Starting phenix.real_space_refine on Tue Feb 20 17:30:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hyj_35086/02_2024/8hyj_35086.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hyj_35086/02_2024/8hyj_35086.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hyj_35086/02_2024/8hyj_35086.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hyj_35086/02_2024/8hyj_35086.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hyj_35086/02_2024/8hyj_35086.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hyj_35086/02_2024/8hyj_35086.pdb" } resolution = 4.3 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= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 4 6.06 5 P 83 5.49 5 Mg 1 5.21 5 S 161 5.16 5 C 17890 2.51 5 N 4986 2.21 5 O 5443 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 34": "OE1" <-> "OE2" Residue "A GLU 64": "OE1" <-> "OE2" Residue "A GLU 89": "OE1" <-> "OE2" Residue "A GLU 182": "OE1" <-> "OE2" Residue "A GLU 204": "OE1" <-> "OE2" Residue "A GLU 238": "OE1" <-> "OE2" Residue "A GLU 260": "OE1" <-> "OE2" Residue "A GLU 265": "OE1" <-> "OE2" Residue "A GLU 338": "OE1" <-> "OE2" Residue "A ARG 348": "NH1" <-> "NH2" Residue "A GLU 353": "OE1" <-> "OE2" Residue "A GLU 476": "OE1" <-> "OE2" Residue "A GLU 504": "OE1" <-> "OE2" Residue "A ARG 505": "NH1" <-> "NH2" Residue "A GLU 551": "OE1" <-> "OE2" Residue "A GLU 583": "OE1" <-> "OE2" Residue "A GLU 591": "OE1" <-> "OE2" Residue "A GLU 615": "OE1" <-> "OE2" Residue "A ARG 640": "NH1" <-> "NH2" Residue "A ARG 650": "NH1" <-> "NH2" Residue "A GLU 815": "OE1" <-> "OE2" Residue "A GLU 856": "OE1" <-> "OE2" Residue "A GLU 961": "OE1" <-> "OE2" Residue "A GLU 988": "OE1" <-> "OE2" Residue "A ARG 993": "NH1" <-> "NH2" Residue "A GLU 1126": "OE1" <-> "OE2" Residue "A GLU 1146": "OE1" <-> "OE2" Residue "A GLU 1195": "OE1" <-> "OE2" Residue "A GLU 1228": "OE1" <-> "OE2" Residue "B TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 73": "OE1" <-> "OE2" Residue "B GLU 77": "OE1" <-> "OE2" Residue "B ARG 91": "NH1" <-> "NH2" Residue "B GLU 113": "OE1" <-> "OE2" Residue "B GLU 139": "OE1" <-> "OE2" Residue "B GLU 214": "OE1" <-> "OE2" Residue "B ARG 227": "NH1" <-> "NH2" Residue "B GLU 265": "OE1" <-> "OE2" Residue "B ARG 370": "NH1" <-> "NH2" Residue "B ARG 387": "NH1" <-> "NH2" Residue "B ARG 396": "NH1" <-> "NH2" Residue "B ARG 409": "NH1" <-> "NH2" Residue "B ARG 419": "NH1" <-> "NH2" Residue "B ARG 420": "NH1" <-> "NH2" Residue "B ARG 454": "NH1" <-> "NH2" Residue "B ARG 491": "NH1" <-> "NH2" Residue "B ARG 507": "NH1" <-> "NH2" Residue "B ARG 516": "NH1" <-> "NH2" Residue "B PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 602": "OE1" <-> "OE2" Residue "B ARG 605": "NH1" <-> "NH2" Residue "B GLU 608": "OE1" <-> "OE2" Residue "B GLU 667": "OE1" <-> "OE2" Residue "B ARG 713": "NH1" <-> "NH2" Residue "B GLU 785": "OE1" <-> "OE2" Residue "B ARG 863": "NH1" <-> "NH2" Residue "B ARG 903": "NH1" <-> "NH2" Residue "B GLU 929": "OE1" <-> "OE2" Residue "B GLU 962": "OE1" <-> "OE2" Residue "B ARG 1016": "NH1" <-> "NH2" Residue "B ARG 1021": "NH1" <-> "NH2" Residue "B GLU 1045": "OE1" <-> "OE2" Residue "B ARG 1109": "NH1" <-> "NH2" Residue "B ARG 1134": "NH1" <-> "NH2" Residue "C ARG 8": "NH1" <-> "NH2" Residue "C ARG 15": "NH1" <-> "NH2" Residue "C ARG 27": "NH1" <-> "NH2" Residue "C GLU 28": "OE1" <-> "OE2" Residue "C ARG 38": "NH1" <-> "NH2" Residue "C GLU 44": "OE1" <-> "OE2" Residue "C GLU 65": "OE1" <-> "OE2" Residue "C PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 85": "NH1" <-> "NH2" Residue "C GLU 105": "OE1" <-> "OE2" Residue "C ARG 123": "NH1" <-> "NH2" Residue "C ARG 170": "NH1" <-> "NH2" Residue "C TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 199": "OE1" <-> "OE2" Residue "C GLU 207": "OE1" <-> "OE2" Residue "C GLU 243": "OE1" <-> "OE2" Residue "D GLU 87": "OE1" <-> "OE2" Residue "D GLU 113": "OE1" <-> "OE2" Residue "D GLU 147": "OE1" <-> "OE2" Residue "D GLU 168": "OE1" <-> "OE2" Residue "D GLU 172": "OE1" <-> "OE2" Residue "D GLU 185": "OE1" <-> "OE2" Residue "D GLU 196": "OE1" <-> "OE2" Residue "E GLU 23": "OE1" <-> "OE2" Residue "E GLU 24": "OE1" <-> "OE2" Residue "E GLU 133": "OE1" <-> "OE2" Residue "E GLU 140": "OE1" <-> "OE2" Residue "E GLU 166": "OE1" <-> "OE2" Residue "E GLU 178": "OE1" <-> "OE2" Residue "F GLU 104": "OE1" <-> "OE2" Residue "F ARG 108": "NH1" <-> "NH2" Residue "F ARG 115": "NH1" <-> "NH2" Residue "G GLU 16": "OE1" <-> "OE2" Residue "G GLU 35": "OE1" <-> "OE2" Residue "G GLU 45": "OE1" <-> "OE2" Residue "G GLU 60": "OE1" <-> "OE2" Residue "G GLU 134": "OE1" <-> "OE2" Residue "G GLU 142": "OE1" <-> "OE2" Residue "G GLU 156": "OE1" <-> "OE2" Residue "G GLU 158": "OE1" <-> "OE2" Residue "G GLU 168": "OE1" <-> "OE2" Residue "G GLU 177": "OE1" <-> "OE2" Residue "G GLU 178": "OE1" <-> "OE2" Residue "I ARG 75": "NH1" <-> "NH2" Residue "I GLU 95": "OE1" <-> "OE2" Residue "I ARG 113": "NH1" <-> "NH2" Residue "J GLU 31": "OE1" <-> "OE2" Residue "J GLU 57": "OE1" <-> "OE2" Residue "K ARG 47": "NH1" <-> "NH2" Residue "K TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 74": "NH1" <-> "NH2" Residue "K GLU 97": "OE1" <-> "OE2" Residue "K GLU 106": "OE1" <-> "OE2" Residue "L ARG 44": "NH1" <-> "NH2" Residue "L GLU 49": "OE1" <-> "OE2" Residue "W GLU 652": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 28568 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 8794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1141, 8794 Classifications: {'peptide': 1141} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 42, 'TRANS': 1098} Chain breaks: 4 Unresolved non-hydrogen bonds: 157 Unresolved non-hydrogen angles: 190 Unresolved non-hydrogen dihedrals: 144 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 88 Chain: "B" Number of atoms: 7912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1054, 7912 Classifications: {'peptide': 1054} Incomplete info: {'truncation_to_alanine': 139} Link IDs: {'PTRANS': 40, 'TRANS': 1013} Chain breaks: 10 Unresolved non-hydrogen bonds: 494 Unresolved non-hydrogen angles: 605 Unresolved non-hydrogen dihedrals: 402 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 7, 'TRP:plan': 1, 'ASP:plan': 21, 'PHE:plan': 1, 'GLU:plan': 38, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 343 Chain: "C" Number of atoms: 2123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2123 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 13, 'TRANS': 271} Chain breaks: 1 Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 152 Unresolved non-hydrogen dihedrals: 98 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 8, 'ASP:plan': 10} Unresolved non-hydrogen planarities: 90 Chain: "D" Number of atoms: 896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 896 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 109} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "E" Number of atoms: 1652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1652 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 3, 'TRANS': 205} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "F" Number of atoms: 554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 554 Classifications: {'peptide': 76} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 4, 'TRANS': 71} Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 7, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 46 Chain: "G" Number of atoms: 1417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1417 Classifications: {'peptide': 178} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 169} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 904 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 5, 'TRANS': 117} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 2, 'HIS:plan': 3, 'ARG:plan': 2, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 54 Chain: "I" Number of atoms: 702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 702 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain breaks: 1 Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 2, 'GLU:plan': 6, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 78 Chain: "J" Number of atoms: 484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 484 Classifications: {'peptide': 62} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 1, 'TRANS': 60} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 20 Chain: "K" Number of atoms: 756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 756 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 3, 'TRANS': 96} Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 4, 'ARG:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 44 Chain: "L" Number of atoms: 309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 309 Classifications: {'peptide': 42} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'TRANS': 41} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "N" Number of atoms: 749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 749 Classifications: {'DNA': 36} Link IDs: {'rna3p': 35} Chain breaks: 1 Chain: "P" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 218 Classifications: {'RNA': 10} Modifications used: {'rna3p_pur': 7, 'rna3p_pyr': 3} Link IDs: {'rna3p': 9} Chain: "T" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 746 Classifications: {'DNA': 37} Link IDs: {'rna3p': 36} Chain: "W" Number of atoms: 347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 347 Classifications: {'peptide': 44} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 17355 SG CYS C 90 60.680 84.146 143.944 1.00 95.55 S ATOM 17378 SG CYS C 93 57.920 83.536 141.364 1.00105.96 S ATOM 17419 SG CYS C 99 57.118 84.814 144.844 1.00 80.86 S ATOM 17441 SG CYS C 102 58.791 86.914 141.950 1.00 77.68 S ATOM 24296 SG CYS I 7 45.093 155.861 39.569 1.00 97.61 S ATOM 24312 SG CYS I 10 42.976 153.903 41.222 1.00 99.01 S ATOM 24439 SG CYS I 29 45.564 153.282 37.551 1.00117.62 S ATOM 24458 SG CYS I 32 42.257 154.176 37.378 1.00116.72 S ATOM 25006 SG CYS J 7 63.320 115.605 129.564 1.00 47.84 S ATOM 25030 SG CYS J 10 65.362 115.545 133.098 1.00 51.10 S ATOM 25284 SG CYS J 44 66.199 118.184 130.418 1.00 53.90 S ATOM 25290 SG CYS J 45 63.042 117.973 132.249 1.00 54.08 S ATOM 26226 SG CYS L 12 24.478 99.768 111.775 1.00 72.87 S ATOM 26244 SG CYS L 15 22.009 100.937 114.195 1.00 85.23 S ATOM 26337 SG CYS L 29 21.755 97.770 111.461 1.00 78.65 S ATOM 26353 SG CYS L 32 21.454 100.798 109.987 1.00 84.11 S Time building chain proxies: 15.13, per 1000 atoms: 0.53 Number of scatterers: 28568 At special positions: 0 Unit cell: (146.3, 173.8, 169.