT: A 456 MET cc_start: 0.8895 (mpp) cc_final: 0.7828 (mpp) REVERT: A 504 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8132 (mm) REVERT: A 521 MET cc_start: 0.8905 (mmm) cc_final: 0.8445 (mmm) REVERT: A 605 MET cc_start: 0.8957 (ttm) cc_final: 0.8598 (mtt) REVERT: A 696 GLU cc_start: 0.9169 (tt0) cc_final: 0.8907 (tp30) REVERT: A 701 LEU cc_start: 0.9141 (pt) cc_final: 0.8306 (pt) REVERT: A 709 THR cc_start: 0.7749 (OUTLIER) cc_final: 0.7535 (p) REVERT: A 748 MET cc_start: 0.8619 (ppp) cc_final: 0.8352 (ppp) REVERT: A 761 MET cc_start: 0.9054 (mtm) cc_final: 0.8595 (mmm) REVERT: A 786 HIS cc_start: 0.8747 (m-70) cc_final: 0.7990 (m-70) REVERT: A 846 GLU cc_start: 0.8830 (mt-10) cc_final: 0.8346 (mt-10) REVERT: A 847 ASP cc_start: 0.8085 (p0) cc_final: 0.7549 (p0) REVERT: A 1120 LEU cc_start: 0.9690 (mt) cc_final: 0.9243 (tp) REVERT: A 1209 MET cc_start: 0.8899 (ppp) cc_final: 0.8626 (ppp) REVERT: A 1227 ILE cc_start: 0.8799 (OUTLIER) cc_final: 0.8543 (mm) REVERT: A 1277 GLU cc_start: 0.9615 (pm20) cc_final: 0.9360 (pm20) REVERT: A 1315 GLU cc_start: 0.8683 (mp0) cc_final: 0.8441 (mp0) REVERT: A 1427 ASN cc_start: 0.8685 (m-40) cc_final: 0.8462 (t0) REVERT: A 1433 MET cc_start: 0.9202 (ppp) cc_final: 0.8875 (tmm) REVERT: B 239 GLU cc_start: 0.7970 (tt0) cc_final: 0.7509 (tm-30) REVERT: B 296 GLU cc_start: 0.9427 (mm-30) cc_final: 0.8983 (mp0) REVERT: B 361 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.8746 (tt) REVERT: B 404 LYS cc_start: 0.9215 (mttt) cc_final: 0.8878 (mttt) REVERT: B 444 MET cc_start: 0.7135 (ppp) cc_final: 0.6704 (ppp) REVERT: B 610 ASN cc_start: 0.8738 (t0) cc_final: 0.8473 (t0) REVERT: B 618 ASP cc_start: 0.8604 (t0) cc_final: 0.8228 (t0) REVERT: B 698 GLU cc_start: 0.8417 (mp0) cc_final: 0.8189 (mp0) REVERT: B 705 MET cc_start: 0.8137 (mmm) cc_final: 0.7343 (mmm) REVERT: B 767 ASN cc_start: 0.8346 (m110) cc_final: 0.8008 (m110) REVERT: B 790 ASP cc_start: 0.8146 (t70) cc_final: 0.7773 (t70) REVERT: B 834 ASN cc_start: 0.8450 (p0) cc_final: 0.7753 (p0) REVERT: B 860 MET cc_start: 0.8328 (ppp) cc_final: 0.7950 (ppp) REVERT: B 963 PHE cc_start: 0.8518 (t80) cc_final: 0.7940 (t80) REVERT: B 967 ARG cc_start: 0.8677 (ttp-170) cc_final: 0.7888 (ttp-110) REVERT: B 1015 HIS cc_start: 0.8395 (m170) cc_final: 0.7895 (m170) REVERT: B 1082 MET cc_start: 0.9041 (tpt) cc_final: 0.8812 (tpt) REVERT: B 1095 LEU cc_start: 0.9298 (mm) cc_final: 0.9070 (mm) REVERT: B 1100 ASP cc_start: 0.8313 (p0) cc_final: 0.8026 (t70) REVERT: C 16 ASP cc_start: 0.9216 (p0) cc_final: 0.7619 (p0) REVERT: C 46 ILE cc_start: 0.9234 (mt) cc_final: 0.8730 (tp) REVERT: C 52 GLU cc_start: 0.8714 (tm-30) cc_final: 0.8481 (tm-30) REVERT: C 157 CYS cc_start: 0.9269 (m) cc_final: 0.8907 (m) REVERT: C 165 LYS cc_start: 0.9093 (tttt) cc_final: 0.8703 (tttm) REVERT: C 233 GLU cc_start: 0.8918 (tt0) cc_final: 0.8414 (tp30) REVERT: D 131 GLU cc_start: 0.6441 (OUTLIER) cc_final: 0.6170 (pt0) REVERT: E 7 ARG cc_start: 0.9138 (ptm-80) cc_final: 0.8727 (ttp80) REVERT: E 58 MET cc_start: 0.9360 (ttp) cc_final: 0.9005 (tmm) REVERT: E 115 ASN cc_start: 0.9298 (p0) cc_final: 0.9074 (p0) REVERT: E 121 MET cc_start: 0.9292 (ppp) cc_final: 0.9025 (ppp) REVERT: E 208 TYR cc_start: 0.7634 (t80) cc_final: 0.7028 (t80) REVERT: E 211 TYR cc_start: 0.8906 (m-80) cc_final: 0.8657 (m-80) REVERT: F 81 THR cc_start: 0.9041 (m) cc_final: 0.8529 (p) REVERT: F 88 TYR cc_start: 0.7750 (m-10) cc_final: 0.7535 (m-10) REVERT: F 103 MET cc_start: 0.9173 (OUTLIER) cc_final: 0.8383 (tmt) REVERT: F 124 GLU cc_start: 0.9227 (tm-30) cc_final: 0.8933 (tm-30) REVERT: F 127 GLU cc_start: 0.8461 (tm-30) cc_final: 0.8240 (tm-30) REVERT: G 44 TYR cc_start: 0.7595 (t80) cc_final: 0.7286 (t80) REVERT: H 1 MET cc_start: 0.1875 (pmm) cc_final: 0.0290 (tpt) REVERT: H 10 PHE cc_start: 0.8355 (m-80) cc_final: 0.7415 (m-80) REVERT: H 97 MET cc_start: 0.8577 (ppp) cc_final: 0.8030 (ppp) REVERT: H 118 PHE cc_start: 0.9181 (m-80) cc_final: 0.8162 (m-10) REVERT: H 123 MET cc_start: 0.9302 (ppp) cc_final: 0.8982 (ppp) REVERT: H 133 ASN cc_start: 0.9120 (t0) cc_final: 0.8917 (t0) REVERT: I 65 ASP cc_start: 0.9278 (t70) cc_final: 0.8748 (t0) REVERT: I 68 LEU cc_start: 0.9439 (mp) cc_final: 0.8918 (mp) REVERT: J 39 LEU cc_start: 0.9350 (tp) cc_final: 0.9015 (tt) REVERT: J 52 THR cc_start: 0.9066 (t) cc_final: 0.8811 (t) REVERT: K 92 ASN cc_start: 0.9373 (m110) cc_final: 0.9011 (m-40) REVERT: K 106 GLU cc_start: 0.9750 (tp30) cc_final: 0.9358 (tp30) REVERT: M 121 ASP cc_start: 0.7957 (OUTLIER) cc_final: 0.7656 (p0) REVERT: M 133 TYR cc_start: 0.8226 (m-80) cc_final: 0.7714 (m-80) outliers start: 142 outliers final: 97 residues processed: 614 average time/residue: 0.4344 time to fit residues: 452.6133 Evaluate side-chains 603 residues out of total 3815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 498 time to evaluate : 4.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain A residue 496 GLU Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain A residue 781 ASP Chi-restraints excluded: chain A residue 834 THR Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 936 LEU Chi-restraints excluded: chain A residue 953 ASN Chi-restraints excluded: chain A residue 1013 ASP Chi-restraints excluded: chain A residue 1062 GLU Chi-restraints excluded: chain A residue 1105 LEU Chi-restraints excluded: chain A residue 1111 MET Chi-restraints excluded: chain A residue 1227 ILE Chi-restraints excluded: chain A residue 1284 MET Chi-restraints excluded: chain A residue 1331 SER Chi-restraints excluded: chain A residue 1341 ILE Chi-restraints excluded: chain A residue 1358 SER Chi-restraints excluded: chain A residue 1385 THR Chi-restraints excluded: chain A residue 1405 THR Chi-restraints excluded: chain A residue 1424 VAL Chi-restraints excluded: chain A residue 1450 LEU Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 310 MET Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 432 MET Chi-restraints excluded: chain B residue 445 LYS Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 465 ASN Chi-restraints excluded: chain B residue 516 ASN Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 639 ILE Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain B residue 737 THR Chi-restraints excluded: chain B residue 789 MET Chi-restraints excluded: chain B residue 854 LEU Chi-restraints excluded: chain B residue 1034 VAL Chi-restraints excluded: chain B residue 1037 LEU Chi-restraints excluded: chain B residue 1049 ASP Chi-restraints excluded: chain B residue 1066 SER Chi-restraints excluded: chain B residue 1103 ILE Chi-restraints excluded: chain B residue 1147 LEU Chi-restraints excluded: chain B residue 1156 ASP Chi-restraints excluded: chain B residue 1175 LEU Chi-restraints excluded: chain B residue 1202 LEU Chi-restraints excluded: chain B residue 1205 GLN Chi-restraints excluded: chain B residue 1206 GLU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 145 CYS Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain D residue 131 GLU Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain G residue 35 GLU Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 168 LEU Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 130 ARG Chi-restraints excluded: chain H residue 134 ASN Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain J residue 57 ILE Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain L residue 31 CYS Chi-restraints excluded: chain L residue 53 HIS Chi-restraints excluded: chain L residue 56 LEU Chi-restraints excluded: chain Q residue 380 ASP Chi-restraints excluded: chain M residue 121 ASP Chi-restraints excluded: chain M residue 214 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 349 optimal weight: 0.6980 chunk 238 optimal weight: 5.9990 chunk 6 optimal weight: 10.0000 chunk 312 optimal weight: 9.9990 chunk 173 optimal weight: 5.9990 chunk 357 optimal weight: 5.9990 chunk 289 optimal weight: 9.9990 chunk 0 optimal weight: 50.0000 chunk 214 optimal weight: 2.9990 chunk 376 optimal weight: 0.8980 chunk 105 optimal weight: 0.7980 overall best weight: 2.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 358 ASN ** A 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1070 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 47 GLN B 481 GLN ** B 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 842 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 GLN ** D 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 179 GLN ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 GLN ** J 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 moved from start: 0.3447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 36958 Z= 0.192 Angle : 0.685 11.899 50326 Z= 0.352 Chirality : 0.044 0.287 5666 Planarity : 0.004 0.062 6198 Dihedral : 15.844 165.402 5803 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 17.65 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.72 % Favored : 90.23 % Rotamer: Outliers : 3.53 % Allowed : 20.51 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.69 % Cis-general : 0.37 % Twisted Proline : 1.08 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.13), residues: 4259 helix: 0.91 (0.14), residues: 1401 sheet: -0.48 (0.21), residues: 660 loop : -1.97 (0.13), residues: 2198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP M 81 HIS 0.011 0.001 HIS B1015 PHE 0.030 0.001 PHE Q 101 TYR 0.023 0.001 TYR Q 373 ARG 0.005 0.000 ARG M 84 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8518 Ramachandran restraints generated. 