Starting phenix.real_space_refine on Sat Apr 13 19:21:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uua_42577/04_2024/8uua_42577_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uua_42577/04_2024/8uua_42577.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uua_42577/04_2024/8uua_42577.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uua_42577/04_2024/8uua_42577.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uua_42577/04_2024/8uua_42577_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uua_42577/04_2024/8uua_42577_updated.pdb" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.084 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians K 1 8.98 5 Zn 3 6.06 5 P 3011 5.49 5 Mg 200 5.21 5 S 78 5.16 5 C 45159 2.51 5 N 16847 2.21 5 O 25709 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "v ASP 96": "OD1" <-> "OD2" Residue "v TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v ASP 327": "OD1" <-> "OD2" Residue "v TYR 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 72": "OD1" <-> "OD2" Residue "C ASP 98": "OD1" <-> "OD2" Residue "C GLU 100": "OE1" <-> "OE2" Residue "C TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 134": "OD1" <-> "OD2" Residue "C TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 44": "OD1" <-> "OD2" Residue "D ASP 55": "OD1" <-> "OD2" Residue "D PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 21": "OD1" <-> "OD2" Residue "E PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 27": "OE1" <-> "OE2" Residue "E TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 185": "OE1" <-> "OE2" Residue "E ASP 190": "OD1" <-> "OD2" Residue "F ASP 32": "OD1" <-> "OD2" Residue "F ASP 98": "OD1" <-> "OD2" Residue "G TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 32": "OE1" <-> "OE2" Residue "L ASP 50": "OD1" <-> "OD2" Residue "L TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 5": "OE1" <-> "OE2" Residue "N GLU 137": "OE1" <-> "OE2" Residue "O GLU 26": "OE1" <-> "OE2" Residue "O TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 23": "OD1" <-> "OD2" Residue "P GLU 39": "OE1" <-> "OE2" Residue "P ASP 101": "OD1" <-> "OD2" Residue "P GLU 133": "OE1" <-> "OE2" Residue "Q GLU 78": "OE1" <-> "OE2" Residue "R GLU 85": "OE1" <-> "OE2" Residue "S TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 89": "OD1" <-> "OD2" Residue "S ASP 97": "OD1" <-> "OD2" Residue "S ASP 102": "OD1" <-> "OD2" Residue "T GLU 63": "OE1" <-> "OE2" Residue "U ASP 82": "OD1" <-> "OD2" Residue "V TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 7": "OD1" <-> "OD2" Residue "Y TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ASP 55": "OD1" <-> "OD2" Residue "4 ASP 50": "OD1" <-> "OD2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 91008 Number of models: 1 Model: "" Number of chains: 48 Chain: "v" Number of atoms: 3294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3294 Classifications: {'peptide': 418} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 407} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 38 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 3, 'GLU:plan': 3, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 39 Chain: "A" Number of atoms: 62168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2894, 62168 Classifications: {'RNA': 2894} Modifications used: {'rna2p_pur': 310, 'rna2p_pyr': 146, 'rna3p_pur': 1389, 'rna3p_pyr': 1049} Link IDs: {'rna2p': 456, 'rna3p': 2437} Chain breaks: 3 Chain: "B" Number of atoms: 2428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 2428 Classifications: {'RNA': 114} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 12, 'rna3p_pur': 54, 'rna3p_pyr': 46} Link IDs: {'rna2p': 14, 'rna3p': 99} Chain: "C" Number of atoms: 2108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2108 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 14, 'TRANS': 258} Chain: "D" Number of atoms: 1583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1583 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 9, 'TRANS': 196} Chain: "E" Number of atoms: 1539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1539 Classifications: {'peptide': 203} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 8, 'TRANS': 194} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 5} Unresolved non-hydrogen planarities: 20 Chain: "F" Number of atoms: 1171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1171 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PTRANS': 7, 'TRANS': 167} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 203 Unresolved non-hydrogen angles: 254 Unresolved non-hydrogen dihedrals: 170 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 5, 'PHE:plan': 3, 'GLU:plan': 3, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 114 Chain: "G" Number of atoms: 1355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1355 Classifications: {'peptide': 177} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 166} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 1117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1117 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 7, 'TRANS': 134} Chain: "M" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 925 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "N" Number of atoms: 1057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1057 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 4, 'TRANS': 139} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 32 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "O" Number of atoms: 1045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1045 Classifications: {'peptide': 133} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 125} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "P" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 957 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain breaks: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "Q" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 913 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain: "R" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 802 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 5, 'TRANS': 97} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "S" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 939 Classifications: {'peptide': 116} Link IDs: {'TRANS': 115} Chain: "T" Number of atoms: 762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 762 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 97} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "U" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 823 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 5, 'TRANS': 104} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "V" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 720 Classifications: {'peptide': 90} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 88} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "W" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 719 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 6, 'TRANS': 95} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 31 Chain: "Y" Number of atoms: 571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 571 Classifications: {'peptide': 76} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 73} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "Z" Number of atoms: 450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 450 Classifications: {'peptide': 59} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 57} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "1" Number of atoms: 483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 483 Classifications: {'peptide': 59} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 58} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "2" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 433 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 3, 'TRANS': 52} Chain: "3" Number of atoms: 292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 292 Classifications: {'peptide': 59} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 4, 'TRANS': 54} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 200 Unresolved non-hydrogen angles: 258 Unresolved non-hydrogen dihedrals: 174 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'HIS:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 4, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 109 Chain: "4" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 425 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 3, 'TRANS': 49} Chain: "5" Number of atoms: 390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 390 Classifications: {'peptide': 47} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 44} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "6" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 365 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "7" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 512 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "8" Number of atoms: 292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 292 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 3, 'TRANS': 32} Chain: "v" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GCP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 192 Unusual residues: {' MG': 192} Classifications: {'undetermined': 192} Link IDs: {None: 191} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "Z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "5" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "6" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "8" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 130 Classifications: {'water': 130} Link IDs: {None: 129} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "8" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 88893 SG CYS 4 30 50.264 37.928 148.203 1.00 63.47 S ATOM 88913 SG CYS 4 33 48.569 40.337 150.658 1.00 65.58 S ATOM 88996 SG CYS 4 43 52.280 40.819 149.600 1.00 57.00 S ATOM 89018 SG CYS 4 46 51.293 38.334 152.040 1.00 60.43 S ATOM 89143 SG CYS 5 9 102.732 175.326 98.161 1.00 58.55 S ATOM 89165 SG CYS 5 12 100.246 177.222 100.748 1.00 61.95 S ATOM 89362 SG CYS 5 36 99.097 174.631 97.750 1.00 54.80 S ATOM 90431 SG CYS 8 11 104.070 67.967 49.243 1.00 62.39 S ATOM 90455 SG CYS 8 14 101.270 68.550 51.734 1.00 60.82 S ATOM 90559 SG CYS 8 27 102.244 64.985 50.828 1.00 60.92 S Time building chain proxies: 35.29, per 1000 atoms: 0.39 Number of scatterers: 91008 At special positions: 0 Unit cell: (186.15, 223.55, 238.85, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 3 29.99 K 1 19.00 S 78 16.00 P 3011 15.00 Mg 200 11.99 O 25709 8.00 N 16847 7.00 C 45159 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: 33.80 Conformation dependent library (CDL) restraints added in 4.