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 S 161 16.00 P 83 15.00 Mg 1 11.99 O 5443 8.00 N 4986 7.00 C 17890 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: 10.94 Conformation dependent library (CDL) restraints added in 5.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 99 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 93 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 90 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 102 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 10 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 32 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 7 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 29 " pdb=" ZN J 200 " pdb="ZN ZN J 200 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 200 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 200 " - pdb=" SG CYS J 7 " pdb="ZN ZN J 200 " - pdb=" SG CYS J 44 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 15 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 32 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 29 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 12 " Number of angles added : 24 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6652 Finding SS restraints... Secondary structure from input PDB file: 113 helices and 39 sheets defined 35.2% alpha, 15.2% beta 21 base pairs and 58 stacking pairs defined. Time for finding SS restraints: 9.49 Creating SS restraints... Processing helix chain 'A' and resid 23 through 31 Processing helix chain 'A' and resid 39 through 45 removed outlier: 3.531A pdb=" N THR A 44 " --> pdb=" O SER A 41 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASN A 45 " --> pdb=" O GLN A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 85 No H-bonds generated for 'chain 'A' and resid 83 through 85' Processing helix chain 'A' and resid 86 through 97 removed outlier: 3.911A pdb=" N LEU A 97 " --> pdb=" O MET A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 164 Processing helix chain 'A' and resid 176 through 186 removed outlier: 3.734A pdb=" N VAL A 180 " --> pdb=" O LEU A 176 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ARG A 186 " --> pdb=" O GLU A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 199 Processing helix chain 'A' and resid 215 through 219 removed outlier: 4.059A pdb=" N LEU A 218 " --> pdb=" O PRO A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 252 Processing helix chain 'A' and resid 258 through 263 Processing helix chain 'A' and resid 266 through 275 removed outlier: 4.040A pdb=" N THR A 275 " --> pdb=" O ARG A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 349 removed outlier: 3.548A pdb=" N ALA A 346 " --> pdb=" O PRO A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 368 removed outlier: 3.610A pdb=" N GLN A 364 " --> pdb=" O ARG A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 423 removed outlier: 3.767A pdb=" N SER A 422 " --> pdb=" O HIS A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 443 Processing helix chain 'A' and resid 462 through 472 Processing helix chain 'A' and resid 492 through 504 Processing helix chain 'A' and resid 509 through 519 removed outlier: 4.320A pdb=" N TYR A 519 " --> pdb=" O GLN A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 549 removed outlier: 3.597A pdb=" N ILE A 544 " --> pdb=" O THR A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 592 removed outlier: 4.213A pdb=" N SER A 579 " --> pdb=" O ASP A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 616 removed outlier: 3.661A pdb=" N THR A 597 " --> pdb=" O GLY A 593 " (cutoff:3.500A) Proline residue: A 606 - end of helix removed outlier: 3.568A pdb=" N ALA A 614 " --> pdb=" O GLU A 610 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU A 615 " --> pdb=" O SER A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 642 Processing helix chain 'A' and resid 643 through 648 removed outlier: 3.580A pdb=" N VAL A 646 " --> pdb=" O SER A 643 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG A 648 " --> pdb=" O MET A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 675 Processing helix chain 'A' and resid 678 through 684 removed outlier: 3.718A pdb=" N ASN A 682 " --> pdb=" O TYR A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 697 Processing helix chain 'A' and resid 715 through 720 Processing helix chain 'A' and resid 721 through 730 Processing helix chain 'A' and resid 750 through 784 Proline residue: A 775 - end of helix Processing helix chain 'A' and resid 828 through 846 Proline residue: A 839 - end of helix Processing helix chain 'A' and resid 848 through 862 removed outlier: 3.654A pdb=" N SER A 854 " --> pdb=" O ASN A 850 " (cutoff:3.500A) Processing helix chain 'A' and resid 871 through 876 removed outlier: 3.752A pdb=" N ARG A 875 " --> pdb=" O THR A 871 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 901 removed outlier: 3.651A pdb=" N ARG A 900 " --> pdb=" O ALA A 896 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASN A 901 " --> pdb=" O CYS A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 907 through 912 removed outlier: 3.729A pdb=" N THR A 911 " --> pdb=" O SER A 907 " (cutoff:3.500A) Processing helix chain 'A' and resid 951 through 967 removed outlier: 3.828A pdb=" N ASP A 955 " --> pdb=" O ILE A 951 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE A 956 " --> pdb=" O SER A 952 " (cutoff:3.500A) Processing helix chain 'A' and resid 978 through 982 removed outlier: 3.875A pdb=" N ARG A 981 " --> pdb=" O ASP A 978 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR A 982 " --> pdb=" O PHE A 979 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 978 through 982' Processing helix chain 'A' and resid 1014 through 1033 removed outlier: 3.627A pdb=" N GLU A1018 " --> pdb=" O ASP A1014 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N THR A1027 " --> pdb=" O VAL A1023 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N VAL A1028 " --> pdb=" O LEU A1024 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR A1029 " --> pdb=" O CYS A1025 " (cutoff:3.500A) Proline residue: A1030 - end of helix Processing helix chain 'A' and resid 1086 through 1095 removed outlier: 3.514A pdb=" N CYS A1095 " --> pdb=" O VAL A1091 " (cutoff:3.500A) Processing helix chain 'A' and resid 1114 through 1119 Processing helix chain 'A' and resid 1120 through 1140 removed outlier: 3.549A pdb=" N ALA A1124 " --> pdb=" O GLY A1120 " (cutoff:3.500A) Processing helix chain 'A' and resid 1144 through 1156 Processing helix chain 'A' and resid 1165 through 1176 Processing helix chain 'A' and resid 1180 through 1188 removed outlier: 3.907A pdb=" N GLU A1184 " --> pdb=" O ALA A1180 " (cutoff:3.500A) Processing helix chain 'A' and resid 1189 through 1201 removed outlier: 4.018A pdb=" N CYS A1193 " --> pdb=" O ALA A1189 " (cutoff:3.500A) Processing helix chain 'A' and resid 1208 through 1213 removed outlier: 4.231A pdb=" N SER A1212 " --> pdb=" O THR A1208 " (cutoff:3.500A) Processing helix chain 'A' and resid 1221 through 1225 removed outlier: 3.637A pdb=" N GLY A1224 " --> pdb=" O VAL A1221 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER A1225 " --> pdb=" O GLY A1222 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1221 through 1225' Processing helix chain 'B' and resid 23 through 27 removed outlier: 3.786A pdb=" N LEU B 26 " --> pdb=" O LEU B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 46 removed outlier: 4.271A pdb=" N CYS B 35 " --> pdb=" O LEU B 31 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N LYS B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ALA B 39 " --> pdb=" O CYS B 35 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER B 41 " --> pdb=" O LYS B 37 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N PHE B 42 " --> pdb=" O ALA B 38 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N PHE B 43 " --> pdb=" O ALA B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 60 removed outlier: 3.922A pdb=" N TYR B 58 " --> pdb=" O ASN B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 70 Processing helix chain 'B' and resid 117 through 125 removed outlier: 3.699A pdb=" N ALA B 121 " --> pdb=" O LEU