4259 Oldfield, 0 Emsley, 4259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8518 Ramachandran restraints generated. 4259 Oldfield, 0 Emsley, 4259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 703 residues out of total 3815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 571 time to evaluate : 4.523 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: A 92 HIS cc_start: 0.7920 (t-90) cc_final: 0.6030 (t-90) REVERT: A 95 PHE cc_start: 0.9411 (m-80) cc_final: 0.8082 (m-80) REVERT: A 117 GLU cc_start: 0.9683 (tt0) cc_final: 0.9409 (tm-30) REVERT: A 122 MET cc_start: 0.9214 (tmm) cc_final: 0.8921 (ppp) REVERT: A 225 ASN cc_start: 0.8971 (t0) cc_final: 0.8613 (t0) REVERT: A 234 MET cc_start: 0.9359 (ttm) cc_final: 0.8814 (tpp) REVERT: A 433 GLU cc_start: 0.7905 (tp30) cc_final: 0.7691 (tp30) REVERT: A 450 LEU cc_start: 0.9087 (mm) cc_final: 0.8640 (tp) REVERT: A 456 MET cc_start: 0.8924 (mpp) cc_final: 0.8558 (mpp) REVERT: A 478 TYR cc_start: 0.8818 (m-80) cc_final: 0.8597 (m-80) REVERT: A 500 GLU cc_start: 0.8482 (tt0) cc_final: 0.8146 (tm-30) REVERT: A 521 MET cc_start: 0.8782 (mmm) cc_final: 0.8178 (mmm) REVERT: A 605 MET cc_start: 0.8803 (ttm) cc_final: 0.8550 (mtt) REVERT: A 696 GLU cc_start: 0.9171 (tt0) cc_final: 0.8923 (tp30) REVERT: A 701 LEU cc_start: 0.9174 (pt) cc_final: 0.8330 (pt) REVERT: A 748 MET cc_start: 0.8556 (ppp) cc_final: 0.8254 (ppp) REVERT: A 761 MET cc_start: 0.9033 (mtm) cc_final: 0.8603 (mmm) REVERT: A 786 HIS cc_start: 0.8691 (m-70) cc_final: 0.7945 (m-70) REVERT: A 804 TYR cc_start: 0.9069 (OUTLIER) cc_final: 0.8241 (m-80) REVERT: A 846 GLU cc_start: 0.8772 (mt-10) cc_final: 0.8277 (mt-10) REVERT: A 847 ASP cc_start: 0.8023 (p0) cc_final: 0.7522 (p0) REVERT: A 956 LEU cc_start: 0.8875 (mt) cc_final: 0.8537 (tt) REVERT: A 1120 LEU cc_start: 0.9694 (mt) cc_final: 0.9259 (tp) REVERT: A 1277 GLU cc_start: 0.9620 (pm20) cc_final: 0.9350 (pm20) REVERT: A 1285 MET cc_start: 0.8695 (mmm) cc_final: 0.8321 (mmm) REVERT: A 1315 GLU cc_start: 0.8685 (mp0) cc_final: 0.8444 (mp0) REVERT: A 1368 MET cc_start: 0.9086 (mtp) cc_final: 0.8851 (mtp) REVERT: A 1419 ASP cc_start: 0.8529 (t0) cc_final: 0.7962 (t0) REVERT: A 1421 CYS cc_start: 0.8124 (t) cc_final: 0.7874 (m) REVERT: A 1427 ASN cc_start: 0.8616 (m-40) cc_final: 0.8395 (t0) REVERT: A 1433 MET cc_start: 0.9247 (ppp) cc_final: 0.9007 (tmm) REVERT: B 239 GLU cc_start: 0.8077 (tt0) cc_final: 0.7436 (tm-30) REVERT: B 296 GLU cc_start: 0.9406 (mm-30) cc_final: 0.8950 (mp0) REVERT: B 404 LYS cc_start: 0.9209 (mttt) cc_final: 0.8813 (mttt) REVERT: B 444 MET cc_start: 0.7137 (ppp) cc_final: 0.6803 (ppp) REVERT: B 481 GLN cc_start: 0.8486 (mt0) cc_final: 0.8185 (mt0) REVERT: B 510 LYS cc_start: 0.5021 (mmtp) cc_final: 0.4804 (mmtt) REVERT: B 542 MET cc_start: 0.8617 (mpp) cc_final: 0.8324 (mpp) REVERT: B 618 ASP cc_start: 0.8576 (t0) cc_final: 0.8262 (t0) REVERT: B 687 GLU cc_start: 0.8637 (tm-30) cc_final: 0.8321 (tm-30) REVERT: B 698 GLU cc_start: 0.8390 (mp0) cc_final: 0.8168 (mp0) REVERT: B 705 MET cc_start: 0.8058 (mmm) cc_final: 0.7254 (mmm) REVERT: B 773 MET cc_start: 0.8594 (ttm) cc_final: 0.8377 (ttm) REVERT: B 790 ASP cc_start: 0.8076 (t70) cc_final: 0.7640 (t70) REVERT: B 834 ASN cc_start: 0.8346 (p0) cc_final: 0.7613 (p0) REVERT: B 860 MET cc_start: 0.8286 (ppp) cc_final: 0.7936 (ppp) REVERT: B 963 PHE cc_start: 0.8302 (t80) cc_final: 0.7660 (t80) REVERT: B 1015 HIS cc_start: 0.8375 (m170) cc_final: 0.8065 (m170) REVERT: B 1095 LEU cc_start: 0.9261 (mm) cc_final: 0.9025 (mm) REVERT: B 1100 ASP cc_start: 0.8254 (p0) cc_final: 0.8000 (t70) REVERT: B 1139 ILE cc_start: 0.9718 (mm) cc_final: 0.9510 (mt) REVERT: B 1169 MET cc_start: 0.8726 (mmt) cc_final: 0.8372 (mmm) REVERT: B 1208 MET cc_start: 0.8859 (ptp) cc_final: 0.8310 (ptp) REVERT: C 16 ASP cc_start: 0.9160 (p0) cc_final: 0.7486 (p0) REVERT: C 37 MET cc_start: 0.9350 (tpp) cc_final: 0.9083 (tpp) REVERT: C 46 ILE cc_start: 0.9206 (mt) cc_final: 0.8730 (tp) REVERT: C 52 GLU cc_start: 0.8581 (tm-30) cc_final: 0.8316 (tm-30) REVERT: C 58 LEU cc_start: 0.8724 (tp) cc_final: 0.8515 (tp) REVERT: C 157 CYS cc_start: 0.9291 (m) cc_final: 0.8906 (m) REVERT: C 165 LYS cc_start: 0.9047 (tttt) cc_final: 0.8750 (tttt) REVERT: C 233 GLU cc_start: 0.8937 (tt0) cc_final: 0.8397 (tp30) REVERT: D 131 GLU cc_start: 0.6410 (OUTLIER) cc_final: 0.6162 (pt0) REVERT: E 7 ARG cc_start: 0.9111 (ptm-80) cc_final: 0.8711 (ttp80) REVERT: E 58 MET cc_start: 0.9335 (ttp) cc_final: 0.8964 (tmm) REVERT: E 75 MET cc_start: 0.6852 (OUTLIER) cc_final: 0.6533 (pmm) REVERT: E 115 ASN cc_start: 0.9334 (p0) cc_final: 0.9109 (p0) REVERT: F 81 THR cc_start: 0.9067 (m) cc_final: 0.8601 (p) REVERT: F 103 MET cc_start: 0.9146 (OUTLIER) cc_final: 0.8436 (tmm) REVERT: F 124 GLU cc_start: 0.9228 (tm-30) cc_final: 0.8955 (tm-30) REVERT: G 57 GLN cc_start: 0.8221 (OUTLIER) cc_final: 0.7884 (pm20) REVERT: H 1 MET cc_start: 0.2253 (pmm) cc_final: 0.0669 (tpt) REVERT: H 10 PHE cc_start: 0.8346 (m-80) cc_final: 0.7367 (m-80) REVERT: H 97 MET cc_start: 0.8485 (ppp) cc_final: 0.8214 (ppp) REVERT: H 118 PHE cc_start: 0.9224 (m-80) cc_final: 0.8663 (m-10) REVERT: H 123 MET cc_start: 0.9306 (ppp) cc_final: 0.8969 (ppp) REVERT: H 133 ASN cc_start: 0.9082 (t0) cc_final: 0.8864 (t0) REVERT: I 47 GLU cc_start: 0.8662 (mm-30) cc_final: 0.8447 (mm-30) REVERT: I 48 LEU cc_start: 0.9433 (tt) cc_final: 0.9113 (pp) REVERT: I 65 ASP cc_start: 0.9302 (t70) cc_final: 0.8811 (t0) REVERT: I 68 LEU cc_start: 0.9514 (mp) cc_final: 0.9050 (mp) REVERT: J 39 LEU cc_start: 0.9308 (tp) cc_final: 0.8992 (tt) REVERT: J 49 MET cc_start: 0.7850 (OUTLIER) cc_final: 0.7628 (mtt) REVERT: K 106 GLU cc_start: 0.9740 (tp30) cc_final: 0.9351 (tp30) REVERT: Q 31 PHE cc_start: 0.4943 (t80) cc_final: 0.4707 (t80) REVERT: M 121 ASP cc_start: 0.7879 (OUTLIER) cc_final: 0.7599 (p0) REVERT: M 228 MET cc_start: 0.4604 (mmm) cc_final: 0.4387 (mmm) outliers start: 132 outliers final: 87 residues processed: 652 average time/residue: 0.4432 time to fit residues: 484.2573 Evaluate side-chains 614 residues out of total 3815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 520 time to evaluate : 4.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 264 PHE Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 444 PHE Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain A residue 496 GLU Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 619 LYS Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain A residue 757 ASN Chi-restraints excluded: chain A residue 804 TYR Chi-restraints excluded: chain A residue 834 THR Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 936 LEU Chi-restraints excluded: chain A residue 953 ASN Chi-restraints excluded: chain A residue 1013 ASP Chi-restraints excluded: chain A residue 1105 LEU Chi-restraints excluded: chain A residue 1111 MET Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain A residue 1284 MET Chi-restraints excluded: chain A residue 1331 SER Chi-restraints excluded: chain A residue 1358 SER Chi-restraints excluded: chain A residue 1385 THR Chi-restraints excluded: chain A residue 1424 VAL Chi-restraints excluded: chain A residue 1450 LEU Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 310 MET Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 445 LYS Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 465 ASN Chi-restraints excluded: chain B residue 516 ASN Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 585 VAL Chi-restraints excluded: chain B residue 639 ILE Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain B residue 737 THR Chi-restraints excluded: chain B residue 812 LEU Chi-restraints excluded: chain B residue 1028 GLU Chi-restraints excluded: chain B residue 1037 LEU Chi-restraints excluded: chain B residue 1049 ASP Chi-restraints excluded: chain B residue 1066 SER Chi-restraints excluded: chain B residue 1147 LEU Chi-restraints excluded: chain B residue 1156 ASP Chi-restraints excluded: chain B residue 1175 LEU Chi-restraints excluded: chain B residue 1202 LEU Chi-restraints excluded: chain B residue 1205 GLN Chi-restraints excluded: chain B residue 1206 GLU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain D residue 131 GLU Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 57 GLN Chi-restraints excluded: chain G residue 168 LEU Chi-restraints excluded: chain H residue 22 LYS Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 49 MET Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain J residue 57 ILE Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain L residue 31 CYS Chi-restraints excluded: chain Q residue 380 ASP Chi-restraints excluded: chain M residue 68 VAL Chi-restraints excluded: chain M residue 85 ASN Chi-restraints excluded: chain M residue 121 ASP Chi-restraints excluded: chain M residue 128 VAL Chi-restraints excluded: chain M residue 214 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 141 optimal weight: 10.0000 chunk 377 optimal weight: 20.0000 chunk 82 optimal weight: 8.9990 chunk 246 optimal weight: 9.9990 chunk 103 optimal weight: 7.9990 chunk 419 optimal weight: 7.9990 chunk 348 optimal weight: 10.0000 chunk 194 optimal weight: 0.0870 chunk 34 optimal weight: 10.0000 chunk 138 optimal weight: 3.9990 chunk 220 optimal weight: 0.0470 overall best weight: 4.0262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 767 GLN ** A 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1070 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 47 GLN ** B 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 153 HIS ** J 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7100 moved from start: 0.3663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 36958 Z= 0.246 Angle : 0.711 11.931 50326 Z= 0.366 Chirality : 0.044 0.210 5666 Planarity : 0.004 0.061 6198 Dihedral : 15.772 162.958 5803 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 19.54 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.75 % Favored : 89.20 % Rotamer: Outliers : 3.96 % Allowed : 21.95 % Favored : 74.