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 4 101 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 46 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 33 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 43 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 30 " pdb=" ZN 5 101 " pdb="ZN ZN 5 101 " - pdb=" SG CYS 5 9 " pdb="ZN ZN 5 101 " - pdb=" SG CYS 5 36 " pdb="ZN ZN 5 101 " - pdb=" SG CYS 5 12 " pdb=" ZN 8 101 " pdb="ZN ZN 8 101 " - pdb=" ND1 HIS 8 32 " pdb="ZN ZN 8 101 " - pdb=" SG CYS 8 14 " pdb="ZN ZN 8 101 " - pdb=" SG CYS 8 11 " pdb="ZN ZN 8 101 " - pdb=" SG CYS 8 27 " Number of angles added : 9 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6228 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 97 helices and 51 sheets defined 27.0% alpha, 19.2% beta 1048 base pairs and 1654 stacking pairs defined. Time for finding SS restraints: 45.39 Creating SS restraints... Processing helix chain 'v' and resid 18 through 30 Processing helix chain 'v' and resid 54 through 67 removed outlier: 3.667A pdb=" N ASP v 58 " --> pdb=" O LYS v 54 " (cutoff:3.500A) Processing helix chain 'v' and resid 80 through 90 Processing helix chain 'v' and resid 97 through 107 removed outlier: 3.681A pdb=" N ASN v 107 " --> pdb=" O ALA v 103 " (cutoff:3.500A) Processing helix chain 'v' and resid 112 through 138 Proline residue: v 128 - end of helix removed outlier: 4.833A pdb=" N PHE v 131 " --> pdb=" O LEU v 127 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N GLY v 132 " --> pdb=" O PRO v 128 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLN v 133 " --> pdb=" O ARG v 129 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASP v 136 " --> pdb=" O GLY v 132 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N MET v 137 " --> pdb=" O GLN v 133 " (cutoff:3.500A) Processing helix chain 'v' and resid 155 through 184 removed outlier: 3.943A pdb=" N GLN v 166 " --> pdb=" O THR v 162 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ILE v 167 " --> pdb=" O ILE v 163 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ARG v 168 " --> pdb=" O LYS v 164 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N HIS v 169 " --> pdb=" O HIS v 165 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL v 183 " --> pdb=" O ASP v 179 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ARG v 184 " --> pdb=" O ASP v 180 " (cutoff:3.500A) Processing helix chain 'v' and resid 186 through 190 Processing helix chain 'v' and resid 206 through 217 Processing helix chain 'v' and resid 264 through 278 removed outlier: 4.047A pdb=" N LYS v 268 " --> pdb=" O HIS v 264 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ALA v 269 " --> pdb=" O GLN v 265 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU v 275 " --> pdb=" O ARG v 271 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N GLU v 276 " --> pdb=" O SER v 272 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N ALA v 277 " --> pdb=" O THR v 273 " (cutoff:3.500A) Processing helix chain 'v' and resid 292 through 308 removed outlier: 4.226A pdb=" N LYS v 295 " --> pdb=" O PRO v 292 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N VAL v 308 " --> pdb=" O LEU v 305 " (cutoff:3.500A) Processing helix chain 'v' and resid 345 through 359 Processing helix chain 'v' and resid 378 through 384 Processing helix chain 'v' and resid 405 through 410 Processing helix chain 'C' and resid 31 through 33 No H-bonds generated for 'chain 'C' and resid 31 through 33' Processing helix chain 'C' and resid 132 through 134 No H-bonds generated for 'chain 'C' and resid 132 through 134' Processing helix chain 'C' and resid 200 through 202 No H-bonds generated for 'chain 'C' and resid 200 through 202' Processing helix chain 'C' and resid 208 through 214 Processing helix chain 'C' and resid 222 through 224 No H-bonds generated for 'chain 'C' and resid 222 through 224' Processing helix chain 'D' and resid 41 through 44 No H-bonds generated for 'chain 'D' and resid 41 through 44' Processing helix chain 'D' and resid 58 through 60 No H-bonds generated for 'chain 'D' and resid 58 through 60' Processing helix chain 'D' and resid 63 through 71 removed outlier: 3.952A pdb=" N LYS D 71 " --> pdb=" O GLY D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 101 No H-bonds generated for 'chain 'D' and resid 99 through 101' Processing helix chain 'D' and resid 122 through 125 No H-bonds generated for 'chain 'D' and resid 122 through 125' Processing helix chain 'E' and resid 21 through 24 No H-bonds generated for 'chain 'E' and resid 21 through 24' Processing helix chain 'E' and resid 30 through 44 removed outlier: 3.624A pdb=" N LEU E 44 " --> pdb=" O GLN E 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 119 Processing helix chain 'E' and resid 136 through 145 Processing helix chain 'E' and resid 163 through 166 No H-bonds generated for 'chain 'E' and resid 163 through 166' Processing helix chain 'E' and resid 183 through 187 Processing helix chain 'E' and resid 196 through 205 Processing helix chain 'F' and resid 3 through 19 removed outlier: 4.788A pdb=" N VAL F 13 " --> pdb=" O LEU F 9 " (cutoff:3.500A) Proline residue: F 14 - end of helix Processing helix chain 'F' and resid 25 through 27 No H-bonds generated for 'chain 'F' and resid 25 through 27' Processing helix chain 'F' and resid 48 through 60 Processing helix chain 'F' and resid 93 through 106 Processing helix chain 'F' and resid 135 through 137 No H-bonds generated for 'chain 'F' and resid 135 through 137' Processing helix chain 'F' and resid 143 through 145 No H-bonds generated for 'chain 'F' and resid 143 through 145' Processing helix chain 'F' and resid 163 through 173 Processing helix chain 'G' and resid 3 through 6 No H-bonds generated for 'chain 'G' and resid 3 through 6' Processing helix chain 'G' and resid 59 through 80 Processing helix chain 'G' and resid 138 through 151 removed outlier: 3.755A pdb=" N VAL G 151 " --> pdb=" O ASN G 147 " (cutoff:3.500A) Processing helix chain 'L' and resid 26 through 38 Processing helix chain 'L' and resid 60 through 62 No H-bonds generated for 'chain 'L' and resid 60 through 62' Processing helix chain 'L' and resid 69 through 72 No H-bonds generated for 'chain 'L' and resid 69 through 72' Processing helix chain 'L' and resid 90 through 96 Processing helix chain 'L' and resid 98 through 109 removed outlier: 3.981A pdb=" N MET L 109 " --> pdb=" O SER L 105 " (cutoff:3.500A) Processing helix chain 'L' and resid 114 through 122 removed outlier: 3.834A pdb=" N LYS L 121 " --> pdb=" O ARG L 117 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N LYS L 122 " --> pdb=" O GLN L 118 " (cutoff:3.500A) Processing helix chain 'L' and resid 134 through 136 No H-bonds generated for 'chain 'L' and resid 134 through 136' Processing helix chain 'M' and resid 104 through 108 Processing helix chain 'M' and resid 112 through 117 Processing helix chain 'N' and resid 23 through 25 No H-bonds generated for 'chain 'N' and resid 23 through 25' Processing helix chain 'N' and resid 57 through 60 Processing helix chain 'N' and resid 81 through 84 removed outlier: 3.552A pdb=" N ARG N 84 " --> pdb=" O VAL N 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 81 through 84' Processing helix chain 'N' and resid 93 through 99 Processing helix chain 'N' and resid 130 through 139 removed outlier: 3.646A pdb=" N ALA N 139 " --> pdb=" O ALA N 135 " (cutoff:3.500A) Processing helix chain 'O' and resid 44 through 58 removed outlier: 3.688A pdb=" N MET O 58 " --> pdb=" O MET O 54 " (cutoff:3.500A) Processing helix chain 'O' and resid 111 through 124 removed outlier: 3.617A pdb=" N HIS O 123 " --> pdb=" O ARG O 119 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N LYS O 124 " --> pdb=" O LEU O 120 " (cutoff:3.500A) Processing helix chain 'P' and resid 10 through 27 Processing helix chain 'P' and resid 34 through 53 removed outlier: 4.589A pdb=" N LYS P 42 " --> pdb=" O LYS P 38 " (cutoff:3.500A) Processing helix chain 'P' and resid 56 through 64 removed outlier: 3.507A pdb=" N ALA P 64 " --> pdb=" O ARG P 60 " (cutoff:3.500A) Processing helix chain 'P' and resid 94 through 100 Processing helix chain 'P' and resid 102 through 106 removed outlier: 3.795A pdb=" N TYR P 106 " --> pdb=" O VAL P 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 102 through 106' Processing helix chain 'Q' and resid 7 through 20 Processing helix chain 'Q' and resid 70 through 87 Processing helix chain 'Q' and resid 104 through 114 Processing helix chain 'R' and resid 3 through 8 Processing helix chain 'R' and resid 54 through 56 No H-bonds generated for 'chain 'R' and resid 54 through 56' Processing helix chain 'R' and resid 98 through 100 No H-bonds generated for 'chain 'R' and resid 98 through 100' Processing helix chain 'S' and resid 9 through 21 removed outlier: 3.630A pdb=" N ALA S 21 " --> pdb=" O ILE S 17 " (cutoff:3.500A) Processing helix chain 'S' and resid 26 through 29 Processing helix chain 'S' and resid 32 through 72 removed outlier: 3.685A pdb=" N GLN S 37 " --> pdb=" O LYS S 33 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ARG S 51 " --> pdb=" O TYR S 47 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N LYS S 54 " --> pdb=" O ARG S 50 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ARG S 55 " --> pdb=" O ARG S 51 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N MET S 71 " --> pdb=" O ALA S 67 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLN S 72 " --> pdb=" O ALA S 68 " (cutoff:3.500A) Processing helix chain 'S' and resid 76 through 85 Processing helix chain 'S' and resid 92 through 101 Processing helix chain 'S' and resid 103 through 116 Processing helix chain 'U' and resid 19 through 29 removed outlier: 4.285A pdb=" N VAL U 25 " --> pdb=" O LYS U 21 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N LEU U 28 " --> pdb=" O ILE U 24 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ILE U 29 " --> pdb=" O VAL U 25 " (cutoff:3.500A) Processing helix chain 'U' and resid 34 through 42 Processing helix chain 'U' and resid 49 through 67 Processing helix chain 'U' and resid 94 through 96 No H-bonds generated for 'chain 'U' and resid 94 through 96' Processing helix chain 'V' and resid 3 through 6 No H-bonds generated for 'chain 'V' and resid 3 through 6' Processing helix chain 'V' and resid 14 through 22 removed outlier: 4.469A pdb=" N ASP V 21 " --> pdb=" O THR V 17 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N ASP V 22 " --> pdb=" O SER V 18 " (cutoff:3.500A) Processing helix chain 'V' and resid 35 through 46 Processing helix chain 'W' and resid 65 through 67 No H-bonds generated for 'chain 'W' and resid 65 through 67' Processing helix chain '1' and resid 6 through 8 No H-bonds generated for 'chain '1' and resid 6 through 8' Processing helix chain '1' and resid 13 through 34 Processing helix chain '1' and resid 42 through 60 Processing helix chain '2' and resid 17 through 25 Processing helix chain '2' and resid 41 through 49 Processing helix chain '2' and resid 51 through 53 No H-bonds generated for 'chain '2' and resid 51 through 53' Processing helix chain '4' and resid 10 through 19 removed outlier: 3.680A pdb=" N THR 4 18 " --> pdb=" O ARG 4 14 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N HIS 4 19 " --> pdb=" O LYS 4 15 " (cutoff:3.500A) Processing helix chain '6' and resid 9 through 16 Processing helix chain '6' and resid 18 through 23 removed outlier: 3.564A pdb=" N SER 6 23 " --> pdb=" O ARG 6 19 " (cutoff:3.500A) Processing helix chain '6' and resid 25 through 37 Processing helix chain '7' and resid 8 through 11 No H-bonds generated for 'chain '7' and resid 8 through 11' Processing helix chain '7' and resid 33 through 35 No H-bonds generated for 'chain '7' and resid 33 through 35' Processing helix chain '7' and resid 38 through 44 Processing helix chain '7' and resid 52 through 58 removed outlier: 3.611A pdb=" N ARG 7 57 " --> pdb=" O GLY 7 53 " (cutoff:3.500A) Processing helix chain '7' and resid 60 through 62 No H-bonds generated for 'chain '7' and resid 60 through 62' Processing helix chain '8' and resid 30 through 32 No H-bonds generated for 'chain '8' and resid 30 through 32' Processing sheet with id= A, first strand: chain 'v' and resid 33 through 35 removed outlier: 6.626A pdb=" N LYS v 3 " --> pdb=" O GLU v 34 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N LEU v 71 " --> pdb=" O LEU v 6 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N VAL v 8 " --> pdb=" O LEU v 71 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ILE v 73 " --> pdb=" O VAL v 8 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'v' and resid 7 through 10 Processing