B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 247 Processing helix chain 'B' and resid 279 through 286 Processing helix chain 'B' and resid 290 through 298 Processing helix chain 'B' and resid 304 through 321 removed outlier: 3.589A pdb=" N ASN B 309 " --> pdb=" O ALA B 305 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER B 310 " --> pdb=" O SER B 306 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL B 321 " --> pdb=" O VAL B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 341 Processing helix chain 'B' and resid 349 through 357 removed outlier: 3.801A pdb=" N HIS B 355 " --> pdb=" O ASP B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 384 removed outlier: 3.668A pdb=" N LEU B 379 " --> pdb=" O MET B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 396 No H-bonds generated for 'chain 'B' and resid 394 through 396' Processing helix chain 'B' and resid 404 through 431 removed outlier: 3.525A pdb=" N GLU B 410 " --> pdb=" O LEU B 406 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS B 428 " --> pdb=" O ARG B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 removed outlier: 4.088A pdb=" N TYR B 442 " --> pdb=" O PRO B 438 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU B 443 " --> pdb=" O ILE B 439 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 438 through 443' Processing helix chain 'B' and resid 445 through 459 Processing helix chain 'B' and resid 482 through 490 removed outlier: 3.768A pdb=" N THR B 486 " --> pdb=" O ASN B 482 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU B 487 " --> pdb=" O PRO B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 555 Processing helix chain 'B' and resid 586 through 599 Processing helix chain 'B' and resid 634 through 640 Processing helix chain 'B' and resid 649 through 656 Processing helix chain 'B' and resid 664 through 670 removed outlier: 3.634A pdb=" N GLU B 668 " --> pdb=" O ILE B 664 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ASP B 669 " --> pdb=" O GLU B 665 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N CYS B 670 " --> pdb=" O GLU B 666 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 664 through 670' Processing helix chain 'B' and resid 675 through 682 removed outlier: 3.660A pdb=" N GLU B 682 " --> pdb=" O GLN B 678 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 697 removed outlier: 3.593A pdb=" N LEU B 697 " --> pdb=" O SER B 694 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 710 removed outlier: 3.799A pdb=" N ASP B 710 " --> pdb=" O ALA B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 711 through 721 Processing helix chain 'B' and resid 755 through 762 Processing helix chain 'B' and resid 949 through 954 removed outlier: 3.707A pdb=" N SER B 953 " --> pdb=" O HIS B 949 " (cutoff:3.500A) Processing helix chain 'B' and resid 956 through 971 removed outlier: 4.577A pdb=" N LEU B 960 " --> pdb=" O THR B 956 " (cutoff:3.500A) Processing helix chain 'B' and resid 996 through 1008 removed outlier: 3.539A pdb=" N GLN B1003 " --> pdb=" O GLU B 999 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N HIS B1005 " --> pdb=" O THR B1001 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ARG B1006 " --> pdb=" O GLU B1002 " (cutoff:3.500A) Processing helix chain 'B' and resid 1043 through 1048 removed outlier: 3.968A pdb=" N LYS B1047 " --> pdb=" O MET B1043 " (cutoff:3.500A) Processing helix chain 'B' and resid 1076 through 1087 Processing helix chain 'B' and resid 1089 through 1098 Processing helix chain 'B' and resid 1148 through 1162 removed outlier: 3.524A pdb=" N LYS B1152 " --> pdb=" O PRO B1148 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 44 removed outlier: 3.607A pdb=" N ALA C 34 " --> pdb=" O ASP C 30 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA C 36 " --> pdb=" O SER C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 65 No H-bonds generated for 'chain 'C' and resid 63 through 65' Processing helix chain 'C' and resid 66 through 73 removed outlier: 3.586A pdb=" N ARG C 70 " --> pdb=" O PHE C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 84 removed outlier: 4.408A pdb=" N MET C 82 " --> pdb=" O GLU C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 181 removed outlier: 3.767A pdb=" N TRP C 180 " --> pdb=" O HIS C 177 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N SER C 181 " --> pdb=" O ALA C 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 177 through 181' Processing helix chain 'C' and resid 199 through 204 removed outlier: 3.570A pdb=" N THR C 203 " --> pdb=" O GLU C 199 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU C 204 " --> pdb=" O MET C 200 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 199 through 204' Processing helix chain 'C' and resid 205 through 210 Processing helix chain 'C' and resid 211 through 216 removed outlier: 4.635A pdb=" N GLU C 214 " --> pdb=" O ASP C 211 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER C 215 " --> pdb=" O LEU C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 238 removed outlier: 3.828A pdb=" N TYR C 238 " --> pdb=" O PRO C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 252 Processing helix chain 'C' and resid 278 through 294 removed outlier: 3.966A pdb=" N ASN C 284 " --> pdb=" O GLN C 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 114 removed outlier: 3.920A pdb=" N VAL D 109 " --> pdb=" O LYS D 105 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N GLY D 110 " --> pdb=" O GLY D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 133 removed outlier: 4.279A pdb=" N ARG D 125 " --> pdb=" O VAL D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 152 removed outlier: 4.048A pdb=" N VAL D 142 " --> pdb=" O ASN D 138 " (cutoff:3.500A) Proline residue: D 148 - end of helix Processing helix chain 'D' and resid 155 through 166 Processing helix chain 'D' and resid 169 through 177 Processing helix chain 'D' and resid 178 through 181 removed outlier: 4.090A pdb=" N LYS D 181 " --> pdb=" O PRO D 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 178 through 181' Processing helix chain 'D' and resid 183 through 201 removed outlier: 6.073A pdb=" N GLN D 189 " --> pdb=" O GLU D 185 " (cutoff:3.500A) Proline residue: D 190 - end of helix Processing helix chain 'E' and resid 22 through 42 removed outlier: 3.756A pdb=" N HIS E 26 " --> pdb=" O SER E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 52 Processing helix chain 'E' and resid 54 through 63 Processing helix chain 'E' and resid 96 through 111 removed outlier: 3.696A pdb=" N ILE E 100 " --> pdb=" O LYS E 96 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 132 Processing helix chain 'E' and resid 133 through 135 No H-bonds generated for 'chain 'E' and resid 133 through 135' Processing helix chain 'F' and resid 66 through 82 Processing helix chain 'F' and resid 96 through 106 removed outlier: 3.773A pdb=" N ILE F 100 " --> pdb=" O ASP F 96 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 38 removed outlier: 3.925A pdb=" N LEU G 25 " --> pdb=" O LYS G 21 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 26 Processing helix chain 'J' and resid 45 through 51 removed outlier: 3.847A pdb=" N LEU J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N MET J 50 " --> pdb=" O ARG J 46 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 62 Processing helix chain 'K' and resid 39 through 51 removed outlier: 3.551A pdb=" N ASN K 44 " --> pdb=" O HIS K 40 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLN K 49 " --> pdb=" O ILE K 45 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 113 removed outlier: 3.506A pdb=" N ALA K 86 " --> pdb=" O SER K 82 " (cutoff:3.500A) Processing helix chain 'W' and resid 650 through 652 No H-bonds generated for 'chain 'W' and resid 650 through 652' Processing sheet with id=AA1, first strand: chain 'A' and resid 18 through 21 Processing sheet with id=AA2, first strand: chain 'A' and resid 132 through 136 Processing sheet with id=AA3, first strand: chain 'A' and resid 323 through 325 removed outlier: 3.906A pdb=" N SER A 323 " --> pdb=" O ARG B1051 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ARG A 325 " --> pdb=" O LYS B1049 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS B1049 " --> pdb=" O ARG A 325 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 328 through 330 Processing sheet with id=AA5, first strand: chain 'A' and resid 338 through 341 Processing sheet with id=AA6, first strand: chain 'A' and resid 350 through 353 removed outlier: 3.754A pdb=" N VAL A 400 " --> pdb=" O GLU A 353 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N HIS A 401 " --> pdb=" O SER A 374 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N SER A 374 " --> pdb=" O HIS A 401 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 789 through 791 removed outlier: 6.618A pdb=" N VAL A 797 " --> pdb=" O ILE A 806 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 877 through 879 removed outlier: 3.868A pdb=" N ASN A1047 " --> pdb=" O ASP A1073 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1227 through 1228 removed outlier: 3.998A pdb=" N ILE F 114 " --> pdb=" O TRP F 126 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N TRP F 126 " --> pdb=" O ILE F 114 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N SER F 122 " --> pdb=" O LEU F 118 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 