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.69 % Cis-general : 0.37 % Twisted Proline : 1.08 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.13), residues: 4259 helix: 0.91 (0.14), residues: 1412 sheet: -0.55 (0.21), residues: 655 loop : -2.00 (0.13), residues: 2192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 556 HIS 0.007 0.001 HIS A1387 PHE 0.026 0.002 PHE J 8 TYR 0.021 0.002 TYR Q 373 ARG 0.010 0.000 ARG C 35 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8518 Ramachandran restraints generated. 4259 Oldfield, 0 Emsley, 4259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8518 Ramachandran restraints generated. 4259 Oldfield, 0 Emsley, 4259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 674 residues out of total 3815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 526 time to evaluate : 4.387 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: A 41 MET cc_start: 0.7489 (tpt) cc_final: 0.6835 (tpt) REVERT: A 117 GLU cc_start: 0.9687 (tt0) cc_final: 0.9425 (tm-30) REVERT: A 122 MET cc_start: 0.9185 (tmm) cc_final: 0.8804 (ppp) REVERT: A 225 ASN cc_start: 0.9031 (t0) cc_final: 0.8685 (t0) REVERT: A 433 GLU cc_start: 0.7875 (tp30) cc_final: 0.7640 (tp30) REVERT: A 450 LEU cc_start: 0.9062 (mm) cc_final: 0.8600 (tp) REVERT: A 456 MET cc_start: 0.9021 (mpp) cc_final: 0.8668 (mpp) REVERT: A 497 THR cc_start: 0.8501 (OUTLIER) cc_final: 0.8296 (t) REVERT: A 504 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8019 (mm) REVERT: A 521 MET cc_start: 0.8753 (mmm) cc_final: 0.8256 (mmm) REVERT: A 547 LEU cc_start: 0.9043 (mt) cc_final: 0.8606 (mt) REVERT: A 605 MET cc_start: 0.8893 (ttm) cc_final: 0.8526 (mtt) REVERT: A 696 GLU cc_start: 0.9189 (tt0) cc_final: 0.8883 (tp30) REVERT: A 701 LEU cc_start: 0.9197 (pt) cc_final: 0.8379 (pt) REVERT: A 748 MET cc_start: 0.8607 (ppp) cc_final: 0.8316 (ppp) REVERT: A 761 MET cc_start: 0.9082 (mtm) cc_final: 0.8643 (mmm) REVERT: A 786 HIS cc_start: 0.8744 (m-70) cc_final: 0.8050 (m-70) REVERT: A 846 GLU cc_start: 0.8784 (mt-10) cc_final: 0.8287 (mt-10) REVERT: A 847 ASP cc_start: 0.8156 (p0) cc_final: 0.7614 (p0) REVERT: A 1111 MET cc_start: 0.8737 (OUTLIER) cc_final: 0.8507 (mmm) REVERT: A 1120 LEU cc_start: 0.9697 (mt) cc_final: 0.9253 (tp) REVERT: A 1227 ILE cc_start: 0.8777 (OUTLIER) cc_final: 0.8560 (mm) REVERT: A 1277 GLU cc_start: 0.9613 (pm20) cc_final: 0.9310 (pm20) REVERT: A 1315 GLU cc_start: 0.8543 (mp0) cc_final: 0.8297 (mp0) REVERT: A 1368 MET cc_start: 0.9058 (mtp) cc_final: 0.8816 (mtp) REVERT: A 1375 MET cc_start: 0.8884 (tmm) cc_final: 0.8356 (tmm) REVERT: A 1400 CYS cc_start: 0.9096 (OUTLIER) cc_final: 0.8565 (p) REVERT: A 1433 MET cc_start: 0.9235 (ppp) cc_final: 0.8999 (tmm) REVERT: B 101 MET cc_start: 0.7970 (tpp) cc_final: 0.7752 (tpp) REVERT: B 239 GLU cc_start: 0.8088 (tt0) cc_final: 0.7458 (tm-30) REVERT: B 296 GLU cc_start: 0.9447 (mm-30) cc_final: 0.8951 (mp0) REVERT: B 373 ARG cc_start: 0.8795 (OUTLIER) cc_final: 0.8515 (mtt90) REVERT: B 393 LYS cc_start: 0.8351 (tppt) cc_final: 0.7738 (tptp) REVERT: B 394 ASP cc_start: 0.8869 (p0) cc_final: 0.8592 (p0) REVERT: B 404 LYS cc_start: 0.9166 (mttt) cc_final: 0.8806 (mttt) REVERT: B 444 MET cc_start: 0.7134 (ppp) cc_final: 0.6672 (ppp) REVERT: B 445 LYS cc_start: 0.8284 (OUTLIER) cc_final: 0.7533 (mmmt) REVERT: B 446 LEU cc_start: 0.8502 (mt) cc_final: 0.7784 (mp) REVERT: B 481 GLN cc_start: 0.8489 (mt0) cc_final: 0.8266 (mm-40) REVERT: B 510 LYS cc_start: 0.5032 (mmtp) cc_final: 0.4798 (mmtt) REVERT: B 542 MET cc_start: 0.8726 (mpp) cc_final: 0.8367 (mpp) REVERT: B 687 GLU cc_start: 0.8742 (tm-30) cc_final: 0.8271 (tm-30) REVERT: B 698 GLU cc_start: 0.8397 (mp0) cc_final: 0.8169 (mp0) REVERT: B 706 GLN cc_start: 0.8037 (mm-40) cc_final: 0.7774 (mm110) REVERT: B 773 MET cc_start: 0.8598 (ttm) cc_final: 0.8347 (ttm) REVERT: B 790 ASP cc_start: 0.8056 (t70) cc_final: 0.7652 (t70) REVERT: B 792 MET cc_start: 0.8237 (mtp) cc_final: 0.8013 (mtp) REVERT: B 834 ASN cc_start: 0.8374 (p0) cc_final: 0.7659 (p0) REVERT: B 860 MET cc_start: 0.8253 (ppp) cc_final: 0.7943 (ppp) REVERT: B 963 PHE cc_start: 0.8181 (t80) cc_final: 0.7569 (t80) REVERT: B 992 ILE cc_start: 0.9126 (pt) cc_final: 0.8862 (pt) REVERT: B 999 MET cc_start: 0.9112 (tpp) cc_final: 0.8373 (mmm) REVERT: B 1015 HIS cc_start: 0.8326 (m170) cc_final: 0.8062 (m170) REVERT: B 1100 ASP cc_start: 0.8255 (p0) cc_final: 0.8021 (t70) REVERT: B 1139 ILE cc_start: 0.9728 (mm) cc_final: 0.9519 (mt) REVERT: B 1169 MET cc_start: 0.8810 (mmt) cc_final: 0.8468 (mmm) REVERT: B 1208 MET cc_start: 0.8881 (ptp) cc_final: 0.8185 (ptp) REVERT: C 16 ASP cc_start: 0.9178 (p0) cc_final: 0.7472 (p0) REVERT: C 37 MET cc_start: 0.9311 (tpp) cc_final: 0.9014 (tpp) REVERT: C 46 ILE cc_start: 0.9179 (mt) cc_final: 0.8690 (tp) REVERT: C 52 GLU cc_start: 0.8613 (tm-30) cc_final: 0.8370 (tm-30) REVERT: C 157 CYS cc_start: 0.9267 (m) cc_final: 0.8892 (m) REVERT: C 165 LYS cc_start: 0.9063 (tttt) cc_final: 0.8726 (tttm) REVERT: C 233 GLU cc_start: 0.8948 (tt0) cc_final: 0.8361 (tp30) REVERT: D 35 LEU cc_start: 0.8753 (mt) cc_final: 0.8502 (pt) REVERT: D 131 GLU cc_start: 0.6349 (OUTLIER) cc_final: 0.6111 (pt0) REVERT: E 7 ARG cc_start: 0.9112 (ptm-80) cc_final: 0.8698 (ttp80) REVERT: E 58 MET cc_start: 0.9329 (ttp) cc_final: 0.9021 (tmm) REVERT: E 75 MET cc_start: 0.6873 (OUTLIER) cc_final: 0.6595 (pmm) REVERT: E 115 ASN cc_start: 0.9340 (p0) cc_final: 0.9125 (p0) REVERT: F 81 THR cc_start: 0.9045 (m) cc_final: 0.8594 (p) REVERT: F 103 MET cc_start: 0.9143 (OUTLIER) cc_final: 0.8378 (tmt) REVERT: F 124 GLU cc_start: 0.9228 (tm-30) cc_final: 0.8925 (tm-30) REVERT: G 44 TYR cc_start: 0.7394 (t80) cc_final: 0.7046 (t80) REVERT: G 57 GLN cc_start: 0.8171 (OUTLIER) cc_final: 0.7778 (pm20) REVERT: H 1 MET cc_start: 0.2287 (pmm) cc_final: 0.0730 (tpt) REVERT: H 10 PHE cc_start: 0.8325 (m-80) cc_final: 0.7369 (m-80) REVERT: H 97 MET cc_start: 0.8535 (ppp) cc_final: 0.8252 (ppp) REVERT: H 118 PHE cc_start: 0.9215 (m-80) cc_final: 0.8656 (m-10) REVERT: H 123 MET cc_start: 0.9334 (ppp) cc_final: 0.8968 (ppp) REVERT: I 48 LEU cc_start: 0.9459 (tt) cc_final: 0.9145 (pp) REVERT: I 65 ASP cc_start: 0.9243 (t70) cc_final: 0.8729 (t0) REVERT: I 68 LEU cc_start: 0.9495 (mp) cc_final: 0.9020 (mp) REVERT: K 106 GLU cc_start: 0.9738 (tp30) cc_final: 0.9351 (tp30) REVERT: Q 31 PHE cc_start: 0.4921 (t80) cc_final: 0.4630 (t80) REVERT: M 121 ASP cc_start: 0.7858 (OUTLIER) cc_final: 0.7601 (p0) REVERT: M 223 GLN cc_start: 0.8826 (OUTLIER) cc_final: 0.8613 (tm-30) outliers start: 148 outliers final: 106 residues processed: 621 average time/residue: 0.4363 time to fit residues: 456.4354 Evaluate side-chains 614 residues out of total 3815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 495 time to evaluate : 4.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 264 PHE Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 444 PHE Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain A residue 496 GLU Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain A residue 767 GLN Chi-restraints excluded: chain A residue 834 THR Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 936 LEU Chi-restraints excluded: chain A residue 953 ASN Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1062 GLU Chi-restraints excluded: chain A residue 1105 LEU Chi-restraints excluded: chain A residue 1111 MET Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain A residue 1227 ILE Chi-restraints excluded: chain A residue 1318 THR Chi-restraints excluded: chain A residue 1331 SER Chi-restraints excluded: chain A residue 1358 SER Chi-restraints excluded: chain A residue 1385 THR Chi-restraints excluded: chain A residue 1400 CYS Chi-restraints excluded: chain A residue 1405 THR Chi-restraints excluded: chain A residue 1424 VAL Chi-restraints excluded: chain A residue 1450 LEU Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 306 ASN Chi-restraints excluded: chain B residue 310 MET Chi-restraints excluded: chain B residue 373 ARG Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 432 MET Chi-restraints excluded: chain B residue 445 LYS Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 465 ASN Chi-restraints excluded: chain B residue 516 ASN Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 585 VAL Chi-restraints excluded: chain B residue 639 ILE Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain B residue 729 ILE Chi-restraints excluded: chain B residue 737 THR Chi-restraints excluded: chain B residue 789 MET Chi-restraints excluded: chain B residue 1023 VAL Chi-restraints excluded: chain B residue 1028 GLU Chi-restraints excluded: chain B residue 1034 VAL Chi-restraints excluded: chain B residue 1040 ASN Chi-restraints excluded: chain B residue 1049 ASP Chi-restraints