sheet with id= C, first strand: chain 'v' and resid 332 through 334 removed outlier: 8.491A pdb=" N ILE v 338 " --> pdb=" O VAL v 315 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N TYR v 317 " --> pdb=" O ILE v 338 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU v 283 " --> pdb=" O ILE v 316 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N ALA v 318 " --> pdb=" O LEU v 283 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N HIS v 285 " --> pdb=" O ALA v 318 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ASN v 320 " --> pdb=" O HIS v 285 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL v 287 " --> pdb=" O ASN v 320 " (cutoff:3.500A) removed outlier: 8.870A pdb=" N VAL v 196 " --> pdb=" O GLN v 249 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LEU v 251 " --> pdb=" O VAL v 196 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N LEU v 198 " --> pdb=" O LEU v 251 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N THR v 253 " --> pdb=" O LEU v 198 " (cutoff:3.500A) removed outlier: 9.391A pdb=" N GLY v 200 " --> pdb=" O THR v 253 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'v' and resid 364 through 371 removed outlier: 3.567A pdb=" N GLU v 389 " --> pdb=" O VAL v 400 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N GLU v 402 " --> pdb=" O ILE v 387 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N ILE v 387 " --> pdb=" O GLU v 402 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 3 through 5 Processing sheet with id= F, first strand: chain 'C' and resid 34 through 36 Processing sheet with id= G, first strand: chain 'C' and resid 101 through 105 removed outlier: 3.579A pdb=" N THR C 80 " --> pdb=" O LEU C 93 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ASN C 95 " --> pdb=" O VAL C 78 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N VAL C 78 " --> pdb=" O ASN C 95 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 129 through 131 Processing sheet with id= I, first strand: chain 'C' and resid 181 through 185 removed outlier: 3.720A pdb=" N GLY C 166 " --> pdb=" O LEU C 173 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ARG C 175 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N VAL C 164 " --> pdb=" O ARG C 175 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 168 through 175 removed outlier: 5.621A pdb=" N ILE D 108 " --> pdb=" O ASN D 173 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N VAL D 113 " --> pdb=" O LEU D 199 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N LEU D 199 " --> pdb=" O VAL D 113 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N VAL D 27 " --> pdb=" O VAL D 10 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N MET D 12 " --> pdb=" O VAL D 25 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL D 25 " --> pdb=" O MET D 12 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N GLN D 14 " --> pdb=" O ILE D 23 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ILE D 23 " --> pdb=" O GLN D 14 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS D 178 " --> pdb=" O LEU D 187 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LYS D 189 " --> pdb=" O ILE D 176 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ILE D 176 " --> pdb=" O LYS D 189 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 80 through 84 removed outlier: 3.615A pdb=" N GLN D 37 " --> pdb=" O GLN D 50 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N GLY D 52 " --> pdb=" O VAL D 35 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N VAL D 35 " --> pdb=" O GLY D 52 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 123 through 126 removed outlier: 6.547A pdb=" N LEU E 192 " --> pdb=" O VAL E 124 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N LEU E 126 " --> pdb=" O LEU E 192 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ILE E 194 " --> pdb=" O LEU E 126 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'F' and resid 128 through 132 removed outlier: 6.735A pdb=" N THR F 68 " --> pdb=" O ILE F 85 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ALA F 87 " --> pdb=" O VAL F 66 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N VAL F 66 " --> pdb=" O ALA F 87 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'G' and resid 16 through 20 Processing sheet with id= O, first strand: chain 'G' and resid 42 through 45 removed outlier: 3.949A pdb=" N THR G 42 " --> pdb=" O SER G 53 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ASN G 51 " --> pdb=" O ASN G 44 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'G' and resid 161 through 164 Processing sheet with id= Q, first strand: chain 'G' and resid 95 through 98 Processing sheet with id= R, first strand: chain 'L' and resid 16 through 20 removed outlier: 6.700A pdb=" N PHE L 54 " --> pdb=" O TYR L 17 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N ILE L 19 " --> pdb=" O PHE L 54 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ILE L 56 " --> pdb=" O ILE L 19 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'L' and resid 74 through 78 Processing sheet with id= T, first strand: chain 'M' and resid 7 through 9 removed outlier: 6.727A pdb=" N VAL M 40 " --> pdb=" O ILE M 22 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N VAL M 24 " --> pdb=" O VAL M 38 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N VAL M 38 " --> pdb=" O VAL M 24 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ALA M 83 " --> pdb=" O VAL M 63 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'M' and resid 101 through 103 removed outlier: 6.430A pdb=" N GLU M 120 " --> pdb=" O VAL M 102 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'N' and resid 75 through 77 Processing sheet with id= W, first strand: chain 'N' and resid 122 through 125 removed outlier: 6.462A pdb=" N LYS N 142 " --> pdb=" O VAL N 123 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N ALA N 125 " --> pdb=" O LYS N 142 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N GLU N 144 " --> pdb=" O ALA N 125 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain 'O' and resid 129 through 133 removed outlier: 3.961A pdb=" N PHE O 104 " --> pdb=" O LEU O 34 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ALA O 36 " --> pdb=" O ILE O 102 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ILE O 102 " --> pdb=" O ALA O 36 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'O' and resid 40 through 43 removed outlier: 6.865A pdb=" N TYR O 74 " --> pdb=" O GLU O 91 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N TRP O 93 " --> pdb=" O LYS O 72 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LYS O 72 " --> pdb=" O TRP O 93 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'P' and resid 29 through 33 removed outlier: 6.083A pdb=" N ILE P 131 " --> pdb=" O LYS P 118 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N LYS P 118 " --> pdb=" O ILE P 131 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N GLU P 133 " --> pdb=" O ILE P 116 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N ILE P 116 " --> pdb=" O GLU P 133 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'P' and resid 70 through 74 removed outlier: 6.806A pdb=" N VAL P 92 " --> pdb=" O VAL P 71 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N VAL P 73 " --> pdb=" O ARG P 90 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ARG P 90 " --> pdb=" O VAL P 73 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'Q' and resid 93 through 95 removed outlier: 3.551A pdb=" N VAL Q 33 " --> pdb=" O ASP Q 95 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ASP Q 46 " --> pdb=" O THR Q 52 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N THR Q 52 " --> pdb=" O ASP Q 46 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'R' and resid 83 through 88 removed outlier: 3.707A pdb=" N LYS R 83 " --> pdb=" O HIS R 29 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N THR R 25 " --> pdb=" O ILE R 87 " (cutoff:3.500A) removed outlier: 8.933A pdb=" N GLU R 44 " --> pdb=" O ILE R 64 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N ILE R 64 " --> pdb=" O GLU R 44 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N THR R 60 " --> pdb=" O ILE R 48 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ARG R 50 " --> pdb=" O THR R 58 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N THR R 58 " --> pdb=" O ARG R 50 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'T' and resid 10 through 14 removed outlier: 3.597A pdb=" N PHE T 40 " --> pdb=" O ILE T 4 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N GLU T 6 " --> pdb=" O VAL T 38 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N VAL T 38 " --> pdb=" O GLU T 6 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'T' and resid 19 through 22 Processing sheet with id= AF, first strand: chain 'T' and resid 32 through 35 removed outlier: 6.208A pdb=" N LYS T 61 " --> pdb=" O ILE T 97 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N ILE T 97 " --> pdb=" O LYS T 61 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'T' and resid 71 through 77 removed outlier: 4.123A pdb=" N TYR T 82 " --> pdb=" O LYS T 77 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'U' and resid 7 through 12 removed outlier: 3.614A pdb=" N GLU U 78 " --> pdb=" O VAL U 111 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N SER U 113 " --> pdb=" O VAL U 76 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N VAL U 76 " --> pdb=" O SER U 113 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'U' and resid 87 through 92 Processing sheet with id= AJ, first strand: chain 'V' and resid 7 through 10 removed outlier: 6.799A pdb=" N GLU V 28 " --> pdb=" O LYS V 8 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N THR V 26 " --> pdb=" O PRO V 10 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ARG V 76 " --> pdb=" O VAL V 29 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'V' and resid 62 through 64 Processing sheet with id= AL, first strand: chain 'W' and resid 20 through 22 Processing sheet with id= AM, first strand: chain 'W' and resid 40 through 45 Processing sheet with id= AN, first strand: chain 'W' and resid 81 through 86 removed outlier: 3.753A pdb=" N LYS W 89 " --> pdb=" O LYS W 86 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'W' and resid 23 through 27 removed outlier: 6.736A pdb=" N LEU W 34 " --> pdb=" O LEU W 24 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N ALA W 26 " --> pdb=" O ARG W 32 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ARG W 32 " --> pdb=" O ALA W 26 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'Y' and resid 59 through 61 Processing sheet with id= AQ, first strand: chain 'Y' and resid 74 through 78 Processing sheet with id= AR, first strand: chain 'Z' and resid 13 through 18 Processing sheet with id= AS, first strand: chain 'Z' and resid 33 through 39 Processing sheet with id= AT, first strand: chain '2' and resid 34 through 37 Processing sheet with id= AU, first strand: chain '3' and resid 22 through 27 removed outlier: 6.885A pdb=" N VAL 3 15 " --> pdb=" O PRO 3 44 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N LEU 3 46 " --> pdb=" O VAL 3 15 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain '4' and resid 27 through 29 Processing sheet with id= AW, first strand: chain '5' and resid 31 through 36 removed outlier: 3.562A pdb=" N ARG 5 41 " --> pdb=" O CYS 5 36 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR 5 17 " --> pdb=" O LEU 5 7 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N CYS 5 9 " --> pdb=" O ARG 5 15 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ARG 5 15 " --> pdb=" O CYS 5 9 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain '7' and resid 23 through 25 Processing sheet with id= AY, first strand: chain '8' and resid 15 through 19 851 hydrogen bonds defined for protein. 