74 through 76 removed outlier: 3.676A pdb=" N ALA B 93 " --> pdb=" O VAL B 76 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 100 through 102 removed outlier: 5.332A pdb=" N ALA B 130 " --> pdb=" O SER B 175 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N SER B 175 " --> pdb=" O ALA B 130 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ILE B 132 " --> pdb=" O ILE B 173 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 106 through 109 Processing sheet with id=AB4, first strand: chain 'B' and resid 208 through 209 Processing sheet with id=AB5, first strand: chain 'B' and resid 398 through 401 removed outlier: 3.527A pdb=" N GLN B 220 " --> pdb=" O GLU B 401 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ALA B 219 " --> pdb=" O ARG B 494 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 236 through 239 removed outlier: 3.844A pdb=" N PHE B 248 " --> pdb=" O PHE B 239 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE B 249 " --> pdb=" O TYR B 271 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N THR B 269 " --> pdb=" O ARG B 251 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE B 277 " --> pdb=" O VAL B 270 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 579 through 584 removed outlier: 5.565A pdb=" N TRP B 580 " --> pdb=" O LEU B 576 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N LEU B 576 " --> pdb=" O TRP B 580 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY B 582 " --> pdb=" O VAL B 574 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 660 through 663 removed outlier: 3.690A pdb=" N ARG B 629 " --> pdb=" O ILE B 662 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 742 through 745 removed outlier: 3.911A pdb=" N LYS B 885 " --> pdb=" O SER B 901 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ARG B 903 " --> pdb=" O VAL B 883 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N VAL B 883 " --> pdb=" O ARG B 903 " (cutoff:3.500A) removed outlier: 9.074A pdb=" N VAL B 905 " --> pdb=" O GLY B 881 " (cutoff:3.500A) removed outlier: 9.684A pdb=" N GLY B 881 " --> pdb=" O VAL B 905 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 742 through 745 removed outlier: 3.911A pdb=" N LYS B 885 " --> pdb=" O SER B 901 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ARG B 903 " --> pdb=" O VAL B 883 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N VAL B 883 " --> pdb=" O ARG B 903 " (cutoff:3.500A) removed outlier: 9.074A pdb=" N VAL B 905 " --> pdb=" O GLY B 881 " (cutoff:3.500A) removed outlier: 9.684A pdb=" N GLY B 881 " --> pdb=" O VAL B 905 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N VAL B 886 " --> pdb=" O LYS L 39 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 1014 through 1015 removed outlier: 7.063A pdb=" N ILE B 788 " --> pdb=" O GLY B 925 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N LEU B 927 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N MET B 790 " --> pdb=" O LEU B 927 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL B 789 " --> pdb=" O VAL B 945 " (cutoff:3.500A) removed outlier: 8.496A pdb=" N ILE B 944 " --> pdb=" O ASN B 771 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ILE B 773 " --> pdb=" O ILE B 944 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N PHE B1031 " --> pdb=" O VAL B 776 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 859 through 861 removed outlier: 3.773A pdb=" N ILE B 861 " --> pdb=" O ILE B 873 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 935 through 936 Processing sheet with id=AC5, first strand: chain 'B' and resid 1114 through 1115 removed outlier: 4.274A pdb=" N HIS B1106 " --> pdb=" O ALA B1115 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL B1145 " --> pdb=" O MET B1105 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILE B1107 " --> pdb=" O VAL B1143 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL B1143 " --> pdb=" O ILE B1107 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 16 through 17 removed outlier: 3.850A pdb=" N GLU C 16 " --> pdb=" O LYS C 23 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 104 through 111 removed outlier: 3.595A pdb=" N VAL C 104 " --> pdb=" O ALA C 169 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU C 52 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N ARG C 170 " --> pdb=" O ILE C 50 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N ILE C 50 " --> pdb=" O ARG C 170 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N GLY C 172 " --> pdb=" O MET C 48 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N MET C 48 " --> pdb=" O GLY C 172 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 118 through 119 Processing sheet with id=AC9, first strand: chain 'C' and resid 192 through 196 Processing sheet with id=AD1, first strand: chain 'E' and resid 87 through 88 Processing sheet with id=AD2, first strand: chain 'E' and resid 160 through 162 removed outlier: 3.726A pdb=" N GLN E 161 " --> pdb=" O LYS E 204 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 2 through 13 removed outlier: 4.140A pdb=" N PHE G 76 " --> pdb=" O LEU G 7 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TRP G 9 " --> pdb=" O VAL G 74 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL G 74 " --> pdb=" O TRP G 9 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE G 13 " --> pdb=" O VAL G 70 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N VAL G 70 " --> pdb=" O ILE G 13 " (cutoff:3.500A) removed outlier: 10.226A pdb=" N ASP G 56 " --> pdb=" O PRO G 73 " (cutoff:3.500A) removed outlier: 8.912A pdb=" N MET G 75 " --> pdb=" O THR G 54 " (cutoff:3.500A) removed outlier: 8.972A pdb=" N THR G 54 " --> pdb=" O MET G 75 " (cutoff:3.500A) removed outlier: 8.417A pdb=" N SER G 77 " --> pdb=" O VAL G 52 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N VAL G 52 " --> pdb=" O SER G 77 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N MET G 79 " --> pdb=" O VAL G 50 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 2 through 13 removed outlier: 4.140A pdb=" N PHE G 76 " --> pdb=" O LEU G 7 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TRP G 9 " --> pdb=" O VAL G 74 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL G 74 " --> pdb=" O TRP G 9 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE G 13 " --> pdb=" O VAL G 70 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N VAL G 70 " --> pdb=" O ILE G 13 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 89 through 96 removed outlier: 6.729A pdb=" N PHE G 102 " --> pdb=" O HIS G 94 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N VAL G 96 " --> pdb=" O GLY G 100 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N GLY G 100 " --> pdb=" O VAL G 96 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N VAL G 101 " --> pdb=" O TYR G 112 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N TYR G 112 " --> pdb=" O VAL G 101 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N MET G 103 " --> pdb=" O ASN G 110 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ASN G 110 " --> pdb=" O MET G 103 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N PHE G 161 " --> pdb=" O ILE G 108 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N ASN G 110 " --> pdb=" O PHE G 161 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ALA G 163 " --> pdb=" O ASN G 110 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N SER G 114 " --> pdb=" O ALA G 165 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLY G 151 " --> pdb=" O LEU G 164 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N SER G 166 " --> pdb=" O VAL G 149 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N VAL G 149 " --> pdb=" O SER G 166 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLY G 91 " --> pdb=" O VAL G 145 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL G 147 " --> pdb=" O ILE G 89 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ILE G 89 " --> pdb=" O VAL G 147 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 122 through 124 removed outlier: 3.887A pdb=" N ILE G 130 " --> pdb=" O ILE G 124 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 8 through 17 removed outlier: 5.667A pdb=" N VAL H 14 " --> pdb=" O THR H 33 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N THR H 33 " --> pdb=" O VAL H 14 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N LEU H 120 " --> pdb=" O ASP H 44 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU H 119 " --> pdb=" O PHE H 116 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N TYR H 113 " --> pdb=" O TYR H 98 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER H 115 " --> pdb=" O LYS H 96 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS H 96 " --> pdb=" O SER H 115 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY H 95 " --> pdb=" O LEU H 139 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU H 139 " --> pdb=" O GLY H 95 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N PHE H 8 " --> pdb=" O LEU H 62 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 14 through 19 Processing sheet with id=AD9, first strand: chain 'I' and resid 84 through 89 removed outlier: 3.788A pdb=" N TRP I 112 " --> pdb=" O PHE I 101 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'K' and resid 19 through 23 removed outlier: 6.378A pdb=" N ILE K 72 " --> pdb=" O TYR K 61 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N TYR K 61 " --> pdb=" O ILE K 72 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ARG K 74 " --> pdb=" O ALA K 59 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ALA K 59 " --> pdb=" O ARG K 74 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N HIS K 76 " --> pdb=" O LEU K 57 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'W' and resid 625 through 626 Processing sheet with id=AE3, first strand: chain 'W' and resid 638 through 639 985 hydrogen bonds defined for protein. 