excluded: chain B residue 1062 HIS Chi-restraints excluded: chain B residue 1066 SER Chi-restraints excluded: chain B residue 1147 LEU Chi-restraints excluded: chain B residue 1156 ASP Chi-restraints excluded: chain B residue 1162 ILE Chi-restraints excluded: chain B residue 1175 LEU Chi-restraints excluded: chain B residue 1202 LEU Chi-restraints excluded: chain B residue 1205 GLN Chi-restraints excluded: chain B residue 1206 GLU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 178 PHE Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain D residue 131 GLU Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 57 GLN Chi-restraints excluded: chain G residue 85 GLU Chi-restraints excluded: chain H residue 22 LYS Chi-restraints excluded: chain H residue 130 ARG Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain J residue 57 ILE Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain L residue 31 CYS Chi-restraints excluded: chain L residue 53 HIS Chi-restraints excluded: chain L residue 56 LEU Chi-restraints excluded: chain Q residue 380 ASP Chi-restraints excluded: chain M residue 68 VAL Chi-restraints excluded: chain M residue 85 ASN Chi-restraints excluded: chain M residue 121 ASP Chi-restraints excluded: chain M residue 128 VAL Chi-restraints excluded: chain M residue 212 THR Chi-restraints excluded: chain M residue 214 ILE Chi-restraints excluded: chain M residue 223 GLN Chi-restraints excluded: chain M residue 224 VAL Chi-restraints excluded: chain M residue 236 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 404 optimal weight: 6.9990 chunk 47 optimal weight: 20.0000 chunk 239 optimal weight: 0.8980 chunk 306 optimal weight: 0.2980 chunk 237 optimal weight: 40.0000 chunk 353 optimal weight: 50.0000 chunk 234 optimal weight: 0.0020 chunk 418 optimal weight: 40.0000 chunk 261 optimal weight: 9.9990 chunk 255 optimal weight: 7.9990 chunk 193 optimal weight: 10.0000 overall best weight: 3.2392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 767 GLN ** A 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1070 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 842 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 112 GLN ** Q 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7092 moved from start: 0.3832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 36958 Z= 0.220 Angle : 0.702 11.831 50326 Z= 0.361 Chirality : 0.044 0.216 5666 Planarity : 0.004 0.061 6198 Dihedral : 15.711 161.253 5803 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 18.72 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.19 % Favored : 89.76 % Rotamer: Outliers : 3.56 % Allowed : 23.37 % Favored : 73.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.69 % Cis-general : 0.37 % Twisted Proline : 0.54 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.13), residues: 4259 helix: 0.96 (0.14), residues: 1410 sheet: -0.50 (0.21), residues: 664 loop : -1.99 (0.13), residues: 2185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 556 HIS 0.009 0.001 HIS B 363 PHE 0.024 0.001 PHE J 8 TYR 0.029 0.001 TYR H 93 ARG 0.010 0.000 ARG C 35 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8518 Ramachandran restraints generated. 4259 Oldfield, 0 Emsley, 4259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8518 Ramachandran restraints generated. 4259 Oldfield, 0 Emsley, 4259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 649 residues out of total 3815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 516 time to evaluate : 4.116 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: A 117 GLU cc_start: 0.9693 (tt0) cc_final: 0.9426 (tm-30) REVERT: A 122 MET cc_start: 0.9198 (tmm) cc_final: 0.8814 (ppp) REVERT: A 225 ASN cc_start: 0.9053 (t0) cc_final: 0.8701 (t0) REVERT: A 433 GLU cc_start: 0.7832 (tp30) cc_final: 0.7588 (tp30) REVERT: A 450 LEU cc_start: 0.9069 (mm) cc_final: 0.8592 (tp) REVERT: A 456 MET cc_start: 0.9056 (mpp) cc_final: 0.8800 (mpp) REVERT: A 478 TYR cc_start: 0.9071 (m-80) cc_final: 0.8679 (m-80) REVERT: A 500 GLU cc_start: 0.8474 (tt0) cc_final: 0.7887 (tm-30) REVERT: A 504 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.7819 (mm) REVERT: A 521 MET cc_start: 0.8732 (mmm) cc_final: 0.8291 (mmm) REVERT: A 605 MET cc_start: 0.8902 (ttm) cc_final: 0.8551 (mtt) REVERT: A 696 GLU cc_start: 0.9189 (tt0) cc_final: 0.8888 (tp30) REVERT: A 701 LEU cc_start: 0.9214 (pt) cc_final: 0.8434 (pt) REVERT: A 748 MET cc_start: 0.8566 (ppp) cc_final: 0.8203 (ppp) REVERT: A 761 MET cc_start: 0.9055 (mtm) cc_final: 0.8582 (mmp) REVERT: A 786 HIS cc_start: 0.8684 (m-70) cc_final: 0.8043 (m-70) REVERT: A 846 GLU cc_start: 0.8779 (mt-10) cc_final: 0.8288 (mt-10) REVERT: A 847 ASP cc_start: 0.8123 (p0) cc_final: 0.7576 (p0) REVERT: A 894 GLU cc_start: 0.9180 (pp20) cc_final: 0.8961 (pp20) REVERT: A 956 LEU cc_start: 0.8966 (mt) cc_final: 0.8514 (tt) REVERT: A 1120 LEU cc_start: 0.9697 (mt) cc_final: 0.9261 (tp) REVERT: A 1227 ILE cc_start: 0.8794 (OUTLIER) cc_final: 0.8585 (mm) REVERT: A 1277 GLU cc_start: 0.9605 (pm20) cc_final: 0.9301 (pm20) REVERT: A 1285 MET cc_start: 0.8598 (mmm) cc_final: 0.8293 (mmm) REVERT: A 1315 GLU cc_start: 0.8476 (mp0) cc_final: 0.8180 (mp0) REVERT: A 1368 MET cc_start: 0.9065 (mtp) cc_final: 0.8838 (mtp) REVERT: A 1375 MET cc_start: 0.8866 (tmm) cc_final: 0.8342 (tmm) REVERT: A 1400 CYS cc_start: 0.9074 (OUTLIER) cc_final: 0.8559 (p) REVERT: A 1421 CYS cc_start: 0.8461 (t) cc_final: 0.7995 (m) REVERT: A 1444 MET cc_start: 0.8702 (mtt) cc_final: 0.8319 (mtm) REVERT: B 112 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8548 (mm) REVERT: B 239 GLU cc_start: 0.8069 (tt0) cc_final: 0.7440 (tm-30) REVERT: B 296 GLU cc_start: 0.9449 (mm-30) cc_final: 0.8929 (mp0) REVERT: B 361 LEU cc_start: 0.9020 (mt) cc_final: 0.8671 (tp) REVERT: B 373 ARG cc_start: 0.8798 (OUTLIER) cc_final: 0.8528 (mtt90) REVERT: B 393 LYS cc_start: 0.8424 (tppt) cc_final: 0.7875 (tmtt) REVERT: B 394 ASP cc_start: 0.8859 (p0) cc_final: 0.8520 (p0) REVERT: B 404 LYS cc_start: 0.9158 (mttt) cc_final: 0.8802 (mttt) REVERT: B 444 MET cc_start: 0.7231 (ppp) cc_final: 0.6806 (ppp) REVERT: B 445 LYS cc_start: 0.8275 (OUTLIER) cc_final: 0.7503 (mmmt) REVERT: B 446 LEU cc_start: 0.8552 (mt) cc_final: 0.7856 (mp) REVERT: B 481 GLN cc_start: 0.8471 (mt0) cc_final: 0.8147 (mt0) REVERT: B 542 MET cc_start: 0.8724 (mpp) cc_final: 0.8390 (mpp) REVERT: B 563 MET cc_start: 0.8316 (mtp) cc_final: 0.8106 (mtp) REVERT: B 687 GLU cc_start: 0.8804 (tm-30) cc_final: 0.8365 (tm-30) REVERT: B 698 GLU cc_start: 0.8394 (mp0) cc_final: 0.8141 (mp0) REVERT: B 790 ASP cc_start: 0.8050 (t70) cc_final: 0.7620 (t70) REVERT: B 792 MET cc_start: 0.8194 (mtp) cc_final: 0.7976 (mtp) REVERT: B 834 ASN cc_start: 0.8369 (p0) cc_final: 0.7635 (p0) REVERT: B 860 MET cc_start: 0.8270 (ppp) cc_final: 0.7987 (ppp) REVERT: B 963 PHE cc_start: 0.8101 (t80) cc_final: 0.7495 (t80) REVERT: B 992 ILE cc_start: 0.9100 (pt) cc_final: 0.8809 (pt) REVERT: B 999 MET cc_start: 0.9126 (tpp) cc_final: 0.8371 (mmt) REVERT: B 1015 HIS cc_start: 0.8319 (m170) cc_final: 0.7884 (m170) REVERT: B 1021 MET cc_start: 0.8265 (tmm) cc_final: 0.7876 (ppp) REVERT: B 1100 ASP cc_start: 0.8256 (p0) cc_final: 0.8015 (t70) REVERT: B 1139 ILE cc_start: 0.9721 (mm) cc_final: 0.9512 (mt) REVERT: B 1169 MET cc_start: 0.8778 (mmt) cc_final: 0.8421 (mmm) REVERT: B 1208 MET cc_start: 0.8871 (ptp) cc_final: 0.8161 (ptp) REVERT: C 16 ASP cc_start: 0.9178 (p0) cc_final: 0.8715 (p0) REVERT: C 35 ARG cc_start: 0.8938 (mtp85) cc_final: 0.8673 (mtp85) REVERT: C 37 MET cc_start: 0.9329 (tpp) cc_final: 0.9012 (tpt) REVERT: C 46 ILE cc_start: 0.9149 (mt) cc_final: 0.8687 (tt) REVERT: C 52 GLU cc_start: 0.8595 (tm-30) cc_final: 0.8353 (tm-30) REVERT: C 157 CYS cc_start: 0.9289 (m) cc_final: 0.8867 (m) REVERT: C 165 LYS cc_start: 0.9002 (tttt) cc_final: 0.8725 (tttm) REVERT: D 131 GLU cc_start: 0.6485 (OUTLIER) cc_final: 0.6260 (pt0) REVERT: E 7 ARG cc_start: 0.9107 (ptm-80) cc_final: 0.8685 (ttp80) REVERT: E 58 MET cc_start: 0.9334 (ttp) cc_final: 0.9025 (tmm) REVERT: E 75 MET cc_start: 0.6792 (OUTLIER) cc_final: 0.6520 (pmm) REVERT: E 115 ASN cc_start: 0.9361 (p0) cc_final: 0.9139 (p0) REVERT: F 81 THR cc_start: 0.9004 (m) cc_final: 0.8564 (p) REVERT: F 103 MET cc_start: 0.9132 (OUTLIER) cc_final: 0.8400 (tmm) REVERT: F 124 GLU cc_start: 0.9234 (tm-30) cc_final: 0.8968 (tm-30) REVERT: G 44 TYR cc_start: 0.7342 (t80) cc_final: 0.6972 (t80) REVERT: G 57 GLN cc_start: 0.8092 (OUTLIER) cc_final: 0.7745 (pm20) REVERT: H 1 MET cc_start: 0.2764 (pmm) cc_final: 0.1241 (tpt) REVERT: H 10 PHE cc_start: 0.8267 (m-80) cc_final: 0.7316 (m-80) REVERT: H 97 MET cc_start: 0.8696 (ppp) cc_final: 0.8377 (ppp) REVERT: H 118 PHE cc_start: 0.9200 (m-80) cc_final: 0.8041 (m-10) REVERT: H 123 MET cc_start: 0.9347 (ppp) cc_final: 0.8960 (ppp) REVERT: I 48 LEU cc_start: 0.9462 (tt) cc_final: 0.9161 (pp) REVERT: I 65 ASP cc_start: 0.9218 (t70) cc_final: 0.8708 (t0) REVERT: I 68 LEU cc_start: 0.9489 (mp) cc_final: 0.9042 (mp) REVERT: K 106 GLU cc_start: 0.9734 (tp30) cc_final: 0.9283 (tp30) REVERT: M 121 ASP cc_start: 0.7872 (OUTLIER) cc_final: 0.7617 (p0) outliers start: 133 outliers final: 103 residues processed: 596 average time/residue: 0.4400 time to fit residues: 442.2885 Evaluate side-chains 613 residues out of total 3815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 499 time to evaluate : 4.