2388 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2617 hydrogen bonds 4118 hydrogen bond angles 0 basepair planarities 1048 basepair parallelities 1654 stacking parallelities Total time for adding SS restraints: 192.00 Time building geometry restraints manager: 37.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 11736 1.32 - 1.45: 43516 1.45 - 1.58: 37364 1.58 - 1.70: 6016 1.70 - 1.83: 144 Bond restraints: 98776 Sorted by residual: bond pdb=" O2B GCP v 501 " pdb=" PB GCP v 501 " ideal model delta sigma weight residual 1.506 1.609 -0.103 2.00e-02 2.50e+03 2.66e+01 bond pdb=" O3A GCP v 501 " pdb=" PB GCP v 501 " ideal model delta sigma weight residual 1.697 1.601 0.096 2.00e-02 2.50e+03 2.31e+01 bond pdb=" C4 GCP v 501 " pdb=" C5 GCP v 501 " ideal model delta sigma weight residual 1.382 1.467 -0.085 2.00e-02 2.50e+03 1.82e+01 bond pdb=" O3G GCP v 501 " pdb=" PG GCP v 501 " ideal model delta sigma weight residual 1.533 1.607 -0.074 2.00e-02 2.50e+03 1.38e+01 bond pdb=" C3B GCP v 501 " pdb=" PG GCP v 501 " ideal model delta sigma weight residual 1.871 1.803 0.068 2.00e-02 2.50e+03 1.14e+01 ... (remaining 98771 not shown) Histogram of bond angle deviations from ideal: 96.79 - 104.59: 12730 104.59 - 112.39: 57519 112.39 - 120.18: 40944 120.18 - 127.98: 31990 127.98 - 135.78: 5164 Bond angle restraints: 148347 Sorted by residual: angle pdb=" C GLU F 55 " pdb=" N GLU F 56 " pdb=" CA GLU F 56 " ideal model delta sigma weight residual 120.31 112.62 7.69 1.52e+00 4.33e-01 2.56e+01 angle pdb=" O4' G A 557 " pdb=" C1' G A 557 " pdb=" N9 G A 557 " ideal model delta sigma weight residual 108.20 115.36 -7.16 1.50e+00 4.44e-01 2.28e+01 angle pdb=" N GLU F 55 " pdb=" CA GLU F 55 " pdb=" CB GLU F 55 " ideal model delta sigma weight residual 110.16 116.97 -6.81 1.48e+00 4.57e-01 2.12e+01 angle pdb=" C4' A A2472 " pdb=" C3' A A2472 " pdb=" O3' A A2472 " ideal model delta sigma weight residual 109.40 115.83 -6.43 1.50e+00 4.44e-01 1.84e+01 angle pdb=" N GLU F 56 " pdb=" CA GLU F 56 " pdb=" CB GLU F 56 " ideal model delta sigma weight residual 110.28 116.89 -6.61 1.55e+00 4.16e-01 1.82e+01 ... (remaining 148342 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.93: 55942 35.93 - 71.87: 6359 71.87 - 107.80: 705 107.80 - 143.73: 11 143.73 - 179.67: 23 Dihedral angle restraints: 63040 sinusoidal: 53351 harmonic: 9689 Sorted by residual: dihedral pdb=" O4' C A1904 " pdb=" C1' C A1904 " pdb=" N1 C A1904 " pdb=" C2 C A1904 " ideal model delta sinusoidal sigma weight residual 200.00 46.78 153.22 1 1.50e+01 4.44e-03 8.08e+01 dihedral pdb=" O4' U A2339 " pdb=" C1' U A2339 " pdb=" N1 U A2339 " pdb=" C2 U A2339 " ideal model delta sinusoidal sigma weight residual 200.00 50.43 149.57 1 1.50e+01 4.44e-03 7.95e+01 dihedral pdb=" O4' C A2507 " pdb=" C1' C A2507 " pdb=" N1 C A2507 " pdb=" C2 C A2507 " ideal model delta sinusoidal sigma weight residual -160.00 -23.94 -136.06 1 1.50e+01 4.44e-03 7.34e+01 ... (remaining 63037 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 17966 0.093 - 0.186: 1024 0.186 - 0.279: 74 0.279 - 0.372: 5 0.372 - 0.465: 2 Chirality restraints: 19071 Sorted by residual: chirality pdb=" C3' A A2472 " pdb=" C4' A A2472 " pdb=" O3' A A2472 " pdb=" C2' A A2472 " both_signs ideal model delta sigma weight residual False -2.74 -2.28 -0.47 2.00e-01 2.50e+01 5.42e+00 chirality pdb=" C3' A A1817 " pdb=" C4' A A1817 " pdb=" O3' A A1817 " pdb=" C2' A A1817 " both_signs ideal model delta sigma weight residual False -2.74 -2.34 -0.40 2.00e-01 2.50e+01 4.02e+00 chirality pdb=" C3' A A2809 " pdb=" C4' A A2809 " pdb=" O3' A A2809 " pdb=" C2' A A2809 " both_signs ideal model delta sigma weight residual False -2.74 -2.39 -0.36 2.00e-01 2.50e+01 3.17e+00 ... (remaining 19068 not shown) Planarity restraints: 7572 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A A1699 " 0.065 2.00e-02 2.50e+03 2.94e-02 2.37e+01 pdb=" N9 A A1699 " -0.068 2.00e-02 2.50e+03 pdb=" C8 A A1699 " -0.006 2.00e-02 2.50e+03 pdb=" N7 A A1699 " 0.003 2.00e-02 2.50e+03 pdb=" C5 A A1699 " 0.002 2.00e-02 2.50e+03 pdb=" C6 A A1699 " 0.012 2.00e-02 2.50e+03 pdb=" N6 A A1699 " 0.014 2.00e-02 2.50e+03 pdb=" N1 A A1699 " 0.004 2.00e-02 2.50e+03 pdb=" C2 A A1699 " -0.004 2.00e-02 2.50e+03 pdb=" N3 A A1699 " -0.009 2.00e-02 2.50e+03 pdb=" C4 A A1699 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A 557 " -0.063 2.00e-02 2.50e+03 2.72e-02 2.21e+01 pdb=" N9 G A 557 " 0.065 2.00e-02 2.50e+03 pdb=" C8 G A 557 " 0.010 2.00e-02 2.50e+03 pdb=" N7 G A 557 " -0.001 2.00e-02 2.50e+03 pdb=" C5 G A 557 " -0.008 2.00e-02 2.50e+03 pdb=" C6 G A 557 " -0.012 2.00e-02 2.50e+03 pdb=" O6 G A 557 " -0.010 2.00e-02 2.50e+03 pdb=" N1 G A 557 " -0.007 2.00e-02 2.50e+03 pdb=" C2 G A 557 " 0.006 2.00e-02 2.50e+03 pdb=" N2 G A 557 " 0.004 2.00e-02 2.50e+03 pdb=" N3 G A 557 " 0.010 2.00e-02 2.50e+03 pdb=" C4 G A 557 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A A1026 " -0.058 2.00e-02 2.50e+03 2.53e-02 1.76e+01 pdb=" N9 A A1026 " 0.056 2.00e-02 2.50e+03 pdb=" C8 A A1026 " 0.005 2.00e-02 2.50e+03 pdb=" N7 A A1026 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A A1026 " 0.003 2.00e-02 2.50e+03 pdb=" C6 A A1026 " -0.009 2.00e-02 2.50e+03 pdb=" N6 A A1026 " -0.016 2.00e-02 2.50e+03 pdb=" N1 A A1026 " -0.004 2.00e-02 2.50e+03 pdb=" C2 A A1026 " 0.003 2.00e-02 2.50e+03 pdb=" N3 A A1026 " 0.010 2.00e-02 2.50e+03 pdb=" C4 A A1026 " 0.010 2.00e-02 2.50e+03 ... (remaining 7569 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.55: 406 2.55 - 3.19: 69656 3.19 - 3.84: 209216 3.84 - 4.49: 302533 4.49 - 5.14: 389254 Nonbonded interactions: 971065 Sorted by model distance: nonbonded pdb=" N1 A A 558 " pdb="MG MG A3180 " model vdw 1.898 2.250 nonbonded pdb=" OP1 G A 345 " pdb="MG MG A3046 " model vdw 2.005 2.170 nonbonded pdb=" O4 U A 449 " pdb="MG MG A3034 " model vdw 2.055 2.170 nonbonded pdb=" O2' G A1791 " pdb="MG MG A3144 " model vdw 2.059 2.170 nonbonded pdb=" OP1 G A 598 " pdb="MG MG A3006 " model vdw 2.068 2.170 ... (remaining 971060 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.160 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: 0.070 Extract box with map and model: 29.070 Check model and map are aligned: 1.180 Set scattering table: 0.650 Process input model: 382.050 Find NCS groups from input model: 1.730 Set up NCS constraints: 0.240 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 433.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8882 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 : 0.007 0.103 98776 Z= 0.432 Angle : 0.720 10.780 148347 Z= 0.379 Chirality : 0.046 0.465 19071 Planarity : 0.006 0.118 7572 Dihedral : 22.614 179.668 56812 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.30 % Favored : 95.64 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.14), residues: 3348 helix: 0.75 (0.18), residues: 912 sheet: 0.23 (0.19), residues: 726 loop : -1.00 (0.14), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP O 65 HIS 0.022 0.002 HIS E 49 PHE 0.025 0.002 PHE D 119 TYR 0.022 0.002 TYR C 257 ARG 0.016 0.001 ARG R 94 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 778 residues out of total 2873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 778 time to evaluate : 3.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 64 LYS cc_start: 0.8639 (mptt) cc_final: 0.8436 (mmtt) REVERT: F 85 ILE cc_start: 0.9233 (tp) cc_final: 0.8992 (tp) REVERT: F 88 LYS cc_start: 0.9087 (ptmt) cc_final: 0.8413 (pptt) REVERT: F 153 ASP cc_start: 0.8740 (m-30) cc_final: 0.8508 (m-30) REVERT: F 168 GLU cc_start: 0.8314 (mt-10) cc_final: 0.7384 (mt-10) REVERT: G 89 LEU cc_start: 0.9402 (mp) cc_final: 0.8537 (mp) outliers start: 0 outliers final: 1 residues processed: 778 average time/residue: 1.7963 time to fit residues: 1858.3837 Evaluate side-chains 666 residues out of total 2873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 665 time to evaluate : 3.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 81 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 628 random chunks: chunk 530 optimal weight: 3.9990 chunk 475 optimal weight: 0.9990 chunk 264 optimal weight: 6.9990 chunk 162 optimal weight: 6.9990 chunk 321 optimal weight: 8.9990 chunk 254 optimal weight: 50.0000 chunk 492 optimal weight: 1.9990 chunk 190 optimal weight: 10.0000 chunk 299 optimal weight: 6.9990 chunk 366 optimal weight: 8.9990 chunk 570 optimal weight: 0.0570 overall best weight: 2.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: v 67 GLN v 382 ASN D 33 ASN D 128 GLN D 152 ASN E 46 GLN E 49 HIS E 75 GLN E 162 ASN G 74 ASN G 147 ASN L 118 GLN L 136 GLN M 4 GLN M 13 ASN N 35 HIS N 70 ASN N 78 ASN Q 15 HIS S 44 GLN S 101 ASN T 81 ASN T 90 GLN U 66 ASN U 107 HIS V 73 ASN Y 58 ASN Z 23 ASN Z 34 GLN 2 24 GLN 5 16 ASN 7 40 GLN 8 36 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8851 moved from start: 0.1092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 98776 Z= 0.229 Angle : 0.550 11.336 148347 Z= 0.295 Chirality : 0.037 0.319 19071 Planarity : 0.004 0.053 7572 Dihedral : 22.823 178.803 50414 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.85 % Favored : 96.09 % Rotamer: Outliers : 2.17 % Allowed : 13.05 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.14), residues: 3348 helix: 1.13 (0.18), residues: 913 sheet: 0.35 (0.19), residues: 712 loop : -0.88 (0.14), residues: 1723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP Z 48 HIS 0.007 0.001 HIS E 49 PHE 0.018 0.001 PHE D 119 TYR 0.018 0.001 TYR v 125 ARG 0.010 0.000 ARG F 80 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 764 residues out of total 2873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 706 time to evaluate : 3.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 273 ARG cc_start: 0.7280 (OUTLIER) cc_final: 0.7017 (mtp180) REVERT: F 26 MET cc_start: 0.7824 (mtm) cc_final: 0.7520 (mtm) REVERT: F 85 ILE cc_start: 0.9285 (tp) cc_final: 0.9003 (tp) REVERT: F 88 LYS cc_start: 0.9116 (ptmt) cc_final: 0.8415 (pptt) REVERT: F 153 ASP cc_start: 0.8613 (m-30) cc_final: 0.8225 (m-30) REVERT: F 158 THR cc_start: 0.9199 (OUTLIER) cc_final: 0.8863 (t) REVERT: F 165 GLU cc_start: 0.9118 (mp0) cc_final: 0.8859 (mp0) REVERT: F 168 GLU cc_start: 0.7705 (mt-10) cc_final: 0.7477 (mt-10) REVERT: G 163 ARG cc_start: 0.8528 (OUTLIER) cc_final: 0.7865 (pmm-80) REVERT: M 3 GLN cc_start: 0.8790 (OUTLIER) cc_final: 0.8291 (pt0) REVERT: M 110 ASN cc_start: 0.8254 (t0) cc_final: 0.8030 (t0) REVERT: S 102 ASP cc_start: 0.7727 (t0) cc_final: 0.7520 (t0) REVERT: V 85 ASP cc_start: 0.7335 (p0) cc_final: 0.7114 (p0) REVERT: 1 47 ARG cc_start: 0.8804 (mtm-85) cc_final: 0.8550 (mtp-110) outliers start: 58 outliers final: 20 residues processed: 713 average time/residue: 1.7839 time to fit residues: 1708.7466 Evaluate side-chains 686 residues out of total 2873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 662 time to evaluate : 3.