2760 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 54 hydrogen bonds 108 hydrogen bond angles 0 basepair planarities 21 basepair parallelities 58 stacking parallelities Total time for adding SS restraints: 12.37 Time building geometry restraints manager: 11.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 4494 1.28 - 1.41: 7309 1.41 - 1.54: 16992 1.54 - 1.68: 221 1.68 - 1.81: 240 Bond restraints: 29256 Sorted by residual: bond pdb=" CA SER B 535 " pdb=" C SER B 535 " ideal model delta sigma weight residual 1.528 1.416 0.112 1.35e-02 5.49e+03 6.89e+01 bond pdb=" CA GLN B 955 " pdb=" C GLN B 955 " ideal model delta sigma weight residual 1.526 1.448 0.078 9.70e-03 1.06e+04 6.46e+01 bond pdb=" CA LYS B 211 " pdb=" C LYS B 211 " ideal model delta sigma weight residual 1.528 1.444 0.084 1.07e-02 8.73e+03 6.15e+01 bond pdb=" CA HIS C 177 " pdb=" C HIS C 177 " ideal model delta sigma weight residual 1.521 1.426 0.095 1.22e-02 6.72e+03 6.04e+01 bond pdb=" C LEU B 406 " pdb=" O LEU B 406 " ideal model delta sigma weight residual 1.236 1.141 0.096 1.25e-02 6.40e+03 5.88e+01 ... (remaining 29251 not shown) Histogram of bond angle deviations from ideal: 91.14 - 100.76: 81 100.76 - 110.38: 8520 110.38 - 119.99: 18818 119.99 - 129.61: 12322 129.61 - 139.23: 210 Bond angle restraints: 39951 Sorted by residual: angle pdb=" N VAL B 634 " pdb=" CA VAL B 634 " pdb=" C VAL B 634 " ideal model delta sigma weight residual 110.42 125.93 -15.51 9.40e-01 1.13e+00 2.72e+02 angle pdb=" N LEU B 356 " pdb=" CA LEU B 356 " pdb=" C LEU B 356 " ideal model delta sigma weight residual 111.36 126.20 -14.84 1.09e+00 8.42e-01 1.85e+02 angle pdb=" N SER B 730 " pdb=" CA SER B 730 " pdb=" C SER B 730 " ideal model delta sigma weight residual 111.07 125.56 -14.49 1.07e+00 8.73e-01 1.84e+02 angle pdb=" N ASP J 33 " pdb=" CA ASP J 33 " pdb=" C ASP J 33 " ideal model delta sigma weight residual 113.61 95.01 18.60 1.50e+00 4.44e-01 1.54e+02 angle pdb=" N GLY B 72 " pdb=" CA GLY B 72 " pdb=" C GLY B 72 " ideal model delta sigma weight residual 112.31 131.45 -19.14 1.59e+00 3.96e-01 1.45e+02 ... (remaining 39946 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.45: 16773 34.45 - 68.89: 669 68.89 - 103.34: 35 103.34 - 137.78: 1 137.78 - 172.23: 8 Dihedral angle restraints: 17486 sinusoidal: 7233 harmonic: 10253 Sorted by residual: dihedral pdb=" CA GLU B 77 " pdb=" C GLU B 77 " pdb=" N PRO B 78 " pdb=" CA PRO B 78 " ideal model delta harmonic sigma weight residual 180.00 150.18 29.82 0 5.00e+00 4.00e-02 3.56e+01 dihedral pdb=" C VAL B 778 " pdb=" N VAL B 778 " pdb=" CA VAL B 778 " pdb=" CB VAL B 778 " ideal model delta harmonic sigma weight residual -122.00 -107.75 -14.25 0 2.50e+00 1.60e-01 3.25e+01 dihedral pdb=" C GLN B 974 " pdb=" N GLN B 974 " pdb=" CA GLN B 974 " pdb=" CB GLN B 974 " ideal model delta harmonic sigma weight residual -122.60 -108.96 -13.64 0 2.50e+00 1.60e-01 2.98e+01 ... (remaining 17483 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.134: 4038 0.134 - 0.269: 456 0.269 - 0.403: 115 0.403 - 0.537: 20 0.537 - 0.672: 7 Chirality restraints: 4636 Sorted by residual: chirality pdb=" CA ARG W 627 " pdb=" N ARG W 627 " pdb=" C ARG W 627 " pdb=" CB ARG W 627 " both_signs ideal model delta sigma weight residual False 2.51 1.84 0.67 2.00e-01 2.50e+01 1.13e+01 chirality pdb=" CA LYS B 181 " pdb=" N LYS B 181 " pdb=" C LYS B 181 " pdb=" CB LYS B 181 " both_signs ideal model delta sigma weight residual False 2.51 1.87 0.64 2.00e-01 2.50e+01 1.02e+01 chirality pdb=" CA GLU C 28 " pdb=" N GLU C 28 " pdb=" C GLU C 28 " pdb=" CB GLU C 28 " both_signs ideal model delta sigma weight residual False 2.51 1.89 0.62 2.00e-01 2.50e+01 9.71e+00 ... (remaining 4633 not shown) Planarity restraints: 4805 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO A1030 " -0.026 2.00e-02 2.50e+03 5.25e-02 2.76e+01 pdb=" C PRO A1030 " 0.091 2.00e-02 2.50e+03 pdb=" O PRO A1030 " -0.034 2.00e-02 2.50e+03 pdb=" N VAL A1031 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR C 133 " -0.074 5.00e-02 4.00e+02 1.14e-01 2.09e+01 pdb=" N PRO C 134 " 0.198 5.00e-02 4.00e+02 pdb=" CA PRO C 134 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO C 134 " -0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 522 " 0.065 5.00e-02 4.00e+02 1.01e-01 1.62e+01 pdb=" N PRO B 523 " -0.174 5.00e-02 4.00e+02 pdb=" CA PRO B 523 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO B 523 " 0.060 5.00e-02 4.00e+02 ... (remaining 4802 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.70: 2306 2.70 - 3.25: 26972 3.25 - 3.80: 44375 3.80 - 4.35: 55494 4.35 - 4.90: 90323 Nonbonded interactions: 219470 Sorted by model distance: nonbonded pdb=" N ASP J 33 " pdb=" N ALA J 34 " model vdw 2.155 2.560 nonbonded pdb=" O SER A 707 " pdb=" OH TYR A 713 " model vdw 2.198 2.440 nonbonded pdb=" CZ PHE B 116 " pdb=" CB ALA B 121 " model vdw 2.200 3.760 nonbonded pdb=" NH2 ARG A1060 " pdb=" CG GLU E 210 " model vdw 2.200 3.520 nonbonded pdb=" O4 DT N 6 " pdb=" N6 DA T -6 " model vdw 2.211 2.520 ... (remaining 219465 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 5.140 Check model and map are aligned: 0.450 Set scattering table: 0.270 Process input model: 86.770 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 97.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5475 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 : 0.015 0.112 29256 Z= 0.994 Angle : 1.483 19.136 39951 Z= 0.994 Chirality : 0.099 0.672 4636 Planarity : 0.007 0.114 4805 Dihedral : 17.343 172.228 10834 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 2.39 % Allowed : 9.01 % Favored : 88.60 % Cbeta Deviations : 0.96 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.61 (0.12), residues: 3465 helix: -1.03 (0.14), residues: 1133 sheet: -1.53 (0.22), residues: 515 loop : -2.28 (0.12), residues: 1817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP B 119 HIS 0.016 0.002 HIS B 51 PHE 0.044 0.002 PHE C 24 TYR 0.033 0.002 TYR C 190 ARG 0.008 0.001 ARG B 629 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 3130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 388 time to evaluate : 3.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 ILE cc_start: 0.7885 (pt) cc_final: 0.7497 (tp) REVERT: A 852 ASN cc_start: 0.6958 (OUTLIER) cc_final: 0.6151 (m110) REVERT: A 1035 ILE cc_start: 0.8575 (OUTLIER) cc_final: 0.8320 (mm) REVERT: B 658 ILE cc_start: 0.6807 (OUTLIER) cc_final: 0.5816 (tp) REVERT: B 740 THR cc_start: 0.6161 (m) cc_final: 0.5838 (p) REVERT: B 902 LEU cc_start: 0.7248 (mp) cc_final: 0.6280 (tp) REVERT: B 1043 MET cc_start: 0.4568 (mtt) cc_final: 0.4266 (mtm) REVERT: B 1097 PHE cc_start: 0.7971 (t80) cc_final: 0.7594 (t80) REVERT: B 1146 TYR cc_start: 0.8627 (m-10) cc_final: 0.8364 (p90) REVERT: D 192 GLN cc_start: 0.9071 (tm-30) cc_final: 0.8829 (pp30) REVERT: F 65 MET cc_start: 0.6230 (ttp) cc_final: 0.6005 (ttt) REVERT: F 74 LEU cc_start: 0.9063 (mt) cc_final: 0.8662 (tt) REVERT: F 98 LEU cc_start: 0.8704 (mt) cc_final: 0.8312 (mm) REVERT: F 102 MET cc_start: 0.9220 (tpt) cc_final: 0.8923 (tmm) REVERT: G 30 LEU cc_start: 0.9194 (mm) cc_final: 0.8943 (pp) REVERT: G 178 GLU cc_start: 0.5304 (mt-10) cc_final: 0.4687 (pm20) outliers start: 67 outliers final: 11 residues processed: 444 average time/residue: 0.4644 time to fit residues: 312.0954 Evaluate side-chains 209 residues out of total 3130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 195 time to evaluate : 3.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 298 optimal weight: 40.0000 chunk 268 optimal weight: 7.9990 chunk 148 optimal weight: 5.9990 chunk 91 optimal weight: 8.9990 chunk 180 optimal weight: 20.0000 chunk 143 optimal weight: 8.9990 chunk 277 optimal weight: 8.9990 chunk 107 optimal weight: 20.0000 chunk 168 optimal weight: 6.9990 chunk 206 optimal weight: 5.9990 chunk 321 optimal weight: 30.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 45 ASN ** A 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 258 ASN A 391 HIS A 398 GLN A 461 GLN ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 490 GLN A 543 GLN A 664 HIS ** A 781 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 947 GLN A 957 HIS A1100 HIS ** A1114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1153 ASN B 54 ASN ** B 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 GLN B 135 ASN B 246 ASN B 397 ASN B 427 GLN B 441 HIS B 510 HIS B 513 HIS B 543 GLN B 577 ASN B 688 HIS ** B 711 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 718 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 722 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 749 GLN B 768 ASN B 770 GLN ** B 853 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 871 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 GLN B1005 HIS ** B1038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1057 HIS ** B1086 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1104 GLN B1116 ASN C 94 ASN ** C 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 GLN C 202 ASN ** C 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 291 GLN D 192 GLN ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 84 ASN ** G 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 67 ASN H 94 HIS H 137 GLN I 11 ASN I 12 ASN I 31 ASN I 88 GLN J 61 ASN ** K 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 55 ASN W 612 GLN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5817 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 29256 Z= 0.301 Angle : 0.687 9.696 39951 Z= 0.368 Chirality : 0.042 0.187 4636 Planarity : 0.005 0.061 4805 Dihedral : 15.945 177.049 4721 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 16.34 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.14 % Favored : 94.83 % Rotamer: Outliers : 0.25 % Allowed : 5.34 % Favored : 94.