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 264 PHE Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 444 PHE Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain A residue 496 GLU Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 767 GLN Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 834 THR Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 936 LEU Chi-restraints excluded: chain A residue 953 ASN Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1105 LEU Chi-restraints excluded: chain A residue 1111 MET Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain A residue 1227 ILE Chi-restraints excluded: chain A residue 1318 THR Chi-restraints excluded: chain A residue 1331 SER Chi-restraints excluded: chain A residue 1338 VAL Chi-restraints excluded: chain A residue 1358 SER Chi-restraints excluded: chain A residue 1385 THR Chi-restraints excluded: chain A residue 1400 CYS Chi-restraints excluded: chain A residue 1424 VAL Chi-restraints excluded: chain A residue 1450 LEU Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 306 ASN Chi-restraints excluded: chain B residue 310 MET Chi-restraints excluded: chain B residue 373 ARG Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 432 MET Chi-restraints excluded: chain B residue 445 LYS Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 465 ASN Chi-restraints excluded: chain B residue 516 ASN Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 585 VAL Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain B residue 729 ILE Chi-restraints excluded: chain B residue 737 THR Chi-restraints excluded: chain B residue 789 MET Chi-restraints excluded: chain B residue 812 LEU Chi-restraints excluded: chain B residue 1023 VAL Chi-restraints excluded: chain B residue 1037 LEU Chi-restraints excluded: chain B residue 1040 ASN Chi-restraints excluded: chain B residue 1049 ASP Chi-restraints excluded: chain B residue 1062 HIS Chi-restraints excluded: chain B residue 1066 SER Chi-restraints excluded: chain B residue 1147 LEU Chi-restraints excluded: chain B residue 1156 ASP Chi-restraints excluded: chain B residue 1162 ILE Chi-restraints excluded: chain B residue 1175 LEU Chi-restraints excluded: chain B residue 1202 LEU Chi-restraints excluded: chain B residue 1205 GLN Chi-restraints excluded: chain B residue 1206 GLU Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 178 PHE Chi-restraints excluded: chain D residue 131 GLU Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 57 GLN Chi-restraints excluded: chain G residue 85 GLU Chi-restraints excluded: chain H residue 130 ARG Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain J residue 57 ILE Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain L residue 31 CYS Chi-restraints excluded: chain L residue 56 LEU Chi-restraints excluded: chain Q residue 380 ASP Chi-restraints excluded: chain M residue 68 VAL Chi-restraints excluded: chain M residue 85 ASN Chi-restraints excluded: chain M residue 121 ASP Chi-restraints excluded: chain M residue 212 THR Chi-restraints excluded: chain M residue 214 ILE Chi-restraints excluded: chain M residue 224 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 258 optimal weight: 5.9990 chunk 167 optimal weight: 7.9990 chunk 249 optimal weight: 10.0000 chunk 126 optimal weight: 5.9990 chunk 82 optimal weight: 8.9990 chunk 81 optimal weight: 20.0000 chunk 265 optimal weight: 7.9990 chunk 284 optimal weight: 2.9990 chunk 206 optimal weight: 9.9990 chunk 38 optimal weight: 6.9990 chunk 328 optimal weight: 10.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 767 GLN ** A 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1070 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 77 HIS B 481 GLN ** B 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 842 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7152 moved from start: 0.4053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 36958 Z= 0.316 Angle : 0.746 11.668 50326 Z= 0.386 Chirality : 0.045 0.241 5666 Planarity : 0.005 0.061 6198 Dihedral : 15.721 158.361 5803 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 22.33 Ramachandran Plot: Outliers : 0.05 % Allowed : 11.58 % Favored : 88.38 % Rotamer: Outliers : 3.88 % Allowed : 23.94 % Favored : 72.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.69 % Cis-general : 0.37 % Twisted Proline : 1.08 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.13), residues: 4259 helix: 0.82 (0.14), residues: 1407 sheet: -0.57 (0.21), residues: 641 loop : -2.04 (0.13), residues: 2211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 556 HIS 0.012 0.001 HIS B1015 PHE 0.024 0.002 PHE J 8 TYR 0.022 0.002 TYR B 486 ARG 0.007 0.000 ARG C 35 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8518 Ramachandran restraints generated. 4259 Oldfield, 0 Emsley, 4259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8518 Ramachandran restraints generated. 4259 Oldfield, 0 Emsley, 4259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 636 residues out of total 3815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 491 time to evaluate : 3.953 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 117 GLU cc_start: 0.9703 (tt0) cc_final: 0.9461 (tm-30) REVERT: A 122 MET cc_start: 0.9113 (tmm) cc_final: 0.8848 (ptt) REVERT: A 225 ASN cc_start: 0.9117 (t0) cc_final: 0.8788 (t0) REVERT: A 234 MET cc_start: 0.9369 (ttm) cc_final: 0.9067 (tpt) REVERT: A 362 ASP cc_start: 0.6858 (p0) cc_final: 0.6620 (p0) REVERT: A 450 LEU cc_start: 0.9080 (mm) cc_final: 0.8738 (tp) REVERT: A 456 MET cc_start: 0.9072 (mpp) cc_final: 0.8642 (mpp) REVERT: A 487 MET cc_start: 0.7649 (mmm) cc_final: 0.7356 (mmm) REVERT: A 500 GLU cc_start: 0.8494 (tt0) cc_final: 0.7838 (tm-30) REVERT: A 504 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.7734 (mm) REVERT: A 521 MET cc_start: 0.8870 (mmm) cc_final: 0.8433 (mmm) REVERT: A 605 MET cc_start: 0.8965 (ttm) cc_final: 0.8592 (mtt) REVERT: A 696 GLU cc_start: 0.9191 (tt0) cc_final: 0.8822 (tp30) REVERT: A 701 LEU cc_start: 0.9257 (pt) cc_final: 0.8507 (pt) REVERT: A 761 MET cc_start: 0.9083 (mtm) cc_final: 0.8597 (mmp) REVERT: A 786 HIS cc_start: 0.8692 (m-70) cc_final: 0.8123 (m-70) REVERT: A 818 MET cc_start: 0.9241 (tpp) cc_final: 0.8683 (mmt) REVERT: A 846 GLU cc_start: 0.8825 (mt-10) cc_final: 0.8427 (mt-10) REVERT: A 894 GLU cc_start: 0.9168 (pp20) cc_final: 0.8925 (pp20) REVERT: A 956 LEU cc_start: 0.9059 (mt) cc_final: 0.8631 (tt) REVERT: A 1111 MET cc_start: 0.8836 (OUTLIER) cc_final: 0.8536 (tpt) REVERT: A 1120 LEU cc_start: 0.9693 (mt) cc_final: 0.9394 (tp) REVERT: A 1277 GLU cc_start: 0.9577 (pm20) cc_final: 0.9264 (pm20) REVERT: A 1309 ASP cc_start: 0.8634 (m-30) cc_final: 0.7914 (p0) REVERT: A 1315 GLU cc_start: 0.8499 (mp0) cc_final: 0.8257 (mp0) REVERT: A 1368 MET cc_start: 0.9070 (mtp) cc_final: 0.8827 (mtp) REVERT: A 1375 MET cc_start: 0.8941 (tmm) cc_final: 0.8462 (tmm) REVERT: A 1400 CYS cc_start: 0.9106 (OUTLIER) cc_final: 0.8731 (p) REVERT: A 1421 CYS cc_start: 0.8657 (t) cc_final: 0.7963 (m) REVERT: B 112 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8627 (mm) REVERT: B 239 GLU cc_start: 0.8179 (tt0) cc_final: 0.7607 (tm-30) REVERT: B 296 GLU cc_start: 0.9473 (mm-30) cc_final: 0.8981 (mp0) REVERT: B 319 GLU cc_start: 0.9369 (tp30) cc_final: 0.9161 (mm-30) REVERT: B 373 ARG cc_start: 0.8864 (OUTLIER) cc_final: 0.8593 (mtt90) REVERT: B 404 LYS cc_start: 0.9180 (mttt) cc_final: 0.8840 (mttt) REVERT: B 444 MET cc_start: 0.7340 (ppp) cc_final: 0.7040 (ppp) REVERT: B 639 ILE cc_start: 0.8943 (pt) cc_final: 0.8703 (pt) REVERT: B 687 GLU cc_start: 0.8951 (tm-30) cc_final: 0.8637 (tm-30) REVERT: B 698 GLU cc_start: 0.8447 (mp0) cc_final: 0.8183 (mp0) REVERT: B 706 GLN cc_start: 0.7989 (mm-40) cc_final: 0.7683 (mm110) REVERT: B 790 ASP cc_start: 0.8159 (t70) cc_final: 0.7664 (t70) REVERT: B 792 MET cc_start: 0.8293 (mtp) cc_final: 0.8048 (mmm) REVERT: B 834 ASN cc_start: 0.8447 (p0) cc_final: 0.7728 (p0) REVERT: B 860 MET cc_start: 0.8243 (ppp) cc_final: 0.7968 (ppp) REVERT: B 963 PHE cc_start: 0.8081 (t80) cc_final: 0.7506 (t80) REVERT: B 992 ILE cc_start: 0.9160 (pt) cc_final: 0.8918 (pt) REVERT: B 999 MET cc_start: 0.9125 (tpp) cc_final: 0.8252 (mmm) REVERT: B 1015 HIS cc_start: 0.8112 (m170) cc_final: 0.7905 (m170) REVERT: B 1021 MET cc_start: 0.8319 (tmm) cc_final: 0.7987 (ppp) REVERT: B 1100 ASP cc_start: 0.8284 (p0) cc_final: 0.7999 (t70) REVERT: B 1153 GLU cc_start: 0.9084 (mm-30) cc_final: 0.8793 (mm-30) REVERT: B 1169 MET cc_start: 0.8879 (mmt) cc_final: 0.8566 (mmm) REVERT: B 1208 MET cc_start: 0.8891 (ptp) cc_final: 0.8191 (ptp) REVERT: C 37 MET cc_start: 0.9306 (tpp) cc_final: 0.9031 (tpt) REVERT: C 46 ILE cc_start: 0.9200 (mt) cc_final: 0.8720 (tp) REVERT: C 52 GLU cc_start: 0.8626 (tm-30) cc_final: 0.8383 (tm-30) REVERT: C 157 CYS cc_start: 0.9313 (m) cc_final: 0.8959 (m) REVERT: E 7 ARG cc_start: 0.9145 (ptm-80) cc_final: 0.8699 (ttp80) REVERT: E 58 MET cc_start: 0.9364 (ttp) cc_final: 0.9083 (tmm) REVERT: E 75 MET cc_start: 0.7163 (OUTLIER) cc_final: 0.6921 (pmm) REVERT: E 115 ASN cc_start: 0.9382 (p0) cc_final: 0.9149 (p0) REVERT: F 81 THR cc_start: 0.9005 (m) cc_final: 0.8525 (p) REVERT: F 103 MET cc_start: 0.9172 (OUTLIER) cc_final: 0.8400 (tmt) REVERT: F 124 GLU cc_start: 0.9220 (tm-30) cc_final: 0.8912 (tm-30) REVERT: G 44 TYR cc_start: 0.7341 (t80) cc_final: 0.6968 (t80) REVERT: G 57 GLN cc_start: 0.8072 (OUTLIER) cc_final: 0.7733 (pm20) REVERT: H 1 MET cc_start: 0.2744 (pmm) cc_final: 0.1321 (tpt) REVERT: H 10 PHE cc_start: 0.8113 (m-80) cc_final: 0.7202 (m-80) REVERT: H 97 MET cc_start: 0.8711 (ppp) cc_final: 0.8437 (ppp) REVERT: H 118 PHE cc_start: 0.9201 (m-80) cc_final: 0.7983 (m-10) REVERT: H 123 MET cc_start: 0.9381 (ppp) cc_final: 0.9002 (ppp) REVERT: I 48 LEU cc_start: 0.9477 (tt) cc_final: 0.9173 (pp) REVERT: I 65 ASP cc_start: 0.9095 (t70) cc_final: 0.8643 (t0) REVERT: I 68 LEU cc_start: 0.9460 (mp) cc_final: 0.9013 (mp) REVERT: K 106 GLU cc_start: 0.9736 (tp30) cc_final: 0.9298 (tp30) REVERT: Q 119 LEU cc_start: 0.8302 (tp) cc_final: 0.8067 (tp) REVERT: M 121 ASP cc_start: 0.7883 (OUTLIER) cc_final: 0.7635 (p0) REVERT: M 132 GLU cc_start: 0.7115 (mm-30) cc_final: 0.6913 (mm-30) REVERT: M 133 TYR cc_start: 0.8172 (m-80) cc_final: 0.7554 (m-10) outliers start: 145 outliers final: 107 residues processed: 586 average time/residue: 0.4442 time to fit residues: 441.4763 Evaluate side-chains 592 residues out of total 3815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 476 time to evaluate : 3.