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain v residue 174 LEU Chi-restraints excluded: chain v residue 177 LEU Chi-restraints excluded: chain C residue 273 ARG Chi-restraints excluded: chain D residue 19 ASN Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain G residue 53 SER Chi-restraints excluded: chain G residue 163 ARG Chi-restraints excluded: chain L residue 87 SER Chi-restraints excluded: chain M residue 3 GLN Chi-restraints excluded: chain M residue 31 LYS Chi-restraints excluded: chain O residue 52 ILE Chi-restraints excluded: chain O residue 76 SER Chi-restraints excluded: chain Q residue 25 THR Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain Q residue 95 ASP Chi-restraints excluded: chain R residue 65 SER Chi-restraints excluded: chain R residue 81 ILE Chi-restraints excluded: chain V residue 32 ARG Chi-restraints excluded: chain Z residue 25 SER Chi-restraints excluded: chain Z residue 56 SER Chi-restraints excluded: chain 1 residue 61 GLU Chi-restraints excluded: chain 2 residue 40 ASN Chi-restraints excluded: chain 7 residue 10 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 628 random chunks: chunk 316 optimal weight: 10.0000 chunk 176 optimal weight: 8.9990 chunk 474 optimal weight: 0.7980 chunk 388 optimal weight: 8.9990 chunk 157 optimal weight: 10.0000 chunk 571 optimal weight: 3.9990 chunk 617 optimal weight: 8.9990 chunk 508 optimal weight: 9.9990 chunk 566 optimal weight: 0.5980 chunk 194 optimal weight: 20.0000 chunk 458 optimal weight: 4.9990 overall best weight: 3.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 163 GLN C 199 GLN F 127 ASN M 4 GLN S 44 GLN T 81 ASN 2 24 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8880 moved from start: 0.1189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 98776 Z= 0.299 Angle : 0.564 8.541 148347 Z= 0.301 Chirality : 0.038 0.352 19071 Planarity : 0.005 0.052 7572 Dihedral : 22.741 179.469 50414 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.76 % Favored : 96.18 % Rotamer: Outliers : 2.88 % Allowed : 15.89 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.14), residues: 3348 helix: 1.27 (0.18), residues: 918 sheet: 0.47 (0.19), residues: 706 loop : -0.89 (0.14), residues: 1724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP Z 48 HIS 0.006 0.001 HIS E 49 PHE 0.019 0.001 PHE D 119 TYR 0.012 0.001 TYR T 74 ARG 0.008 0.000 ARG v 168 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 756 residues out of total 2873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 679 time to evaluate : 3.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: v 112 LYS cc_start: 0.8777 (OUTLIER) cc_final: 0.8562 (ptmm) REVERT: C 273 ARG cc_start: 0.7215 (OUTLIER) cc_final: 0.6928 (mtp180) REVERT: D 128 GLN cc_start: 0.8833 (OUTLIER) cc_final: 0.7986 (mm-40) REVERT: F 26 MET cc_start: 0.7812 (mtm) cc_final: 0.7424 (mtm) REVERT: F 32 ASP cc_start: 0.8437 (t0) cc_final: 0.8220 (t0) REVERT: F 42 ASP cc_start: 0.7972 (p0) cc_final: 0.7764 (p0) REVERT: F 85 ILE cc_start: 0.9355 (tp) cc_final: 0.9051 (tp) REVERT: F 88 LYS cc_start: 0.9119 (ptmt) cc_final: 0.8429 (pptt) REVERT: F 153 ASP cc_start: 0.8613 (m-30) cc_final: 0.8164 (m-30) REVERT: F 156 ILE cc_start: 0.9567 (mm) cc_final: 0.9358 (tp) REVERT: F 158 THR cc_start: 0.9101 (OUTLIER) cc_final: 0.8808 (t) REVERT: F 165 GLU cc_start: 0.9094 (mp0) cc_final: 0.8890 (mp0) REVERT: G 89 LEU cc_start: 0.9040 (mp) cc_final: 0.8794 (mp) REVERT: G 163 ARG cc_start: 0.8699 (OUTLIER) cc_final: 0.7379 (pmm-80) REVERT: M 110 ASN cc_start: 0.8183 (t0) cc_final: 0.7972 (t0) REVERT: Q 78 GLU cc_start: 0.7734 (tp30) cc_final: 0.7154 (tp30) REVERT: R 1 MET cc_start: 0.8499 (OUTLIER) cc_final: 0.8076 (ttp) REVERT: S 102 ASP cc_start: 0.7787 (t0) cc_final: 0.7443 (t0) REVERT: U 95 GLN cc_start: 0.8718 (OUTLIER) cc_final: 0.7901 (mp10) REVERT: Y 84 LYS cc_start: 0.8875 (OUTLIER) cc_final: 0.7857 (mmtp) REVERT: 1 47 ARG cc_start: 0.8847 (mtm-85) cc_final: 0.8586 (mtp-110) outliers start: 77 outliers final: 29 residues processed: 701 average time/residue: 1.8236 time to fit residues: 1707.6003 Evaluate side-chains 689 residues out of total 2873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 652 time to evaluate : 3.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain v residue 8 VAL Chi-restraints excluded: chain v residue 112 LYS Chi-restraints excluded: chain v residue 196 VAL Chi-restraints excluded: chain v residue 258 PHE Chi-restraints excluded: chain C residue 273 ARG Chi-restraints excluded: chain D residue 12 MET Chi-restraints excluded: chain D residue 19 ASN Chi-restraints excluded: chain D residue 128 GLN Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain F residue 56 GLU Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 164 GLU Chi-restraints excluded: chain G residue 53 SER Chi-restraints excluded: chain G residue 116 VAL Chi-restraints excluded: chain G residue 163 ARG Chi-restraints excluded: chain L residue 87 SER Chi-restraints excluded: chain L residue 114 SER Chi-restraints excluded: chain N residue 81 VAL Chi-restraints excluded: chain N residue 113 SER Chi-restraints excluded: chain O residue 55 THR Chi-restraints excluded: chain Q residue 25 THR Chi-restraints excluded: chain Q residue 40 ILE Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 65 SER Chi-restraints excluded: chain T residue 12 ILE Chi-restraints excluded: chain U residue 14 THR Chi-restraints excluded: chain U residue 95 GLN Chi-restraints excluded: chain Y residue 84 LYS Chi-restraints excluded: chain Z residue 25 SER Chi-restraints excluded: chain Z residue 59 VAL Chi-restraints excluded: chain 1 residue 16 ASP Chi-restraints excluded: chain 2 residue 40 ASN Chi-restraints excluded: chain 7 residue 10 SER Chi-restraints excluded: chain 8 residue 13 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 628 random chunks: chunk 564 optimal weight: 2.9990 chunk 429 optimal weight: 2.9990 chunk 296 optimal weight: 8.9990 chunk 63 optimal weight: 10.0000 chunk 272 optimal weight: 10.0000 chunk 383 optimal weight: 0.7980 chunk 573 optimal weight: 0.9980 chunk 607 optimal weight: 0.6980 chunk 299 optimal weight: 8.9990 chunk 543 optimal weight: 0.6980 chunk 163 optimal weight: 8.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 163 GLN F 127 ASN M 4 GLN S 44 GLN T 81 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.106 98776 Z= 0.146 Angle : 0.535 13.135 148347 Z= 0.286 Chirality : 0.035 0.302 19071 Planarity : 0.004 0.087 7572 Dihedral : 22.782 179.142 50412 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.52 % Favored : 96.42 % Rotamer: Outliers : 2.65 % Allowed : 18.02 % Favored : 79.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.14), residues: 3348 helix: 1.32 (0.18), residues: 910 sheet: 0.54 (0.19), residues: 701 loop : -0.82 (0.14), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP Z 48 HIS 0.005 0.001 HIS S 29 PHE 0.011 0.001 PHE R 74 TYR 0.013 0.001 TYR T 74 ARG 0.011 0.000 ARG F 78 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 743 residues out of total 2873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 672 time to evaluate : 3.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: v 14 GLN cc_start: 0.8276 (OUTLIER) cc_final: 0.7804 (mp10) REVERT: v 112 LYS cc_start: 0.8804 (OUTLIER) cc_final: 0.8387 (ptmm) REVERT: C 273 ARG cc_start: 0.7186 (OUTLIER) cc_final: 0.6910 (mtp180) REVERT: F 26 MET cc_start: 0.7741 (OUTLIER) cc_final: 0.7519 (mtm) REVERT: F 32 ASP cc_start: 0.8460 (t0) cc_final: 0.8199 (t0) REVERT: F 42 ASP cc_start: 0.8027 (p0) cc_final: 0.7748 (p0) REVERT: F 69 LYS cc_start: 0.9232 (mppt) cc_final: 0.8385 (ttmm) REVERT: F 88 LYS cc_start: 0.9114 (ptmt) cc_final: 0.8454 (pptt) REVERT: F 153 ASP cc_start: 0.8535 (m-30) cc_final: 0.8105 (m-30) REVERT: F 158 THR cc_start: 0.9186 (OUTLIER) cc_final: 0.8844 (t) REVERT: F 165 GLU cc_start: 0.9219 (mp0) cc_final: 0.8853 (mp0) REVERT: G 163 ARG cc_start: 0.8637 (OUTLIER) cc_final: 0.7253 (pmm-80) REVERT: M 110 ASN cc_start: 0.8124 (t0) cc_final: 0.7900 (t0) REVERT: O 76 SER cc_start: 0.8638 (OUTLIER) cc_final: 0.8348 (p) REVERT: R 1 MET cc_start: 0.8473 (OUTLIER) cc_final: 0.8058 (ttp) REVERT: S 102 ASP cc_start: 0.7668 (t0) cc_final: 0.7322 (t0) REVERT: Y 84 LYS cc_start: 0.8822 (OUTLIER) cc_final: 0.7810 (mmtp) REVERT: 1 47 ARG cc_start: 0.8773 (mtm-85) cc_final: 0.8542 (mtp-110) outliers start: 71 outliers final: 35 residues processed: 700 average time/residue: 1.7879 time to fit residues: 1679.2159 Evaluate side-chains 701 residues out of total 2873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 657 time to evaluate : 3.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain v residue 8 VAL Chi-restraints excluded: chain v residue 14 GLN Chi-restraints excluded: chain v residue 112 LYS Chi-restraints excluded: chain v residue 177 LEU Chi-restraints excluded: chain v residue 196 VAL Chi-restraints excluded: chain v residue 258 PHE Chi-restraints excluded: chain C residue 273 ARG Chi-restraints excluded: chain D residue 19 ASN Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain E residue 100 LYS Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain F residue 26 MET Chi-restraints excluded: chain F residue 56 GLU Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain G residue 163 ARG Chi-restraints excluded: chain L residue 87 SER Chi-restraints excluded: chain L residue 114 SER Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 31 LYS Chi-restraints excluded: chain M residue 66 LYS Chi-restraints excluded: chain O residue 52 ILE Chi-restraints excluded: chain O residue 76 SER Chi-restraints excluded: chain P residue 42 LYS Chi-restraints excluded: chain Q residue 25 THR Chi-restraints excluded: chain Q residue 40 ILE Chi-restraints excluded: chain Q residue 53 LEU Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 81 ILE Chi-restraints excluded: chain U residue 14 THR Chi-restraints excluded: chain W residue 68 VAL Chi-restraints excluded: chain W residue 79 THR Chi-restraints excluded: chain Y residue 39 VAL Chi-restraints excluded: chain Y residue 84 LYS Chi-restraints excluded: chain 1 residue 16 ASP Chi-restraints excluded: chain 1 residue 17 GLN Chi-restraints excluded: chain 2 residue 40 ASN Chi-restraints excluded: chain 2 residue 54 VAL Chi-restraints excluded: chain 4 residue 3 VAL Chi-restraints excluded: chain 5 residue 20 THR Chi-restraints excluded: chain 8 residue 12 GLU Chi-restraints excluded: chain 8 residue 13 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 628 random chunks: chunk 505 optimal weight: 8.9990 chunk 344 optimal weight: 6.9990 chunk 8 optimal weight: 0.7980 chunk 451 optimal weight: 0.1980 chunk 250 optimal weight: 20.0000 chunk 518 optimal weight: 8.9990 chunk 419 optimal weight: 40.0000 chunk 0 optimal weight: 20.0000 chunk 309 optimal weight: 10.0000 chunk 544 optimal weight: 9.9990 chunk 153 optimal weight: 20.0000 overall best weight: 5.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 163 GLN C 199 GLN F 127 ASN L 118 GLN M 4 GLN Q 32 ASN T 81 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8899 moved from start: 0.1293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 98776 Z= 0.393 Angle : 0.601 8.489 148347 Z= 0.318 Chirality : 0.040 0.375 19071 Planarity : 0.005 0.052 7572 Dihedral : 22.697 179.837 50412 Min Nonbonded Distance : 1.778 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.91 % Favored : 96.03 % Rotamer: Outliers : 3.44 % Allowed : 18.43 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.14), residues: 3348 helix: 1.35 (0.18), residues: 908 sheet: 0.42 (0.19), residues: 734 loop : -0.83 (0.14), residues: 1706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP Z 48 HIS 0.006 0.001 HIS E 49 PHE 0.019 0.001 PHE D 119 TYR 0.023 0.002 TYR v 125 ARG 0.010 0.001 ARG v 168 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 739 residues out of total 2873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 647 time to evaluate : 3.