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.13), residues: 3465 helix: -0.34 (0.15), residues: 1174 sheet: -1.34 (0.21), residues: 564 loop : -1.86 (0.13), residues: 1727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 855 HIS 0.008 0.002 HIS B 316 PHE 0.019 0.002 PHE B 951 TYR 0.017 0.002 TYR B 442 ARG 0.008 0.001 ARG B 597 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 3130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 226 time to evaluate : 3.534 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: B 740 THR cc_start: 0.6785 (m) cc_final: 0.6483 (p) REVERT: B 1043 MET cc_start: 0.4910 (mtt) cc_final: 0.4703 (mtt) REVERT: C 201 MET cc_start: 0.8772 (tmm) cc_final: 0.8547 (tmm) REVERT: C 251 MET cc_start: 0.5751 (mtt) cc_final: 0.5511 (mtt) REVERT: D 147 GLU cc_start: 0.8603 (tm-30) cc_final: 0.8202 (tm-30) REVERT: F 102 MET cc_start: 0.9217 (tpt) cc_final: 0.8922 (tmm) REVERT: G 18 MET cc_start: 0.0707 (mmm) cc_final: 0.0448 (mmt) REVERT: G 132 MET cc_start: 0.6266 (ptp) cc_final: 0.6018 (tpp) REVERT: G 138 ARG cc_start: 0.7681 (ptt-90) cc_final: 0.7328 (ptp90) REVERT: G 178 GLU cc_start: 0.5564 (mt-10) cc_final: 0.4500 (pm20) REVERT: H 121 MET cc_start: 0.7283 (ttm) cc_final: 0.7032 (ttm) REVERT: I 97 MET cc_start: 0.8850 (tpt) cc_final: 0.8626 (tpp) REVERT: K 48 MET cc_start: 0.7125 (mmm) cc_final: 0.6917 (mmm) outliers start: 7 outliers final: 0 residues processed: 233 average time/residue: 0.4243 time to fit residues: 158.6722 Evaluate side-chains 166 residues out of total 3130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 166 time to evaluate : 2.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 178 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 267 optimal weight: 0.9990 chunk 218 optimal weight: 1.9990 chunk 88 optimal weight: 30.0000 chunk 322 optimal weight: 20.0000 chunk 347 optimal weight: 20.0000 chunk 286 optimal weight: 30.0000 chunk 319 optimal weight: 8.9990 chunk 109 optimal weight: 7.9990 chunk 258 optimal weight: 9.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS A 71 HIS ** A 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 216 ASN A 364 GLN A 515 GLN ** A 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 781 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 441 HIS ** B 711 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 718 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 853 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 918 HIS ** B 947 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1086 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 159 GLN ** E 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 HIS ** G 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 137 GLN ** I 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 653 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5855 moved from start: 0.3998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 29256 Z= 0.193 Angle : 0.576 9.996 39951 Z= 0.305 Chirality : 0.040 0.200 4636 Planarity : 0.004 0.061 4805 Dihedral : 15.830 173.785 4721 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.65 % Favored : 95.32 % Rotamer: Outliers : 0.14 % Allowed : 4.20 % Favored : 95.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.14), residues: 3465 helix: 0.06 (0.15), residues: 1179 sheet: -1.13 (0.22), residues: 530 loop : -1.57 (0.14), residues: 1756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1050 HIS 0.011 0.001 HIS B 722 PHE 0.015 0.001 PHE B 729 TYR 0.014 0.001 TYR A 163 ARG 0.008 0.001 ARG W 627 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 3130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 214 time to evaluate : 3.594 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 406 ASP cc_start: 0.8665 (m-30) cc_final: 0.8465 (m-30) REVERT: A 470 MET cc_start: 0.8549 (mtm) cc_final: 0.8097 (mpp) REVERT: C 201 MET cc_start: 0.8653 (tmm) cc_final: 0.8431 (tmm) REVERT: C 251 MET cc_start: 0.5909 (mtt) cc_final: 0.5471 (mtt) REVERT: D 93 MET cc_start: -0.0164 (mmp) cc_final: -0.0570 (mmm) REVERT: F 102 MET cc_start: 0.9253 (tpt) cc_final: 0.8938 (tmm) REVERT: G 132 MET cc_start: 0.6697 (ptp) cc_final: 0.6394 (tpp) REVERT: G 138 ARG cc_start: 0.7613 (ptt-90) cc_final: 0.7134 (ptp90) REVERT: G 178 GLU cc_start: 0.5887 (mt-10) cc_final: 0.4568 (pm20) REVERT: H 121 MET cc_start: 0.7228 (ttm) cc_final: 0.6739 (tpp) REVERT: I 97 MET cc_start: 0.8957 (tpt) cc_final: 0.8753 (tpp) REVERT: W 616 ILE cc_start: 0.4878 (mp) cc_final: 0.4669 (mp) outliers start: 4 outliers final: 1 residues processed: 217 average time/residue: 0.4113 time to fit residues: 144.2790 Evaluate side-chains 165 residues out of total 3130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 164 time to evaluate : 3.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 318 optimal weight: 30.0000 chunk 242 optimal weight: 1.9990 chunk 167 optimal weight: 0.8980 chunk 35 optimal weight: 6.9990 chunk 153 optimal weight: 10.0000 chunk 216 optimal weight: 40.0000 chunk 323 optimal weight: 20.0000 chunk 342 optimal weight: 8.9990 chunk 168 optimal weight: 9.9990 chunk 306 optimal weight: 8.9990 chunk 92 optimal weight: 5.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 781 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1233 GLN ** B 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 HIS ** B 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 711 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 718 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN ** B 853 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 947 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 HIS ** B1038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1104 GLN ** C 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 42 HIS H 137 GLN ** I 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 80 GLN I 110 HIS ** J 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6018 moved from start: 0.5098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 29256 Z= 0.228 Angle : 0.598 9.378 39951 Z= 0.317 Chirality : 0.041 0.226 4636 Planarity : 0.004 0.054 4805 Dihedral : 15.865 175.073 4721 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 17.65 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.57 % Favored : 94.40 % Rotamer: Outliers : 0.04 % Allowed : 4.49 % Favored : 95.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.14), residues: 3465 helix: 0.17 (0.15), residues: 1166 sheet: -1.17 (0.22), residues: 554 loop : -1.44 (0.14), residues: 1745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A1050 HIS 0.010 0.001 HIS B 722 PHE 0.031 0.002 PHE A 724 TYR 0.014 0.001 TYR B1037 ARG 0.009 0.001 ARG E 184 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 3130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 199 time to evaluate : 3.180 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 631 MET cc_start: 0.8025 (mmm) cc_final: 0.7404 (tpt) REVERT: C 201 MET cc_start: 0.8544 (tmm) cc_final: 0.8288 (tmm) REVERT: C 251 MET cc_start: 0.5750 (mtt) cc_final: 0.5317 (mtt) REVERT: D 152 TYR cc_start: 0.6529 (m-80) cc_final: 0.6221 (t80) REVERT: F 102 MET cc_start: 0.9291 (tpt) cc_final: 0.9020 (tmm) REVERT: G 24 MET cc_start: 0.6311 (tmm) cc_final: 0.4762 (tmm) REVERT: G 132 MET cc_start: 0.6789 (ptp) cc_final: 0.6469 (tpp) REVERT: G 138 ARG cc_start: 0.7658 (ptt-90) cc_final: 0.7236 (ptp90) REVERT: G 178 GLU cc_start: 0.6136 (mt-10) cc_final: 0.4440 (pm20) outliers start: 1 outliers final: 0 residues processed: 200 average time/residue: 0.4194 time to fit residues: 134.5515 Evaluate side-chains 150 residues out of total 3130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 3.