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 264 PHE Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 552 TRP Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 834 THR Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 936 LEU Chi-restraints excluded: chain A residue 953 ASN Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1105 LEU Chi-restraints excluded: chain A residue 1111 MET Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain A residue 1318 THR Chi-restraints excluded: chain A residue 1331 SER Chi-restraints excluded: chain A residue 1338 VAL Chi-restraints excluded: chain A residue 1358 SER Chi-restraints excluded: chain A residue 1385 THR Chi-restraints excluded: chain A residue 1400 CYS Chi-restraints excluded: chain A residue 1405 THR Chi-restraints excluded: chain A residue 1424 VAL Chi-restraints excluded: chain A residue 1450 LEU Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 129 PHE Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 306 ASN Chi-restraints excluded: chain B residue 310 MET Chi-restraints excluded: chain B residue 357 GLN Chi-restraints excluded: chain B residue 373 ARG Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 432 MET Chi-restraints excluded: chain B residue 445 LYS Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 465 ASN Chi-restraints excluded: chain B residue 516 ASN Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 585 VAL Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain B residue 729 ILE Chi-restraints excluded: chain B residue 737 THR Chi-restraints excluded: chain B residue 789 MET Chi-restraints excluded: chain B residue 1023 VAL Chi-restraints excluded: chain B residue 1037 LEU Chi-restraints excluded: chain B residue 1040 ASN Chi-restraints excluded: chain B residue 1049 ASP Chi-restraints excluded: chain B residue 1062 HIS Chi-restraints excluded: chain B residue 1066 SER Chi-restraints excluded: chain B residue 1147 LEU Chi-restraints excluded: chain B residue 1156 ASP Chi-restraints excluded: chain B residue 1162 ILE Chi-restraints excluded: chain B residue 1175 LEU Chi-restraints excluded: chain B residue 1202 LEU Chi-restraints excluded: chain B residue 1205 GLN Chi-restraints excluded: chain B residue 1206 GLU Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 145 CYS Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain G residue 18 PHE Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 57 GLN Chi-restraints excluded: chain H residue 130 ARG Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain J residue 57 ILE Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain L residue 31 CYS Chi-restraints excluded: chain L residue 53 HIS Chi-restraints excluded: chain L residue 56 LEU Chi-restraints excluded: chain Q residue 380 ASP Chi-restraints excluded: chain M residue 68 VAL Chi-restraints excluded: chain M residue 85 ASN Chi-restraints excluded: chain M residue 121 ASP Chi-restraints excluded: chain M residue 128 VAL Chi-restraints excluded: chain M residue 212 THR Chi-restraints excluded: chain M residue 214 ILE Chi-restraints excluded: chain M residue 224 VAL Chi-restraints excluded: chain M residue 236 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 380 optimal weight: 7.9990 chunk 400 optimal weight: 20.0000 chunk 365 optimal weight: 9.9990 chunk 389 optimal weight: 5.9990 chunk 234 optimal weight: 7.9990 chunk 169 optimal weight: 7.9990 chunk 306 optimal weight: 0.4980 chunk 119 optimal weight: 6.9990 chunk 352 optimal weight: 40.0000 chunk 368 optimal weight: 2.9990 chunk 388 optimal weight: 5.9990 overall best weight: 4.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 994 GLN ** A1070 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 481 GLN ** B 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 842 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 moved from start: 0.4178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 36958 Z= 0.262 Angle : 0.742 12.132 50326 Z= 0.380 Chirality : 0.045 0.286 5666 Planarity : 0.005 0.060 6198 Dihedral : 15.667 158.256 5803 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 20.50 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.75 % Favored : 89.20 % Rotamer: Outliers : 3.51 % Allowed : 24.77 % Favored : 71.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.69 % Cis-general : 0.37 % Twisted Proline : 0.54 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.13), residues: 4259 helix: 0.84 (0.14), residues: 1412 sheet: -0.52 (0.21), residues: 634 loop : -2.05 (0.13), residues: 2213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP M 81 HIS 0.007 0.001 HIS A1387 PHE 0.022 0.002 PHE J 8 TYR 0.020 0.001 TYR E 211 ARG 0.011 0.000 ARG J 47 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8518 Ramachandran restraints generated. 4259 Oldfield, 0 Emsley, 4259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8518 Ramachandran restraints generated. 4259 Oldfield, 0 Emsley, 4259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 627 residues out of total 3815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 496 time to evaluate : 3.812 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 62 ASP cc_start: 0.9284 (p0) cc_final: 0.9007 (t0) REVERT: A 117 GLU cc_start: 0.9699 (tt0) cc_final: 0.9462 (tm-30) REVERT: A 122 MET cc_start: 0.9138 (tmm) cc_final: 0.8890 (ptt) REVERT: A 225 ASN cc_start: 0.9175 (t0) cc_final: 0.8894 (t0) REVERT: A 234 MET cc_start: 0.9372 (ttm) cc_final: 0.9080 (tpt) REVERT: A 304 MET cc_start: 0.9316 (tpp) cc_final: 0.9115 (mmt) REVERT: A 362 ASP cc_start: 0.6846 (p0) cc_final: 0.6628 (p0) REVERT: A 450 LEU cc_start: 0.9005 (mm) cc_final: 0.8614 (tp) REVERT: A 456 MET cc_start: 0.9073 (mpp) cc_final: 0.8804 (mpp) REVERT: A 487 MET cc_start: 0.7640 (mmm) cc_final: 0.7307 (mmm) REVERT: A 500 GLU cc_start: 0.8480 (tt0) cc_final: 0.7976 (tm-30) REVERT: A 504 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.7797 (mm) REVERT: A 521 MET cc_start: 0.8748 (mmm) cc_final: 0.8265 (mmm) REVERT: A 605 MET cc_start: 0.8943 (ttm) cc_final: 0.8641 (mtt) REVERT: A 696 GLU cc_start: 0.9198 (tt0) cc_final: 0.8820 (tp30) REVERT: A 701 LEU cc_start: 0.9262 (pt) cc_final: 0.8504 (pt) REVERT: A 748 MET cc_start: 0.9069 (ttt) cc_final: 0.8669 (ppp) REVERT: A 761 MET cc_start: 0.9091 (mtm) cc_final: 0.8673 (mmp) REVERT: A 786 HIS cc_start: 0.8691 (m-70) cc_final: 0.8090 (m-70) REVERT: A 818 MET cc_start: 0.9196 (tpp) cc_final: 0.8620 (mmt) REVERT: A 894 GLU cc_start: 0.9125 (pp20) cc_final: 0.8843 (pp20) REVERT: A 956 LEU cc_start: 0.9018 (mt) cc_final: 0.8613 (tt) REVERT: A 1111 MET cc_start: 0.8737 (OUTLIER) cc_final: 0.8442 (tpt) REVERT: A 1120 LEU cc_start: 0.9697 (mt) cc_final: 0.9396 (tp) REVERT: A 1277 GLU cc_start: 0.9577 (pm20) cc_final: 0.9254 (pm20) REVERT: A 1309 ASP cc_start: 0.8656 (m-30) cc_final: 0.7923 (p0) REVERT: A 1315 GLU cc_start: 0.8455 (mp0) cc_final: 0.8235 (mp0) REVERT: A 1368 MET cc_start: 0.9099 (mtp) cc_final: 0.8881 (mtp) REVERT: A 1375 MET cc_start: 0.8854 (tmm) cc_final: 0.8487 (tmm) REVERT: A 1400 CYS cc_start: 0.9106 (OUTLIER) cc_final: 0.8619 (p) REVERT: B 112 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8586 (mm) REVERT: B 239 GLU cc_start: 0.8181 (tt0) cc_final: 0.7618 (tm-30) REVERT: B 296 GLU cc_start: 0.9482 (mm-30) cc_final: 0.8986 (mp0) REVERT: B 373 ARG cc_start: 0.8837 (OUTLIER) cc_final: 0.8544 (mtt90) REVERT: B 404 LYS cc_start: 0.9182 (mttt) cc_final: 0.8836 (mttt) REVERT: B 444 MET cc_start: 0.7353 (ppp) cc_final: 0.6947 (ppp) REVERT: B 445 LYS cc_start: 0.8165 (OUTLIER) cc_final: 0.7204 (mmmt) REVERT: B 446 LEU cc_start: 0.8241 (mt) cc_final: 0.7587 (mp) REVERT: B 481 GLN cc_start: 0.8435 (mt0) cc_final: 0.8232 (mm-40) REVERT: B 639 ILE cc_start: 0.8947 (pt) cc_final: 0.8713 (pt) REVERT: B 698 GLU cc_start: 0.8392 (mp0) cc_final: 0.8109 (mp0) REVERT: B 706 GLN cc_start: 0.8044 (mm-40) cc_final: 0.7698 (mm110) REVERT: B 790 ASP cc_start: 0.8120 (t70) cc_final: 0.7630 (t70) REVERT: B 834 ASN cc_start: 0.8469 (p0) cc_final: 0.7744 (p0) REVERT: B 860 MET cc_start: 0.8202 (ppp) cc_final: 0.7941 (ppp) REVERT: B 963 PHE cc_start: 0.7955 (t80) cc_final: 0.7424 (t80) REVERT: B 992 ILE cc_start: 0.9122 (pt) cc_final: 0.8858 (pt) REVERT: B 999 MET cc_start: 0.9122 (tpp) cc_final: 0.8281 (mmm) REVERT: B 1021 MET cc_start: 0.8406 (tmm) cc_final: 0.8056 (ppp) REVERT: B 1100 ASP cc_start: 