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: v 14 GLN cc_start: 0.8356 (OUTLIER) cc_final: 0.7839 (mp10) REVERT: v 112 LYS cc_start: 0.8812 (OUTLIER) cc_final: 0.8577 (ptmm) REVERT: C 273 ARG cc_start: 0.7192 (OUTLIER) cc_final: 0.6823 (mtp180) REVERT: D 128 GLN cc_start: 0.8880 (OUTLIER) cc_final: 0.8411 (mt0) REVERT: E 74 ARG cc_start: 0.9278 (OUTLIER) cc_final: 0.7277 (ptp-170) REVERT: F 26 MET cc_start: 0.7848 (OUTLIER) cc_final: 0.7052 (mtt) REVERT: F 32 ASP cc_start: 0.8476 (t0) cc_final: 0.8275 (t0) REVERT: F 42 ASP cc_start: 0.8185 (p0) cc_final: 0.7834 (p0) REVERT: F 69 LYS cc_start: 0.9247 (OUTLIER) cc_final: 0.8516 (ttpp) REVERT: F 88 LYS cc_start: 0.9135 (ptmt) cc_final: 0.8436 (pptt) REVERT: F 153 ASP cc_start: 0.8567 (m-30) cc_final: 0.8190 (m-30) REVERT: F 156 ILE cc_start: 0.9553 (mm) cc_final: 0.9314 (tp) REVERT: F 158 THR cc_start: 0.9198 (OUTLIER) cc_final: 0.8894 (t) REVERT: F 165 GLU cc_start: 0.8894 (mp0) cc_final: 0.8595 (mp0) REVERT: G 163 ARG cc_start: 0.8791 (OUTLIER) cc_final: 0.7431 (pmm-80) REVERT: M 110 ASN cc_start: 0.8213 (t0) cc_final: 0.7986 (t0) REVERT: O 76 SER cc_start: 0.8808 (OUTLIER) cc_final: 0.8555 (p) REVERT: R 1 MET cc_start: 0.8524 (OUTLIER) cc_final: 0.8118 (ttp) REVERT: S 102 ASP cc_start: 0.7834 (t0) cc_final: 0.7583 (t0) REVERT: Y 84 LYS cc_start: 0.8874 (OUTLIER) cc_final: 0.7864 (mmtp) REVERT: Z 37 ARG cc_start: 0.7367 (OUTLIER) cc_final: 0.6900 (ttp-110) outliers start: 92 outliers final: 46 residues processed: 687 average time/residue: 1.7937 time to fit residues: 1652.6101 Evaluate side-chains 696 residues out of total 2873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 637 time to evaluate : 3.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain v residue 8 VAL Chi-restraints excluded: chain v residue 14 GLN Chi-restraints excluded: chain v residue 112 LYS Chi-restraints excluded: chain v residue 177 LEU Chi-restraints excluded: chain v residue 196 VAL Chi-restraints excluded: chain v residue 258 PHE Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 273 ARG Chi-restraints excluded: chain D residue 19 ASN Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 128 GLN Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain E residue 74 ARG Chi-restraints excluded: chain E residue 100 LYS Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain F residue 26 MET Chi-restraints excluded: chain F residue 56 GLU Chi-restraints excluded: chain F residue 69 LYS Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain G residue 116 VAL Chi-restraints excluded: chain G residue 163 ARG Chi-restraints excluded: chain L residue 87 SER Chi-restraints excluded: chain L residue 114 SER Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 31 LYS Chi-restraints excluded: chain M residue 66 LYS Chi-restraints excluded: chain N residue 81 VAL Chi-restraints excluded: chain O residue 55 THR Chi-restraints excluded: chain O residue 76 SER Chi-restraints excluded: chain O residue 103 MET Chi-restraints excluded: chain O residue 112 ASP Chi-restraints excluded: chain P residue 31 GLU Chi-restraints excluded: chain P residue 42 LYS Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain Q residue 110 GLU Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 65 SER Chi-restraints excluded: chain S residue 117 LEU Chi-restraints excluded: chain T residue 12 ILE Chi-restraints excluded: chain U residue 14 THR Chi-restraints excluded: chain V residue 81 THR Chi-restraints excluded: chain W residue 68 VAL Chi-restraints excluded: chain W residue 79 THR Chi-restraints excluded: chain Y residue 39 VAL Chi-restraints excluded: chain Y residue 78 GLU Chi-restraints excluded: chain Y residue 84 LYS Chi-restraints excluded: chain Z residue 25 SER Chi-restraints excluded: chain Z residue 37 ARG Chi-restraints excluded: chain Z residue 59 VAL Chi-restraints excluded: chain 1 residue 16 ASP Chi-restraints excluded: chain 2 residue 40 ASN Chi-restraints excluded: chain 2 residue 54 VAL Chi-restraints excluded: chain 4 residue 3 VAL Chi-restraints excluded: chain 5 residue 20 THR Chi-restraints excluded: chain 6 residue 33 SER Chi-restraints excluded: chain 7 residue 58 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 628 random chunks: chunk 204 optimal weight: 7.9990 chunk 546 optimal weight: 5.9990 chunk 119 optimal weight: 7.9990 chunk 356 optimal weight: 5.9990 chunk 149 optimal weight: 20.0000 chunk 607 optimal weight: 5.9990 chunk 504 optimal weight: 2.9990 chunk 281 optimal weight: 7.9990 chunk 50 optimal weight: 10.0000 chunk 200 optimal weight: 10.0000 chunk 318 optimal weight: 7.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 127 ASN M 4 GLN N 78 ASN Q 32 ASN T 81 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8914 moved from start: 0.1355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.079 98776 Z= 0.433 Angle : 0.628 14.150 148347 Z= 0.332 Chirality : 0.042 0.394 19071 Planarity : 0.005 0.054 7572 Dihedral : 22.723 179.652 50412 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.12 % Favored : 95.82 % Rotamer: Outliers : 3.70 % Allowed : 19.63 % Favored : 76.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.14), residues: 3348 helix: 1.24 (0.18), residues: 913 sheet: 0.40 (0.19), residues: 728 loop : -0.88 (0.14), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP Z 48 HIS 0.006 0.001 HIS E 49 PHE 0.019 0.001 PHE D 119 TYR 0.014 0.002 TYR T 74 ARG 0.007 0.001 ARG C 272 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 747 residues out of total 2873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 648 time to evaluate : 3.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: v 112 LYS cc_start: 0.8971 (OUTLIER) cc_final: 0.8656 (ptmm) REVERT: C 273 ARG cc_start: 0.7198 (OUTLIER) cc_final: 0.6786 (mtp180) REVERT: D 128 GLN cc_start: 0.8883 (OUTLIER) cc_final: 0.8423 (mt0) REVERT: E 20 ASN cc_start: 0.8877 (t0) cc_final: 0.8651 (t0) REVERT: E 74 ARG cc_start: 0.9290 (OUTLIER) cc_final: 0.7485 (ptp-170) REVERT: F 26 MET cc_start: 0.7822 (OUTLIER) cc_final: 0.7037 (mtt) REVERT: F 32 ASP cc_start: 0.8499 (t0) cc_final: 0.8284 (t0) REVERT: F 42 ASP cc_start: 0.8176 (p0) cc_final: 0.7843 (p0) REVERT: F 69 LYS cc_start: 0.9271 (OUTLIER) cc_final: 0.8502 (ttpt) REVERT: F 88 LYS cc_start: 0.9161 (ptmt) cc_final: 0.8445 (pptt) REVERT: F 92 ARG cc_start: 0.8469 (OUTLIER) cc_final: 0.8251 (ptm160) REVERT: F 153 ASP cc_start: 0.8558 (m-30) cc_final: 0.8236 (m-30) REVERT: F 158 THR cc_start: 0.9245 (OUTLIER) cc_final: 0.8904 (t) REVERT: F 165 GLU cc_start: 0.8870 (mp0) cc_final: 0.8596 (mp0) REVERT: G 163 ARG cc_start: 0.8870 (OUTLIER) cc_final: 0.7839 (pmm-80) REVERT: M 110 ASN cc_start: 0.8267 (t0) cc_final: 0.8060 (t0) REVERT: R 1 MET cc_start: 0.8525 (OUTLIER) cc_final: 0.8130 (ttp) REVERT: S 102 ASP cc_start: 0.7839 (t0) cc_final: 0.7567 (t0) REVERT: U 95 GLN cc_start: 0.8730 (OUTLIER) cc_final: 0.7942 (mp10) REVERT: Y 84 LYS cc_start: 0.8876 (OUTLIER) cc_final: 0.7869 (mmtp) REVERT: Z 37 ARG cc_start: 0.7393 (OUTLIER) cc_final: 0.6872 (ttp-110) REVERT: 5 33 LYS cc_start: 0.9153 (OUTLIER) cc_final: 0.8793 (mttt) outliers start: 99 outliers final: 57 residues processed: 689 average time/residue: 1.8020 time to fit residues: 1667.3598 Evaluate side-chains 704 residues out of total 2873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 633 time to evaluate : 3.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain v residue 8 VAL Chi-restraints excluded: chain v residue 112 LYS Chi-restraints excluded: chain v residue 177 LEU Chi-restraints excluded: chain v residue 196 VAL Chi-restraints excluded: chain v residue 258 PHE Chi-restraints excluded: chain v residue 267 VAL Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 273 ARG Chi-restraints excluded: chain D residue 19 ASN Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 128 GLN Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain E residue 74 ARG Chi-restraints excluded: chain E residue 100 LYS Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain F residue 26 MET Chi-restraints excluded: chain F residue 56 GLU Chi-restraints excluded: chain F residue 69 LYS Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain G residue 53 SER Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 116 VAL Chi-restraints excluded: chain G residue 163 ARG Chi-restraints excluded: chain L residue 87 SER Chi-restraints excluded: chain L residue 114 SER Chi-restraints excluded: chain L residue 139 GLU Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 31 LYS Chi-restraints excluded: chain M residue 66 LYS Chi-restraints excluded: chain N residue 81 VAL Chi-restraints excluded: chain O residue 55 THR Chi-restraints excluded: chain O residue 103 MET Chi-restraints excluded: chain O residue 131 ILE Chi-restraints excluded: chain P residue 31 GLU Chi-restraints excluded: chain P residue 42 LYS Chi-restraints excluded: chain P residue 130 VAL Chi-restraints excluded: chain Q residue 3 THR Chi-restraints excluded: chain Q residue 40 ILE Chi-restraints excluded: chain Q residue 53 LEU Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain Q residue 110 GLU Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 64 ILE Chi-restraints excluded: chain R residue 65 SER Chi-restraints excluded: chain S residue 117 LEU Chi-restraints excluded: chain T residue 12 ILE Chi-restraints excluded: chain T residue 95 LEU Chi-restraints excluded: chain U residue 95 GLN Chi-restraints excluded: chain V residue 81 THR Chi-restraints excluded: chain W residue 68 VAL Chi-restraints excluded: chain W residue 79 THR Chi-restraints excluded: chain Y residue 39 VAL Chi-restraints excluded: chain Y residue 84 LYS Chi-restraints excluded: chain Z residue 37 ARG Chi-restraints excluded: chain Z residue 56 SER Chi-restraints excluded: chain Z residue 59 VAL Chi-restraints excluded: chain 1 residue 5 ASP Chi-restraints excluded: chain 2 residue 40 ASN Chi-restraints excluded: chain 2 residue 54 VAL Chi-restraints excluded: chain 4 residue 3 VAL Chi-restraints excluded: chain 5 residue 20 THR Chi-restraints excluded: chain 5 residue 33 LYS Chi-restraints excluded: chain 6 residue 33 SER Chi-restraints excluded: chain 7 residue 10 SER Chi-restraints excluded: chain 7 residue 58 ILE Chi-restraints excluded: chain 8 residue 24 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 628 random chunks: chunk 585 optimal weight: 6.9990 chunk 68 optimal weight: 10.0000 chunk 346 optimal weight: 3.9990 chunk 443 optimal weight: 1.9990 chunk 343 optimal weight: 4.9990 chunk 511 optimal weight: 6.9990 chunk 339 optimal weight: 10.0000 chunk 605 optimal weight: 50.0000 chunk 378 optimal weight: 8.9990 chunk 369 optimal weight: 3.9990 chunk 279 optimal weight: 8.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 4 GLN Q 32 ASN T 81 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8902 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 98776 Z= 0.341 Angle : 0.603 13.729 148347 Z= 0.320 Chirality : 0.040 0.374 19071 Planarity : 0.005 0.065 7572 Dihedral : 22.734 179.795 50412 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.03 % Favored : 95.91 % Rotamer: Outliers : 3.29 % Allowed : 21.01 % Favored : 75.