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 284 optimal weight: 6.9990 chunk 194 optimal weight: 8.9990 chunk 4 optimal weight: 50.0000 chunk 254 optimal weight: 4.9990 chunk 141 optimal weight: 5.9990 chunk 291 optimal weight: 0.9990 chunk 236 optimal weight: 8.9990 chunk 0 optimal weight: 50.0000 chunk 174 optimal weight: 9.9990 chunk 307 optimal weight: 20.0000 chunk 86 optimal weight: 7.9990 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 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 45 ASN ** A 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 781 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 441 HIS B 450 ASN ** B 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 711 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 718 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 724 GLN B 771 ASN ** B 853 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 947 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 988 HIS ** B1038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 215 HIS H 137 GLN I 31 ASN ** J 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6074 moved from start: 0.5669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 29256 Z= 0.225 Angle : 0.591 12.164 39951 Z= 0.311 Chirality : 0.041 0.234 4636 Planarity : 0.004 0.053 4805 Dihedral : 15.903 172.998 4721 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 17.72 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.63 % Favored : 94.34 % Rotamer: Outliers : 0.04 % Allowed : 2.81 % Favored : 97.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.14), residues: 3465 helix: 0.22 (0.15), residues: 1176 sheet: -1.24 (0.22), residues: 535 loop : -1.38 (0.14), residues: 1754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 229 HIS 0.005 0.001 HIS K 65 PHE 0.021 0.001 PHE G 131 TYR 0.024 0.001 TYR A 163 ARG 0.008 0.001 ARG E 184 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 3130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 192 time to evaluate : 3.180 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: A 631 MET cc_start: 0.7999 (mmm) cc_final: 0.7515 (tpt) REVERT: C 201 MET cc_start: 0.8467 (tmm) cc_final: 0.8226 (tmm) REVERT: C 251 MET cc_start: 0.5795 (mtt) cc_final: 0.5412 (mtt) REVERT: D 152 TYR cc_start: 0.6522 (m-80) cc_final: 0.6183 (t80) REVERT: F 102 MET cc_start: 0.9351 (tpt) cc_final: 0.9111 (tmm) REVERT: G 24 MET cc_start: 0.6438 (tmm) cc_final: 0.6020 (tmm) REVERT: G 132 MET cc_start: 0.6774 (ptp) cc_final: 0.6516 (tpp) REVERT: G 138 ARG cc_start: 0.7686 (ptt-90) cc_final: 0.7218 (ptp90) REVERT: G 178 GLU cc_start: 0.6300 (mt-10) cc_final: 0.4483 (pm20) REVERT: I 97 MET cc_start: 0.9098 (tpt) cc_final: 0.8889 (tpp) outliers start: 1 outliers final: 0 residues processed: 193 average time/residue: 0.4165 time to fit residues: 129.4833 Evaluate side-chains 147 residues out of total 3130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 147 time to evaluate : 3.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 115 optimal weight: 9.9990 chunk 308 optimal weight: 20.0000 chunk 67 optimal weight: 8.9990 chunk 200 optimal weight: 30.0000 chunk 84 optimal weight: 40.0000 chunk 342 optimal weight: 30.0000 chunk 284 optimal weight: 5.9990 chunk 158 optimal weight: 7.9990 chunk 28 optimal weight: 40.0000 chunk 113 optimal weight: 0.8980 chunk 179 optimal weight: 30.0000 overall best weight: 6.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 413 ASN ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 672 ASN ** A 781 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 711 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 718 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 771 ASN B 779 HIS ** B 853 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 877 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 947 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1106 HIS ** C 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 137 GLN ** J 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6217 moved from start: 0.6719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 29256 Z= 0.272 Angle : 0.646 10.462 39951 Z= 0.342 Chirality : 0.042 0.241 4636 Planarity : 0.005 0.073 4805 Dihedral : 16.179 173.450 4721 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 22.46 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.93 % Favored : 93.04 % Rotamer: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.14), residues: 3465 helix: 0.08 (0.15), residues: 1165 sheet: -1.22 (0.22), residues: 506 loop : -1.52 (0.14), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A1050 HIS 0.011 0.002 HIS B 355 PHE 0.026 0.002 PHE B 746 TYR 0.037 0.002 TYR B1037 ARG 0.013 0.001 ARG E 184 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 3130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 185 time to evaluate : 3.449 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: C 201 MET cc_start: 0.8529 (tmm) cc_final: 0.8019 (ppp) REVERT: C 251 MET cc_start: 0.5862 (mtt) cc_final: 0.5375 (mtt) REVERT: D 93 MET cc_start: 0.0111 (mmp) cc_final: -0.1727 (mtt) REVERT: D 144 LYS cc_start: 0.8038 (mmmt) cc_final: 0.7817 (ptmm) REVERT: G 18 MET cc_start: 0.2345 (mtp) cc_final: 0.2082 (mtp) REVERT: G 24 MET cc_start: 0.6500 (tmm) cc_final: 0.5941 (tmm) REVERT: G 79 MET cc_start: 0.4523 (mpp) cc_final: 0.4029 (mmt) REVERT: G 138 ARG cc_start: 0.7737 (ptt-90) cc_final: 0.7225 (ptp90) REVERT: G 178 GLU cc_start: 0.6447 (mt-10) cc_final: 0.4711 (pm20) REVERT: H 121 MET cc_start: 0.6603 (tpt) cc_final: 0.6336 (tpt) REVERT: I 97 MET cc_start: 0.9074 (tpt) cc_final: 0.8841 (tpp) outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.4159 time to fit residues: 122.9325 Evaluate side-chains 150 residues out of total 3130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 3.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 330 optimal weight: 10.0000 chunk 38 optimal weight: 0.5980 chunk 195 optimal weight: 7.9990 chunk 250 optimal weight: 0.9990 chunk 193 optimal weight: 6.9990 chunk 288 optimal weight: 30.0000 chunk 191 optimal weight: 20.0000 chunk 341 optimal weight: 9.9990 chunk 213 optimal weight: 5.9990 chunk 208 optimal weight: 9.9990 chunk 157 optimal weight: 20.0000 overall best weight: 4.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 781 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 HIS A1116 GLN ** B 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 124 GLN B 330 ASN ** B 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 711 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 718 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 877 HIS ** B 947 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1052 ASN ** B1104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 197 ASN C 202 ASN ** C 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 137 GLN ** J 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 51 HIS K 65 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6190 moved from start: 0.6943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 29256 Z= 0.206 Angle : 0.584 10.389 39951 Z= 0.307 Chirality : 0.041 0.231 4636 Planarity : 0.004 0.056 4805 Dihedral : 16.200 173.740 4721 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 19.23 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.89 % Favored : 94.08 % Rotamer: Outliers : 0.04 % Allowed : 1.28 % Favored : 98.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.14), residues: 3465 helix: 0.25 (0.16), residues: 1164 sheet: -1.23 (0.22), residues: 522 loop : -1.47 (0.14), residues: 1779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 229 HIS 0.008 0.001 HIS A 25 PHE 0.032 0.002 PHE B 283 TYR 0.021 0.001 TYR D 152 ARG 0.020 0.001 ARG B 714 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 3130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 188 time to evaluate : 3.220 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 405 MET cc_start: 0.8911 (pmm) cc_final: 0.8681 (pmm) REVERT: A 406 ASP cc_start: 0.8859 (m-30) cc_final: 0.8524 (m-30) REVERT: A 631 MET cc_start: 0.7328 (mtp) cc_final: 0.6016 (mtp) REVERT: C 201 MET cc_start: 0.8444 (tmm) cc_final: 0.8025 (ppp) REVERT: C 251 MET cc_start: 0.5716 (mtt) cc_final: 0.5272 (mtt) REVERT: D 93 MET cc_start: 0.0149 (mmp) cc_final: -0.1549 (mtp) REVERT: D 144 LYS cc_start: 0.8272 (mmmt) cc_final: 0.7775 (ptmm) REVERT: E 52 ASN cc_start: 0.8843 (m-40) cc_final: 0.8493 (p0) REVERT: G 18 MET cc_start: 0.2497 (mtp) cc_final: 0.2273 (mtp) REVERT: G 118 MET cc_start: -0.0046 (tpp) cc_final: -0.0309 (tpt) REVERT: G 138 ARG cc_start: 0.7653 (ptt-90) cc_final: 0.7311 (ptp90) REVERT: G 178 GLU cc_start: 0.6511 (mt-10) cc_final: 0.4774 (pm20) REVERT: I 97 MET cc_start: 0.9030 (tpt) cc_final: 0.8651 (tpp) outliers start: 1 outliers final: 1 residues processed: 189 average time/residue: 0.4199 time to fit residues: 128.7661 Evaluate side-chains 151 residues out of total 3130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 150 time to evaluate : 3.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 211 optimal weight: 6.9990 chunk 136 optimal weight: 0.9980 chunk 203 optimal weight: 30.0000 chunk 102 optimal weight: 5.9990 chunk 67 optimal weight: 10.0000 chunk 66 optimal weight: 6.9990 chunk 216 optimal weight: 0.1980 chunk 232 optimal weight: 20.0000 chunk 168 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 chunk 268 optimal weight: 30.0000 overall best weight: 4.