0.8267 (p0) cc_final: 0.7976 (t70) REVERT: B 1153 GLU cc_start: 0.9082 (mm-30) cc_final: 0.8788 (mm-30) REVERT: B 1169 MET cc_start: 0.8880 (mmm) cc_final: 0.8574 (mmm) REVERT: B 1208 MET cc_start: 0.8943 (ptp) cc_final: 0.8155 (ptp) REVERT: C 37 MET cc_start: 0.9299 (tpp) cc_final: 0.9023 (tpt) REVERT: C 46 ILE cc_start: 0.9173 (mt) cc_final: 0.8709 (tp) REVERT: C 52 GLU cc_start: 0.8554 (tm-30) cc_final: 0.8302 (tm-30) REVERT: C 157 CYS cc_start: 0.9353 (m) cc_final: 0.9036 (m) REVERT: C 165 LYS cc_start: 0.8867 (tttt) cc_final: 0.8657 (tttt) REVERT: E 7 ARG cc_start: 0.9139 (ptm-80) cc_final: 0.8699 (ttp80) REVERT: E 58 MET cc_start: 0.9351 (ttp) cc_final: 0.9059 (tmm) REVERT: E 115 ASN cc_start: 0.9390 (p0) cc_final: 0.9158 (p0) REVERT: F 81 THR cc_start: 0.9004 (m) cc_final: 0.8611 (t) REVERT: F 103 MET cc_start: 0.9170 (OUTLIER) cc_final: 0.8408 (tmt) REVERT: F 124 GLU cc_start: 0.9238 (tm-30) cc_final: 0.8952 (tm-30) REVERT: G 44 TYR cc_start: 0.7437 (t80) cc_final: 0.7083 (t80) REVERT: G 51 TYR cc_start: 0.7123 (t80) cc_final: 0.6891 (t80) REVERT: G 57 GLN cc_start: 0.8075 (OUTLIER) cc_final: 0.7761 (pm20) REVERT: H 1 MET cc_start: 0.2777 (pmm) cc_final: 0.1407 (tpt) REVERT: H 10 PHE cc_start: 0.8131 (m-80) cc_final: 0.7130 (m-80) REVERT: H 97 MET cc_start: 0.8763 (ppp) cc_final: 0.8500 (ppp) REVERT: H 118 PHE cc_start: 0.9193 (m-80) cc_final: 0.8056 (m-10) REVERT: H 123 MET cc_start: 0.9388 (ppp) cc_final: 0.9022 (ppp) REVERT: I 48 LEU cc_start: 0.9459 (tt) cc_final: 0.9155 (pp) REVERT: I 65 ASP cc_start: 0.9069 (t70) cc_final: 0.8643 (t0) REVERT: I 68 LEU cc_start: 0.9456 (mp) cc_final: 0.9021 (mp) REVERT: K 106 GLU cc_start: 0.9728 (tp30) cc_final: 0.9273 (tp30) REVERT: Q 27 MET cc_start: 0.8040 (tpt) cc_final: 0.7652 (tpp) REVERT: Q 119 LEU cc_start: 0.8281 (tp) cc_final: 0.8027 (tp) REVERT: M 121 ASP cc_start: 0.7845 (OUTLIER) cc_final: 0.7606 (p0) REVERT: M 133 TYR cc_start: 0.8185 (m-80) cc_final: 0.7526 (m-10) outliers start: 131 outliers final: 108 residues processed: 580 average time/residue: 0.4385 time to fit residues: 430.9217 Evaluate side-chains 592 residues out of total 3815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 475 time to evaluate : 4.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 95 PHE Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 264 PHE Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 444 PHE Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 552 TRP Chi-restraints excluded: chain A residue 573 SER Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 834 THR Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 936 LEU Chi-restraints excluded: chain A residue 953 ASN Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1062 GLU Chi-restraints excluded: chain A residue 1105 LEU Chi-restraints excluded: chain A residue 1111 MET Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain A residue 1318 THR Chi-restraints excluded: chain A residue 1331 SER Chi-restraints excluded: chain A residue 1338 VAL Chi-restraints excluded: chain A residue 1358 SER Chi-restraints excluded: chain A residue 1385 THR Chi-restraints excluded: chain A residue 1400 CYS Chi-restraints excluded: chain A residue 1405 THR Chi-restraints excluded: chain A residue 1424 VAL Chi-restraints excluded: chain A residue 1450 LEU Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 129 PHE Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 306 ASN Chi-restraints excluded: chain B residue 310 MET Chi-restraints excluded: chain B residue 373 ARG Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 432 MET Chi-restraints excluded: chain B residue 445 LYS Chi-restraints excluded: chain B residue 465 ASN Chi-restraints excluded: chain B residue 516 ASN Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 585 VAL Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain B residue 729 ILE Chi-restraints excluded: chain B residue 737 THR Chi-restraints excluded: chain B residue 789 MET Chi-restraints excluded: chain B residue 812 LEU Chi-restraints excluded: chain B residue 1023 VAL Chi-restraints excluded: chain B residue 1037 LEU Chi-restraints excluded: chain B residue 1040 ASN Chi-restraints excluded: chain B residue 1049 ASP Chi-restraints excluded: chain B residue 1062 HIS Chi-restraints excluded: chain B residue 1066 SER Chi-restraints excluded: chain B residue 1147 LEU Chi-restraints excluded: chain B residue 1156 ASP Chi-restraints excluded: chain B residue 1162 ILE Chi-restraints excluded: chain B residue 1175 LEU Chi-restraints excluded: chain B residue 1202 LEU Chi-restraints excluded: chain B residue 1205 GLN Chi-restraints excluded: chain B residue 1206 GLU Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 145 CYS Chi-restraints excluded: chain D residue 137 ASN Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 57 GLN Chi-restraints excluded: chain H residue 130 ARG Chi-restraints excluded: chain H residue 134 ASN Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain J residue 57 ILE Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain L residue 31 CYS Chi-restraints excluded: chain L residue 56 LEU Chi-restraints excluded: chain Q residue 380 ASP Chi-restraints excluded: chain M residue 68 VAL Chi-restraints excluded: chain M residue 85 ASN Chi-restraints excluded: chain M residue 121 ASP Chi-restraints excluded: chain M residue 128 VAL Chi-restraints excluded: chain M residue 212 THR Chi-restraints excluded: chain M residue 214 ILE Chi-restraints excluded: chain M residue 224 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 255 optimal weight: 9.9990 chunk 412 optimal weight: 20.0000 chunk 251 optimal weight: 4.9990 chunk 195 optimal weight: 9.9990 chunk 286 optimal weight: 6.9990 chunk 432 optimal weight: 5.9990 chunk 397 optimal weight: 5.9990 chunk 344 optimal weight: 6.9990 chunk 35 optimal weight: 5.9990 chunk 265 optimal weight: 4.9990 chunk 211 optimal weight: 1.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1070 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 842 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 28 GLN ** D 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 moved from start: 0.4316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 36958 Z= 0.275 Angle : 0.760 12.435 50326 Z= 0.387 Chirality : 0.045 0.240 5666 Planarity : 0.005 0.062 6198 Dihedral : 15.658 158.473 5803 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 21.58 Ramachandran Plot: Outliers : 0.05 % Allowed : 11.36 % Favored : 88.59 % Rotamer: Outliers : 3.37 % Allowed : 25.44 % Favored : 71.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.69 % Cis-general : 0.37 % Twisted Proline : 0.54 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.13), residues: 4259 helix: 0.79 (0.14), residues: 1413 sheet: -0.46 (0.21), residues: 626 loop : -2.07 (0.13), residues: 2220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP M 81 HIS 0.034 0.001 HIS B1015 PHE 0.032 0.002 PHE Q 31 TYR 0.018 0.002 TYR B 486 ARG 0.007 0.000 ARG C 35 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8518 Ramachandran restraints generated. 4259 Oldfield, 0 Emsley, 4259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8518 Ramachandran restraints generated. 4259 Oldfield, 0 Emsley, 4259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 612 residues out of total 3815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 486 time to evaluate : 4.149 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 62 ASP cc_start: 0.9281 (p0) cc_final: 0.8997 (t0) REVERT: A 117 GLU cc_start: 0.9696 (tt0) cc_final: 0.9446 (tm-30) REVERT: A 122 MET cc_start: 0.9089 (tmm) cc_final: 0.8858 (ptt) REVERT: A 225 ASN cc_start: 0.9196 (t0) cc_final: 0.8927 (t0) REVERT: A 304 MET cc_start: 0.9273 (tpp) cc_final: 0.9071 (mmt) REVERT: A 362 ASP cc_start: 0.6829 (p0) cc_final: 0.6629 (p0) REVERT: A 450 LEU cc_start: 0.8997 (mm) cc_final: 0.8667 (tp) REVERT: A 456 MET cc_start: 0.9050 (mpp) cc_final: 0.8803 (mpp) REVERT: A 487 MET cc_start: 0.7659 (mmm) cc_final: 0.7310 (mmm) REVERT: A 504 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.7939 (mm) REVERT: A 521 MET cc_start: 0.8864 (mmm) cc_final: 0.8399 (mmm) REVERT: A 605 MET cc_start: 0.8951 (ttm) cc_final: 0.8639 (mtt) REVERT: A 696 GLU cc_start: 0.9186 (tt0) cc_final: 0.8814 (tp30) REVERT: A 701 LEU cc_start: 0.9329 (pt) cc_final: 0.8605 (pt) REVERT: A 748 MET cc_start: 0.9009 (ttt) cc_final: 0.8623 (ppp) REVERT: A 761 MET cc_start: 0.9096 (mtm) cc_final: 0.8679 (mmp) REVERT: A 786 HIS cc_start: 0.8702 (m-70) cc_final: 0.8258 (m-70) REVERT: A 818 MET cc_start: 0.9199 (tpp) cc_final: 0.8617 (mmt) REVERT: A 846 GLU cc_start: 0.8863 (mt-10) cc_final: 0.8642 (mt-10) REVERT: A 847 ASP cc_start: 0.8175 (p0) cc_final: 0.7559 (p0) REVERT: A 894 GLU cc_start: 0.9096 (pp20) cc_final: 0.8798 (pp20) REVERT: A 956 LEU cc_start: 0.9051 (mt) cc_final: 0.8614 (tt) REVERT: A 1079 MET cc_start: 0.6311 (ttp) cc_final: 0.5992 (mtp) REVERT: A 1120 LEU cc_start: 0.9699 (mt) cc_final: 0.9394 (tp) REVERT: A 1277 GLU cc_start: 0.9568 (pm20) cc_final: 0.9238 (pm20) REVERT: A 1315 GLU cc_start: 0.8532 (mp0) cc_final: 0.8323 (mp0) REVERT: A 1368 MET cc_start: 0.9056 (mtp) cc_final: 0.8814 (mtp) REVERT: A 1375 MET cc_start: 0.8875 (tmm) cc_final: 0.8404 (tmm) REVERT: A 1400 CYS cc_start: 0.9125 (OUTLIER) cc_final: 0.8752 (p) REVERT: B 112 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8551 (mm) REVERT: B 239 