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.14), residues: 3348 helix: 1.31 (0.18), residues: 906 sheet: 0.42 (0.19), residues: 714 loop : -0.86 (0.14), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP Z 48 HIS 0.005 0.001 HIS S 29 PHE 0.016 0.001 PHE D 119 TYR 0.012 0.001 TYR O 32 ARG 0.012 0.000 ARG v 168 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 724 residues out of total 2873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 636 time to evaluate : 3.883 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: v 112 LYS cc_start: 0.8925 (OUTLIER) cc_final: 0.8632 (ptmm) REVERT: C 273 ARG cc_start: 0.7178 (OUTLIER) cc_final: 0.6781 (mtp180) REVERT: D 128 GLN cc_start: 0.8860 (OUTLIER) cc_final: 0.7894 (mm-40) REVERT: E 74 ARG cc_start: 0.9279 (OUTLIER) cc_final: 0.7296 (ptp-170) REVERT: F 26 MET cc_start: 0.7800 (OUTLIER) cc_final: 0.6971 (mtt) REVERT: F 32 ASP cc_start: 0.8512 (t0) cc_final: 0.8294 (t0) REVERT: F 42 ASP cc_start: 0.8209 (p0) cc_final: 0.7986 (p0) REVERT: F 69 LYS cc_start: 0.9248 (OUTLIER) cc_final: 0.8516 (ttpt) REVERT: F 88 LYS cc_start: 0.9156 (ptmt) cc_final: 0.8454 (pptt) REVERT: F 92 ARG cc_start: 0.8484 (mtp85) cc_final: 0.8078 (ptp-170) REVERT: F 153 ASP cc_start: 0.8544 (m-30) cc_final: 0.8215 (m-30) REVERT: F 165 GLU cc_start: 0.8859 (mp0) cc_final: 0.8608 (mp0) REVERT: G 163 ARG cc_start: 0.8868 (OUTLIER) cc_final: 0.7882 (pmm-80) REVERT: M 110 ASN cc_start: 0.8270 (t0) cc_final: 0.8045 (t0) REVERT: Q 115 ASN cc_start: 0.8134 (OUTLIER) cc_final: 0.7918 (m-40) REVERT: R 1 MET cc_start: 0.8510 (OUTLIER) cc_final: 0.8119 (ttp) REVERT: S 102 ASP cc_start: 0.7797 (t0) cc_final: 0.7560 (t0) REVERT: T 1 MET cc_start: 0.7760 (ttt) cc_final: 0.7430 (ttt) REVERT: Y 84 LYS cc_start: 0.8884 (OUTLIER) cc_final: 0.7885 (mmtp) REVERT: Z 37 ARG cc_start: 0.7406 (OUTLIER) cc_final: 0.6879 (ttp-110) REVERT: 5 33 LYS cc_start: 0.9141 (OUTLIER) cc_final: 0.8788 (mttt) outliers start: 88 outliers final: 59 residues processed: 673 average time/residue: 1.8014 time to fit residues: 1630.8478 Evaluate side-chains 701 residues out of total 2873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 630 time to evaluate : 3.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain v residue 8 VAL Chi-restraints excluded: chain v residue 112 LYS Chi-restraints excluded: chain v residue 177 LEU Chi-restraints excluded: chain v residue 196 VAL Chi-restraints excluded: chain v residue 258 PHE Chi-restraints excluded: chain v residue 267 VAL Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 273 ARG Chi-restraints excluded: chain D residue 19 ASN Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 128 GLN Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain E residue 74 ARG Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain F residue 26 MET Chi-restraints excluded: chain F residue 56 GLU Chi-restraints excluded: chain F residue 69 LYS Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain G residue 53 SER Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 116 VAL Chi-restraints excluded: chain G residue 163 ARG Chi-restraints excluded: chain L residue 87 SER Chi-restraints excluded: chain L residue 114 SER Chi-restraints excluded: chain L residue 139 GLU Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 31 LYS Chi-restraints excluded: chain M residue 66 LYS Chi-restraints excluded: chain O residue 55 THR Chi-restraints excluded: chain O residue 94 VAL Chi-restraints excluded: chain O residue 103 MET Chi-restraints excluded: chain P residue 31 GLU Chi-restraints excluded: chain P residue 42 LYS Chi-restraints excluded: chain P residue 53 LYS Chi-restraints excluded: chain P residue 66 ILE Chi-restraints excluded: chain P residue 130 VAL Chi-restraints excluded: chain Q residue 40 ILE Chi-restraints excluded: chain Q residue 53 LEU Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain Q residue 110 GLU Chi-restraints excluded: chain Q residue 115 ASN Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 64 ILE Chi-restraints excluded: chain R residue 65 SER Chi-restraints excluded: chain S residue 117 LEU Chi-restraints excluded: chain T residue 12 ILE Chi-restraints excluded: chain T residue 95 LEU Chi-restraints excluded: chain V residue 81 THR Chi-restraints excluded: chain W residue 68 VAL Chi-restraints excluded: chain W residue 79 THR Chi-restraints excluded: chain Y residue 39 VAL Chi-restraints excluded: chain Y residue 84 LYS Chi-restraints excluded: chain Z residue 25 SER Chi-restraints excluded: chain Z residue 37 ARG Chi-restraints excluded: chain Z residue 56 SER Chi-restraints excluded: chain Z residue 59 VAL Chi-restraints excluded: chain 1 residue 5 ASP Chi-restraints excluded: chain 1 residue 16 ASP Chi-restraints excluded: chain 2 residue 40 ASN Chi-restraints excluded: chain 2 residue 54 VAL Chi-restraints excluded: chain 4 residue 3 VAL Chi-restraints excluded: chain 5 residue 20 THR Chi-restraints excluded: chain 5 residue 33 LYS Chi-restraints excluded: chain 6 residue 33 SER Chi-restraints excluded: chain 7 residue 30 SER Chi-restraints excluded: chain 7 residue 58 ILE Chi-restraints excluded: chain 8 residue 24 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 628 random chunks: chunk 374 optimal weight: 3.9990 chunk 241 optimal weight: 7.9990 chunk 361 optimal weight: 2.9990 chunk 182 optimal weight: 8.9990 chunk 118 optimal weight: 7.9990 chunk 117 optimal weight: 20.0000 chunk 384 optimal weight: 3.9990 chunk 412 optimal weight: 30.0000 chunk 299 optimal weight: 8.9990 chunk 56 optimal weight: 10.0000 chunk 475 optimal weight: 0.9980 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 157 ASN M 4 GLN Q 32 ASN T 81 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8894 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 98776 Z= 0.311 Angle : 0.591 13.237 148347 Z= 0.314 Chirality : 0.039 0.362 19071 Planarity : 0.005 0.076 7572 Dihedral : 22.733 179.991 50412 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.97 % Favored : 95.97 % Rotamer: Outliers : 3.36 % Allowed : 21.12 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.14), residues: 3348 helix: 1.31 (0.18), residues: 906 sheet: 0.46 (0.19), residues: 705 loop : -0.87 (0.14), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP Z 48 HIS 0.005 0.001 HIS S 29 PHE 0.014 0.001 PHE D 119 TYR 0.027 0.001 TYR v 125 ARG 0.011 0.000 ARG v 271 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 729 residues out of total 2873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 639 time to evaluate : 3.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: v 112 LYS cc_start: 0.8932 (OUTLIER) cc_final: 0.8632 (ptmm) REVERT: C 273 ARG cc_start: 0.7175 (OUTLIER) cc_final: 0.6738 (mtp180) REVERT: D 128 GLN cc_start: 0.8849 (OUTLIER) cc_final: 0.7896 (mm-40) REVERT: E 74 ARG cc_start: 0.9265 (OUTLIER) cc_final: 0.7274 (ptp-170) REVERT: F 26 MET cc_start: 0.7751 (OUTLIER) cc_final: 0.6914 (mtt) REVERT: F 32 ASP cc_start: 0.8463 (t0) cc_final: 0.8243 (t0) REVERT: F 42 ASP cc_start: 0.8206 (p0) cc_final: 0.7954 (p0) REVERT: F 69 LYS cc_start: 0.9255 (OUTLIER) cc_final: 0.8541 (ttpt) REVERT: F 88 LYS cc_start: 0.9177 (ptmt) cc_final: 0.8447 (pptt) REVERT: F 92 ARG cc_start: 0.8490 (OUTLIER) cc_final: 0.8206 (ptm160) REVERT: F 153 ASP cc_start: 0.8570 (m-30) cc_final: 0.8239 (m-30) REVERT: F 165 GLU cc_start: 0.8869 (mp0) cc_final: 0.8617 (mp0) REVERT: G 163 ARG cc_start: 0.8858 (OUTLIER) cc_final: 0.7872 (pmm-80) REVERT: M 110 ASN cc_start: 0.8243 (t0) cc_final: 0.8020 (t0) REVERT: R 1 MET cc_start: 0.8520 (OUTLIER) cc_final: 0.8125 (ttp) REVERT: S 102 ASP cc_start: 0.7771 (t0) cc_final: 0.7526 (t0) REVERT: T 1 MET cc_start: 0.7449 (ttt) cc_final: 0.7153 (ttm) REVERT: U 95 GLN cc_start: 0.8721 (OUTLIER) cc_final: 0.7913 (mp10) REVERT: Y 84 LYS cc_start: 0.8875 (OUTLIER) cc_final: 0.7879 (mmtp) REVERT: Z 37 ARG cc_start: 0.7404 (OUTLIER) cc_final: 0.6876 (ttp-110) REVERT: 5 33 LYS cc_start: 0.9135 (OUTLIER) cc_final: 0.8785 (mttt) REVERT: 7 56 LYS cc_start: 0.8919 (OUTLIER) cc_final: 0.8524 (mtmm) outliers start: 90 outliers final: 63 residues processed: 674 average time/residue: 1.7768 time to fit residues: 1612.1727 Evaluate side-chains 707 residues out of total 2873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 630 time to evaluate : 3.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain v residue 8 VAL Chi-restraints excluded: chain v residue 112 LYS Chi-restraints excluded: chain v residue 158 THR Chi-restraints excluded: chain v residue 177 LEU Chi-restraints excluded: chain v residue 196 VAL Chi-restraints excluded: chain v residue 258 PHE Chi-restraints excluded: chain v residue 267 VAL Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 273 ARG Chi-restraints excluded: chain D residue 19 ASN Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 128 GLN Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain E residue 74 ARG Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain F residue 26 MET Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 56 GLU Chi-restraints excluded: chain F residue 69 LYS Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 53 SER Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 116 VAL Chi-restraints excluded: chain G residue 163 ARG Chi-restraints excluded: chain L residue 87 SER Chi-restraints excluded: chain L residue 114 SER Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 31 LYS Chi-restraints excluded: chain M residue 66 LYS Chi-restraints excluded: chain N residue 113 SER Chi-restraints excluded: chain O residue 55 THR Chi-restraints excluded: chain O residue 94 VAL Chi-restraints excluded: chain O residue 103 MET Chi-restraints excluded: chain O residue 131 ILE Chi-restraints excluded: chain P residue 31 GLU Chi-restraints excluded: chain P residue 42 LYS Chi-restraints excluded: chain P residue 53 LYS Chi-restraints excluded: chain P residue 66 ILE Chi-restraints excluded: chain P residue 130 VAL Chi-restraints excluded: chain Q residue 3 THR Chi-restraints excluded: chain Q residue 53 LEU Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain Q residue 110 GLU Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 65 SER Chi-restraints excluded: chain S residue 117 LEU Chi-restraints excluded: chain T residue 12 ILE Chi-restraints excluded: chain T residue 95 LEU Chi-restraints excluded: chain U residue 95 GLN Chi-restraints excluded: chain V residue 81 THR Chi-restraints excluded: chain W residue 68 VAL Chi-restraints excluded: chain W residue 79 THR Chi-restraints excluded: chain Y residue 39 VAL Chi-restraints excluded: chain Y residue 84 LYS Chi-restraints excluded: chain Z residue 25 SER Chi-restraints excluded: chain Z residue 37 ARG Chi-restraints excluded: chain Z residue 56 SER Chi-restraints excluded: chain Z residue 59 VAL Chi-restraints excluded: chain 1 residue 5 ASP Chi-restraints excluded: chain 1 residue 16 ASP Chi-restraints excluded: chain 2 residue 40 ASN Chi-restraints excluded: chain 2 residue 54 VAL Chi-restraints excluded: chain 4 residue 3 VAL Chi-restraints excluded: chain 5 residue 20 THR Chi-restraints excluded: chain 5 residue 33 LYS Chi-restraints excluded: chain 6 residue 33 SER Chi-restraints excluded: chain 7 residue 10 SER Chi-restraints excluded: chain 7 residue 30 SER Chi-restraints excluded: chain 7 residue 56 LYS Chi-restraints excluded: chain 7 residue 58 ILE Chi-restraints excluded: chain 8 residue 24 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 628 random chunks: chunk 550 optimal weight: 7.9990 chunk 579 optimal weight: 0.8980 chunk 529 optimal weight: 2.9990 chunk 564 optimal weight: 5.9990 chunk 339 optimal weight: 10.0000 chunk 245 optimal weight: 7.9990 chunk 442 optimal weight: 8.9990 chunk 173 optimal weight: 8.9990 chunk 509 optimal weight: 0.3980 chunk 533 optimal weight: 2.9990 chunk 562 optimal weight: 3.