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 781 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 711 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 718 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 877 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 947 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 137 GLN ** J 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 653 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6194 moved from start: 0.7179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 29256 Z= 0.195 Angle : 0.573 9.942 39951 Z= 0.301 Chirality : 0.040 0.223 4636 Planarity : 0.004 0.055 4805 Dihedral : 16.216 174.034 4721 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 18.96 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.18 % Favored : 93.80 % Rotamer: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.14), residues: 3465 helix: 0.34 (0.16), residues: 1152 sheet: -1.22 (0.22), residues: 546 loop : -1.44 (0.14), residues: 1767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 229 HIS 0.008 0.001 HIS A 25 PHE 0.027 0.001 PHE H 24 TYR 0.017 0.001 TYR D 129 ARG 0.008 0.001 ARG E 184 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 3130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 3.187 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: A 406 ASP cc_start: 0.8858 (m-30) cc_final: 0.8530 (m-30) REVERT: C 201 MET cc_start: 0.8380 (tmm) cc_final: 0.8024 (tmm) REVERT: C 251 MET cc_start: 0.5859 (mtt) cc_final: 0.5454 (mtt) REVERT: D 93 MET cc_start: -0.0190 (mmp) cc_final: -0.1978 (mtt) REVERT: D 192 GLN cc_start: 0.9240 (tm-30) cc_final: 0.9031 (pp30) REVERT: E 52 ASN cc_start: 0.8905 (m-40) cc_final: 0.8476 (p0) REVERT: G 24 MET cc_start: 0.6442 (tmm) cc_final: 0.5915 (tmm) REVERT: G 178 GLU cc_start: 0.6361 (mt-10) cc_final: 0.4705 (pm20) REVERT: I 97 MET cc_start: 0.9110 (tpt) cc_final: 0.8661 (tpp) outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.3961 time to fit residues: 117.5164 Evaluate side-chains 148 residues out of total 3130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 2.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 310 optimal weight: 10.0000 chunk 326 optimal weight: 3.9990 chunk 298 optimal weight: 30.0000 chunk 317 optimal weight: 0.6980 chunk 191 optimal weight: 30.0000 chunk 138 optimal weight: 30.0000 chunk 249 optimal weight: 20.0000 chunk 97 optimal weight: 30.0000 chunk 287 optimal weight: 0.8980 chunk 300 optimal weight: 20.0000 chunk 316 optimal weight: 10.0000 overall best weight: 5.1190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 781 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 ASN ** B 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 709 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 711 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 718 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 877 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 947 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 143 GLN ** E 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 137 GLN ** J 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6238 moved from start: 0.7560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 29256 Z= 0.222 Angle : 0.610 9.412 39951 Z= 0.319 Chirality : 0.041 0.214 4636 Planarity : 0.004 0.058 4805 Dihedral : 16.318 174.747 4721 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 20.79 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.61 % Favored : 93.33 % Rotamer: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.14), residues: 3465 helix: 0.30 (0.16), residues: 1144 sheet: -1.26 (0.22), residues: 543 loop : -1.40 (0.14), residues: 1778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.002 TRP B 280 HIS 0.012 0.001 HIS B 877 PHE 0.023 0.002 PHE H 24 TYR 0.021 0.002 TYR A 163 ARG 0.008 0.001 ARG E 184 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 3130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 181 time to evaluate : 3.315 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 405 MET cc_start: 0.8941 (pmm) cc_final: 0.8683 (pmm) REVERT: A 470 MET cc_start: 0.8677 (mpp) cc_final: 0.8410 (mpp) REVERT: A 502 MET cc_start: 0.8561 (mpp) cc_final: 0.8193 (mmm) REVERT: A 721 MET cc_start: 0.1694 (tmm) cc_final: 0.1012 (ttp) REVERT: C 201 MET cc_start: 0.8313 (tmm) cc_final: 0.7995 (tmm) REVERT: C 251 MET cc_start: 0.5748 (mtt) cc_final: 0.5309 (mtt) REVERT: D 93 MET cc_start: 0.0025 (mmp) cc_final: -0.1796 (mtt) REVERT: E 52 ASN cc_start: 0.9006 (m-40) cc_final: 0.8571 (p0) REVERT: G 178 GLU cc_start: 0.6343 (mt-10) cc_final: 0.4514 (pm20) REVERT: I 97 MET cc_start: 0.9119 (tpt) cc_final: 0.8653 (tpp) outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.3934 time to fit residues: 117.2673 Evaluate side-chains 144 residues out of total 3130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 3.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 208 optimal weight: 6.9990 chunk 336 optimal weight: 5.9990 chunk 205 optimal weight: 2.9990 chunk 159 optimal weight: 3.9990 chunk 233 optimal weight: 20.0000 chunk 352 optimal weight: 0.4980 chunk 324 optimal weight: 0.7980 chunk 280 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 216 optimal weight: 0.0270 chunk 172 optimal weight: 5.9990 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 546 GLN A 672 ASN ** A 781 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 57 ASN B 543 GLN ** B 709 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 711 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 718 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 722 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 877 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 947 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1042 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1086 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 154 HIS H 137 GLN J 16 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6113 moved from start: 0.7399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 29256 Z= 0.146 Angle : 0.573 12.049 39951 Z= 0.293 Chirality : 0.041 0.187 4636 Planarity : 0.004 0.055 4805 Dihedral : 16.155 174.847 4721 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.94 % Favored : 95.01 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.14), residues: 3465 helix: 0.49 (0.16), residues: 1161 sheet: -1.11 (0.22), residues: 533 loop : -1.33 (0.14), residues: 1771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 229 HIS 0.012 0.001 HIS B 877 PHE 0.022 0.001 PHE H 24 TYR 0.015 0.001 TYR K 87 ARG 0.005 0.000 ARG B1134 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 3130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 183 time to evaluate : 3.037 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 405 MET cc_start: 0.8787 (pmm) cc_final: 0.8558 (pmm) REVERT: A 406 ASP cc_start: 0.8733 (m-30) cc_final: 0.8444 (m-30) REVERT: A 470 MET cc_start: 0.8517 (mpp) cc_final: 0.8308 (mpp) REVERT: A 502 MET cc_start: 0.8199 (mpp) cc_final: 0.7957 (mmm) REVERT: C 201 MET cc_start: 0.8274 (tmm) cc_final: 0.7865 (ppp) REVERT: C 251 MET cc_start: 0.5358 (mtt) cc_final: 0.5004 (mtt) REVERT: D 93 MET cc_start: -0.0354 (mmp) cc_final: -0.1907 (mtt) REVERT: E 94 MET cc_start: 0.6460 (tpp) cc_final: 0.6179 (tpp) REVERT: F 65 MET cc_start: 0.8235 (ttm) cc_final: 0.7738 (tpp) REVERT: G 24 MET cc_start: 0.6552 (tmm) cc_final: 0.6023 (tmm) REVERT: G 178 GLU cc_start: 0.6449 (mt-10) cc_final: 0.4658 (pm20) REVERT: H 121 MET cc_start: 0.6227 (mmp) cc_final: 0.6014 (mmm) REVERT: I 97 MET cc_start: 0.9214 (tpt) cc_final: 0.8678 (tpp) outliers start: 0 outliers final: 0 residues processed: 183 average time/residue: 0.3783 time to fit residues: 113.6439 Evaluate side-chains 147 residues out of total 3130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 147 time to evaluate : 2.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 223 optimal weight: 1.9990 chunk 299 optimal weight: 7.9990 chunk 86 optimal weight: 5.9990 chunk 258 optimal weight: 30.0000 chunk 41 optimal weight: 20.0000 chunk 78 optimal weight: 30.0000 chunk 281 optimal weight: 8.9990 chunk 117 optimal weight: 8.9990 chunk 288 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 781 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 709 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 711 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 718 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 853 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 877 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 947 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1104 GLN ** C 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 137 GLN ** I 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.062406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.049485 restraints weight = 414214.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.050208 restraints weight = 294750.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.050776 restraints weight = 231891.223| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.7750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 29256 Z= 0.200 Angle : 0.589 9.720 39951 Z= 0.305 Chirality : 0.040 0.181 4636 Planarity : 0.004 0.051 4805 Dihedral : 16.239 175.087 4721 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 19.19 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.06 % Favored : 93.88 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.14), residues: 3465 helix: 0.49 (0.16), residues: 1153 sheet: -1.12 (0.22), residues: 542 loop : -1.29 (0.14), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 280 HIS 0.008 0.001 HIS B 877 PHE 0.020 0.001 PHE H 24 TYR 0.019 0.001 TYR G 121 ARG 0.007 0.001 ARG E 184 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4702.15 seconds wall clock time: 88 minutes 20.96 seconds (5300.96 seconds total)