GLU cc_start: 0.8179 (tt0) cc_final: 0.7612 (tm-30) REVERT: B 296 GLU cc_start: 0.9479 (mm-30) cc_final: 0.8986 (mp0) REVERT: B 373 ARG cc_start: 0.8826 (OUTLIER) cc_final: 0.8545 (mtt90) REVERT: B 404 LYS cc_start: 0.9187 (mttt) cc_final: 0.8852 (mttt) REVERT: B 444 MET cc_start: 0.7296 (ppp) cc_final: 0.6920 (ppp) REVERT: B 445 LYS cc_start: 0.8132 (OUTLIER) cc_final: 0.7210 (mmmt) REVERT: B 446 LEU cc_start: 0.8275 (mt) cc_final: 0.7590 (mp) REVERT: B 481 GLN cc_start: 0.8443 (mt0) cc_final: 0.8225 (mm-40) REVERT: B 540 SER cc_start: 0.8878 (t) cc_final: 0.8057 (m) REVERT: B 639 ILE cc_start: 0.8939 (pt) cc_final: 0.8702 (pt) REVERT: B 698 GLU cc_start: 0.8425 (mp0) cc_final: 0.8138 (mp0) REVERT: B 790 ASP cc_start: 0.8131 (t70) cc_final: 0.7642 (t70) REVERT: B 834 ASN cc_start: 0.8421 (p0) cc_final: 0.7667 (p0) REVERT: B 860 MET cc_start: 0.8196 (ppp) cc_final: 0.7958 (ppp) REVERT: B 963 PHE cc_start: 0.7931 (t80) cc_final: 0.7429 (t80) REVERT: B 992 ILE cc_start: 0.9133 (pt) cc_final: 0.8880 (pt) REVERT: B 999 MET cc_start: 0.9123 (tpp) cc_final: 0.8221 (mmm) REVERT: B 1021 MET cc_start: 0.8320 (tmm) cc_final: 0.8024 (ppp) REVERT: B 1100 ASP cc_start: 0.8280 (p0) cc_final: 0.7970 (t70) REVERT: B 1153 GLU cc_start: 0.9052 (mm-30) cc_final: 0.8742 (mm-30) REVERT: B 1169 MET cc_start: 0.8912 (mmm) cc_final: 0.8559 (mmm) REVERT: B 1208 MET cc_start: 0.8963 (ptp) cc_final: 0.8703 (ptt) REVERT: B 1210 MET cc_start: 0.8822 (mtp) cc_final: 0.8468 (ttp) REVERT: C 37 MET cc_start: 0.9287 (tpp) cc_final: 0.9014 (tpt) REVERT: C 46 ILE cc_start: 0.9176 (mt) cc_final: 0.8714 (tp) REVERT: C 52 GLU cc_start: 0.8541 (tm-30) cc_final: 0.8287 (tm-30) REVERT: C 157 CYS cc_start: 0.9361 (m) cc_final: 0.9048 (m) REVERT: C 192 TRP cc_start: 0.9075 (t60) cc_final: 0.8467 (t60) REVERT: E 7 ARG cc_start: 0.9126 (ptm-80) cc_final: 0.8687 (ttp80) REVERT: E 58 MET cc_start: 0.9357 (ttp) cc_final: 0.9069 (tmm) REVERT: E 115 ASN cc_start: 0.9397 (p0) cc_final: 0.9162 (p0) REVERT: E 208 TYR cc_start: 0.7496 (t80) cc_final: 0.7024 (t80) REVERT: F 81 THR cc_start: 0.8954 (m) cc_final: 0.8576 (t) REVERT: F 103 MET cc_start: 0.9182 (OUTLIER) cc_final: 0.8421 (tmt) REVERT: F 124 GLU cc_start: 0.9243 (tm-30) cc_final: 0.8965 (tm-30) REVERT: G 44 TYR cc_start: 0.7395 (t80) cc_final: 0.7052 (t80) REVERT: G 51 TYR cc_start: 0.7227 (t80) cc_final: 0.7010 (t80) REVERT: G 57 GLN cc_start: 0.8029 (OUTLIER) cc_final: 0.7715 (pm20) REVERT: H 1 MET cc_start: 0.2885 (pmm) cc_final: 0.1550 (tpt) REVERT: H 10 PHE cc_start: 0.8154 (m-80) cc_final: 0.7173 (m-80) REVERT: H 118 PHE cc_start: 0.9166 (m-80) cc_final: 0.8028 (m-10) REVERT: H 123 MET cc_start: 0.9419 (ppp) cc_final: 0.9013 (ppp) REVERT: I 48 LEU cc_start: 0.9461 (tt) cc_final: 0.9158 (pp) REVERT: I 65 ASP cc_start: 0.9038 (t70) cc_final: 0.8577 (t0) REVERT: I 68 LEU cc_start: 0.9448 (mp) cc_final: 0.9015 (mp) REVERT: K 106 GLU cc_start: 0.9725 (tp30) cc_final: 0.9279 (tp30) REVERT: Q 30 ASN cc_start: 0.5802 (p0) cc_final: 0.5496 (p0) REVERT: Q 31 PHE cc_start: 0.5233 (t80) cc_final: 0.5004 (t80) REVERT: Q 119 LEU cc_start: 0.8291 (tp) cc_final: 0.8027 (tp) REVERT: M 121 ASP cc_start: 0.7835 (OUTLIER) cc_final: 0.7599 (p0) REVERT: M 132 GLU cc_start: 0.7019 (mm-30) cc_final: 0.6814 (mm-30) REVERT: M 133 TYR cc_start: 0.8151 (m-80) cc_final: 0.7464 (m-10) outliers start: 126 outliers final: 108 residues processed: 573 average time/residue: 0.4440 time to fit residues: 431.8855 Evaluate side-chains 588 residues out of total 3815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 472 time to evaluate : 4.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 264 PHE Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 444 PHE Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 552 TRP Chi-restraints excluded: chain A residue 573 SER Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 834 THR Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 936 LEU Chi-restraints excluded: chain A residue 953 ASN Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1062 GLU Chi-restraints excluded: chain A residue 1064 VAL Chi-restraints excluded: chain A residue 1105 LEU Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain A residue 1318 THR Chi-restraints excluded: chain A residue 1331 SER Chi-restraints excluded: chain A residue 1338 VAL Chi-restraints excluded: chain A residue 1358 SER Chi-restraints excluded: chain A residue 1385 THR Chi-restraints excluded: chain A residue 1400 CYS Chi-restraints excluded: chain A residue 1405 THR Chi-restraints excluded: chain A residue 1424 VAL Chi-restraints excluded: chain A residue 1450 LEU Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 129 PHE Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 306 ASN Chi-restraints excluded: chain B residue 310 MET Chi-restraints excluded: chain B residue 373 ARG Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 432 MET Chi-restraints excluded: chain B residue 445 LYS Chi-restraints excluded: chain B residue 465 ASN Chi-restraints excluded: chain B residue 516 ASN Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 585 VAL Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain B residue 729 ILE Chi-restraints excluded: chain B residue 737 THR Chi-restraints excluded: chain B residue 789 MET Chi-restraints excluded: chain B residue 812 LEU Chi-restraints excluded: chain B residue 1023 VAL Chi-restraints excluded: chain B residue 1037 LEU Chi-restraints excluded: chain B residue 1040 ASN Chi-restraints excluded: chain B residue 1049 ASP Chi-restraints excluded: chain B residue 1062 HIS Chi-restraints excluded: chain B residue 1066 SER Chi-restraints excluded: chain B residue 1147 LEU Chi-restraints excluded: chain B residue 1156 ASP Chi-restraints excluded: chain B residue 1162 ILE Chi-restraints excluded: chain B residue 1175 LEU Chi-restraints excluded: chain B residue 1202 LEU Chi-restraints excluded: chain B residue 1205 GLN Chi-restraints excluded: chain B residue 1206 GLU Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 145 CYS Chi-restraints excluded: chain D residue 137 ASN Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain G residue 12 THR Chi-restraints excluded: chain G residue 18 PHE Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 57 GLN Chi-restraints excluded: chain H residue 130 ARG Chi-restraints excluded: chain H residue 134 ASN Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain J residue 57 ILE Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain L residue 31 CYS Chi-restraints excluded: chain L residue 56 LEU Chi-restraints excluded: chain Q residue 380 ASP Chi-restraints excluded: chain M residue 85 ASN Chi-restraints excluded: chain M residue 121 ASP Chi-restraints excluded: chain M residue 128 VAL Chi-restraints excluded: chain M residue 212 THR Chi-restraints excluded: chain M residue 214 ILE Chi-restraints excluded: chain M residue 224 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 273 optimal weight: 5.9990 chunk 366 optimal weight: 20.0000 chunk 105 optimal weight: 0.2980 chunk 317 optimal weight: 2.9990 chunk 50 optimal weight: 0.0670 chunk 95 optimal weight: 9.9990 chunk 344 optimal weight: 10.0000 chunk 144 optimal weight: 0.1980 chunk 354 optimal weight: 4.9990 chunk 43 optimal weight: 6.9990 chunk 63 optimal weight: 0.0060 overall best weight: 0.7136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 654 ASN ** A 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1070 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 776 GLN ** B 834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 842 ASN C 31 ASN ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 40 HIS ** Q 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.129997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.088511 restraints weight = 117303.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.091362 restraints weight = 54213.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.093301 restraints weight = 33429.070| |-----------------------------------------------------------------------------| r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3640 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3640 r_free = 0.3640 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.95 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3640 r_free = 0.3640 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3640 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.4487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 36958 Z= 0.189 Angle : 0.762 12.534 50326 Z= 0.378 Chirality : 0.045 0.291 5666 Planarity : 0.004 0.059 6198 Dihedral : 15.525 160.229 5803 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 16.83 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.32 % Favored : 90.63 % Rotamer: Outliers : 2.22 % Allowed : 26.64 % Favored : 71.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.69 % Cis-general : 0.37 % Twisted Proline : 0.54 % 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: -1.02 (0.13), residues: 4259 helix: 1.01 (0.14), residues: 1407 sheet: -0.37 (0.21), residues: 628 loop : -1.98 (0.13), residues: 2224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP M 81 HIS 0.005 0.001 HIS A 80 PHE 0.033 0.001 PHE Q 31 TYR 0.015 0.001 TYR B 833 ARG 0.007 0.000 ARG B1150 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9124.16 seconds wall clock time: 166 minutes 1.22 seconds (9961.22 seconds total)