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 157 ASN M 4 GLN Q 32 ASN T 81 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8876 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 98776 Z= 0.200 Angle : 0.574 12.779 148347 Z= 0.305 Chirality : 0.036 0.335 19071 Planarity : 0.005 0.096 7572 Dihedral : 22.767 179.894 50412 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.03 % Favored : 95.91 % Rotamer: Outliers : 2.88 % Allowed : 21.79 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.14), residues: 3348 helix: 1.38 (0.18), residues: 899 sheet: 0.54 (0.19), residues: 713 loop : -0.82 (0.14), residues: 1736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP Z 48 HIS 0.006 0.001 HIS R 29 PHE 0.011 0.001 PHE D 119 TYR 0.017 0.001 TYR T 82 ARG 0.015 0.000 ARG v 271 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 719 residues out of total 2873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 642 time to evaluate : 4.274 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: v 112 LYS cc_start: 0.8891 (OUTLIER) cc_final: 0.8618 (ptmm) REVERT: C 273 ARG cc_start: 0.7179 (OUTLIER) cc_final: 0.6764 (mtp180) REVERT: D 128 GLN cc_start: 0.8811 (OUTLIER) cc_final: 0.7867 (mm-40) REVERT: E 74 ARG cc_start: 0.9244 (OUTLIER) cc_final: 0.7272 (ptp-170) REVERT: F 26 MET cc_start: 0.7736 (OUTLIER) cc_final: 0.7011 (mtt) REVERT: F 32 ASP cc_start: 0.8449 (t0) cc_final: 0.8226 (t0) REVERT: F 42 ASP cc_start: 0.8178 (p0) cc_final: 0.7967 (p0) REVERT: F 69 LYS cc_start: 0.9253 (OUTLIER) cc_final: 0.8596 (tmmt) REVERT: F 88 LYS cc_start: 0.9159 (ptmt) cc_final: 0.8430 (pptt) REVERT: F 92 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.8248 (ptm160) REVERT: F 153 ASP cc_start: 0.8546 (m-30) cc_final: 0.8235 (m-30) REVERT: F 158 THR cc_start: 0.9216 (OUTLIER) cc_final: 0.8922 (t) REVERT: G 163 ARG cc_start: 0.8833 (OUTLIER) cc_final: 0.7841 (pmm-80) REVERT: L 15 LYS cc_start: 0.8782 (OUTLIER) cc_final: 0.8576 (mmmm) REVERT: M 110 ASN cc_start: 0.8196 (t0) cc_final: 0.7943 (t0) REVERT: Q 115 ASN cc_start: 0.8166 (OUTLIER) cc_final: 0.7879 (m-40) REVERT: R 1 MET cc_start: 0.8500 (OUTLIER) cc_final: 0.8111 (ttp) REVERT: S 102 ASP cc_start: 0.7655 (t0) cc_final: 0.7385 (t0) REVERT: T 1 MET cc_start: 0.7320 (ttt) cc_final: 0.7081 (ttm) REVERT: Y 84 LYS cc_start: 0.8861 (OUTLIER) cc_final: 0.7861 (mmtp) REVERT: Z 37 ARG cc_start: 0.7391 (OUTLIER) cc_final: 0.6867 (ttp-110) REVERT: 5 33 LYS cc_start: 0.9125 (OUTLIER) cc_final: 0.8776 (mttt) REVERT: 7 56 LYS cc_start: 0.8895 (OUTLIER) cc_final: 0.8498 (mtmm) outliers start: 77 outliers final: 45 residues processed: 674 average time/residue: 1.8255 time to fit residues: 1652.5496 Evaluate side-chains 698 residues out of total 2873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 637 time to evaluate : 3.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain v residue 8 VAL Chi-restraints excluded: chain v residue 112 LYS Chi-restraints excluded: chain v residue 177 LEU Chi-restraints excluded: chain v residue 196 VAL Chi-restraints excluded: chain v residue 258 PHE Chi-restraints excluded: chain v residue 267 VAL Chi-restraints excluded: chain C residue 273 ARG Chi-restraints excluded: chain D residue 19 ASN Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 128 GLN Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain E residue 74 ARG Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain F residue 26 MET Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 56 GLU Chi-restraints excluded: chain F residue 69 LYS Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 116 VAL Chi-restraints excluded: chain G residue 163 ARG Chi-restraints excluded: chain L residue 15 LYS Chi-restraints excluded: chain L residue 87 SER Chi-restraints excluded: chain L residue 114 SER Chi-restraints excluded: chain L residue 139 GLU Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain O residue 94 VAL Chi-restraints excluded: chain O residue 103 MET Chi-restraints excluded: chain O residue 131 ILE Chi-restraints excluded: chain P residue 53 LYS Chi-restraints excluded: chain P residue 130 VAL Chi-restraints excluded: chain Q residue 53 LEU Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain Q residue 110 GLU Chi-restraints excluded: chain Q residue 115 ASN Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 65 SER Chi-restraints excluded: chain S residue 117 LEU Chi-restraints excluded: chain T residue 95 LEU Chi-restraints excluded: chain V residue 36 THR Chi-restraints excluded: chain V residue 81 THR Chi-restraints excluded: chain W residue 68 VAL Chi-restraints excluded: chain W residue 79 THR Chi-restraints excluded: chain Y residue 39 VAL Chi-restraints excluded: chain Y residue 84 LYS Chi-restraints excluded: chain Z residue 37 ARG Chi-restraints excluded: chain Z residue 56 SER Chi-restraints excluded: chain Z residue 59 VAL Chi-restraints excluded: chain 1 residue 5 ASP Chi-restraints excluded: chain 2 residue 40 ASN Chi-restraints excluded: chain 2 residue 54 VAL Chi-restraints excluded: chain 4 residue 3 VAL Chi-restraints excluded: chain 5 residue 20 THR Chi-restraints excluded: chain 5 residue 33 LYS Chi-restraints excluded: chain 6 residue 33 SER Chi-restraints excluded: chain 7 residue 30 SER Chi-restraints excluded: chain 7 residue 56 LYS Chi-restraints excluded: chain 7 residue 58 ILE Chi-restraints excluded: chain 8 residue 24 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 628 random chunks: chunk 370 optimal weight: 0.6980 chunk 596 optimal weight: 10.0000 chunk 364 optimal weight: 0.9980 chunk 282 optimal weight: 10.0000 chunk 414 optimal weight: 8.9990 chunk 625 optimal weight: 5.9990 chunk 575 optimal weight: 1.9990 chunk 498 optimal weight: 1.9990 chunk 51 optimal weight: 10.0000 chunk 384 optimal weight: 4.9990 chunk 305 optimal weight: 10.0000 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 157 ASN M 4 GLN Q 32 ASN T 81 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8860 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 98776 Z= 0.192 Angle : 0.557 12.744 148347 Z= 0.297 Chirality : 0.036 0.322 19071 Planarity : 0.004 0.123 7572 Dihedral : 22.741 179.309 50412 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.97 % Favored : 95.97 % Rotamer: Outliers : 2.39 % Allowed : 22.54 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.14), residues: 3348 helix: 1.35 (0.18), residues: 906 sheet: 0.53 (0.19), residues: 722 loop : -0.80 (0.14), residues: 1720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP Z 48 HIS 0.005 0.001 HIS R 29 PHE 0.010 0.001 PHE R 74 TYR 0.016 0.001 TYR T 82 ARG 0.015 0.000 ARG v 271 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 718 residues out of total 2873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 654 time to evaluate : 3.821 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: v 112 LYS cc_start: 0.8921 (OUTLIER) cc_final: 0.8674 (ptmm) REVERT: C 273 ARG cc_start: 0.7197 (OUTLIER) cc_final: 0.6779 (mtp180) REVERT: D 128 GLN cc_start: 0.8804 (OUTLIER) cc_final: 0.7870 (mm-40) REVERT: E 74 ARG cc_start: 0.9214 (OUTLIER) cc_final: 0.7232 (ptp-170) REVERT: F 26 MET cc_start: 0.7756 (OUTLIER) cc_final: 0.6992 (mtt) REVERT: F 69 LYS cc_start: 0.9242 (mppt) cc_final: 0.8583 (ttpt) REVERT: F 88 LYS cc_start: 0.9178 (ptmt) cc_final: 0.8430 (pptt) REVERT: F 153 ASP cc_start: 0.8508 (m-30) cc_final: 0.8200 (m-30) REVERT: G 163 ARG cc_start: 0.8822 (OUTLIER) cc_final: 0.7809 (pmm-80) REVERT: L 15 LYS cc_start: 0.8785 (OUTLIER) cc_final: 0.8567 (mmmm) REVERT: M 110 ASN cc_start: 0.8215 (t0) cc_final: 0.7949 (t0) REVERT: R 1 MET cc_start: 0.8492 (OUTLIER) cc_final: 0.8112 (ttp) REVERT: S 102 ASP cc_start: 0.7665 (t0) cc_final: 0.7372 (t0) REVERT: T 1 MET cc_start: 0.7379 (ttt) cc_final: 0.7141 (ttm) REVERT: Y 84 LYS cc_start: 0.8832 (OUTLIER) cc_final: 0.7831 (mmtp) REVERT: Z 37 ARG cc_start: 0.7388 (OUTLIER) cc_final: 0.6870 (ttp-110) REVERT: 5 33 LYS cc_start: 0.9119 (OUTLIER) cc_final: 0.8766 (mttt) outliers start: 64 outliers final: 48 residues processed: 681 average time/residue: 1.7934 time to fit residues: 1648.7799 Evaluate side-chains 708 residues out of total 2873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 649 time to evaluate : 3.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain v residue 8 VAL Chi-restraints excluded: chain v residue 112 LYS Chi-restraints excluded: chain v residue 177 LEU Chi-restraints excluded: chain v residue 196 VAL Chi-restraints excluded: chain v residue 258 PHE Chi-restraints excluded: chain v residue 267 VAL Chi-restraints excluded: chain C residue 273 ARG Chi-restraints excluded: chain D residue 19 ASN Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 128 GLN Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain E residue 74 ARG Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain F residue 26 MET Chi-restraints excluded: chain F residue 56 GLU Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 116 VAL Chi-restraints excluded: chain G residue 163 ARG Chi-restraints excluded: chain L residue 15 LYS Chi-restraints excluded: chain L residue 87 SER Chi-restraints excluded: chain L residue 114 SER Chi-restraints excluded: chain L residue 139 GLU Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain O residue 94 VAL Chi-restraints excluded: chain O residue 103 MET Chi-restraints excluded: chain O residue 131 ILE Chi-restraints excluded: chain P residue 53 LYS Chi-restraints excluded: chain P residue 130 VAL Chi-restraints excluded: chain Q residue 53 LEU Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain Q residue 110 GLU Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 65 SER Chi-restraints excluded: chain S residue 117 LEU Chi-restraints excluded: chain T residue 95 LEU Chi-restraints excluded: chain V residue 36 THR Chi-restraints excluded: chain V residue 81 THR Chi-restraints excluded: chain W residue 68 VAL Chi-restraints excluded: chain W residue 79 THR Chi-restraints excluded: chain Y residue 39 VAL Chi-restraints excluded: chain Y residue 84 LYS Chi-restraints excluded: chain Z residue 37 ARG Chi-restraints excluded: chain Z residue 56 SER Chi-restraints excluded: chain Z residue 59 VAL Chi-restraints excluded: chain 1 residue 5 ASP Chi-restraints excluded: chain 1 residue 16 ASP Chi-restraints excluded: chain 2 residue 40 ASN Chi-restraints excluded: chain 2 residue 54 VAL Chi-restraints excluded: chain 4 residue 3 VAL Chi-restraints excluded: chain 5 residue 20 THR Chi-restraints excluded: chain 5 residue 33 LYS Chi-restraints excluded: chain 6 residue 33 SER Chi-restraints excluded: chain 7 residue 30 SER Chi-restraints excluded: chain 7 residue 58 ILE Chi-restraints excluded: chain 8 residue 24 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 628 random chunks: chunk 395 optimal weight: 7.9990 chunk 530 optimal weight: 5.9990 chunk 152 optimal weight: 30.0000 chunk 459 optimal weight: 6.9990 chunk 73 optimal weight: 10.0000 chunk 138 optimal weight: 8.9990 chunk 498 optimal weight: 6.9990 chunk 208 optimal weight: 8.9990 chunk 512 optimal weight: 0.0670 chunk 63 optimal weight: 10.0000 chunk 91 optimal weight: 8.9990 overall best weight: 5.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 157 ASN L 118 GLN M 4 GLN Q 32 ASN T 81 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.069548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2469 r_free = 0.2469 target = 0.045760 restraints weight = 236822.282| |-----------------------------------------------------------------------------| r_work (start): 0.2465 rms_B_bonded: 1.12 r_work: 0.2355 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2274 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.2274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9195 moved from start: 0.1466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 98776 Z= 0.421 Angle : 0.626 12.482 148347 Z= 0.330 Chirality : 0.042 0.387 19071 Planarity : 0.005 0.080 7572 Dihedral : 22.694 179.979 50412 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.18 % Favored : 95.76 % Rotamer: Outliers : 2.47 % Allowed : 22.65 % Favored : 74.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.14), residues: 3348 helix: 1.21 (0.18), residues: 915 sheet: 0.37 (0.19), residues: 737 loop : -0.84 (0.14), residues: 1696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP Z 48 HIS 0.005 0.001 HIS E 49 PHE 0.018 0.001 PHE D 119 TYR 0.022 0.002 TYR T 82 ARG 0.023 0.001 ARG v 168 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 27333.74 seconds wall clock time: 475 minutes 35.52 seconds (28535.52 seconds total)