Starting phenix.real_space_refine on Sat Feb 24 15:57:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xyu_6790/02_2024/5xyu_6790_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xyu_6790/02_2024/5xyu_6790.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xyu_6790/02_2024/5xyu_6790.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xyu_6790/02_2024/5xyu_6790.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xyu_6790/02_2024/5xyu_6790_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xyu_6790/02_2024/5xyu_6790_neut.pdb" } resolution = 3.45 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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: 6 Type Number sf(0) Gaussians P 1379 5.49 5 Mg 48 5.21 5 S 32 5.16 5 C 22881 2.51 5 N 8466 2.21 5 O 12351 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ARG 11": "NH1" <-> "NH2" Residue "C ARG 21": "NH1" <-> "NH2" Residue "C ARG 58": "NH1" <-> "NH2" Residue "C ARG 150": "NH1" <-> "NH2" Residue "C PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 169": "NH1" <-> "NH2" Residue "C ARG 179": "NH1" <-> "NH2" Residue "D ARG 14": "NH1" <-> "NH2" Residue "D ARG 68": "NH1" <-> "NH2" Residue "D ARG 69": "NH1" <-> "NH2" Residue "D ARG 76": "NH1" <-> "NH2" Residue "D ARG 99": "NH1" <-> "NH2" Residue "D ARG 110": "NH1" <-> "NH2" Residue "D PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 98": "NH1" <-> "NH2" Residue "E ASP 188": "OD1" <-> "OD2" Residue "F TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 10": "NH1" <-> "NH2" Residue "G TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 51": "NH1" <-> "NH2" Residue "G ARG 76": "NH1" <-> "NH2" Residue "G ARG 92": "NH1" <-> "NH2" Residue "G ARG 149": "NH1" <-> "NH2" Residue "H TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 50": "NH1" <-> "NH2" Residue "H ARG 55": "NH1" <-> "NH2" Residue "H ARG 72": "NH1" <-> "NH2" Residue "H ARG 79": "NH1" <-> "NH2" Residue "H ARG 96": "NH1" <-> "NH2" Residue "I ARG 32": "NH1" <-> "NH2" Residue "I PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 126": "NH1" <-> "NH2" Residue "I ASP 127": "OD1" <-> "OD2" Residue "I ARG 133": "NH1" <-> "NH2" Residue "I TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 89": "NH1" <-> "NH2" Residue "K ARG 102": "NH1" <-> "NH2" Residue "L ARG 9": "NH1" <-> "NH2" Residue "L ARG 12": "NH1" <-> "NH2" Residue "L ARG 13": "NH1" <-> "NH2" Residue "L TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 99": "NH1" <-> "NH2" Residue "L ARG 116": "NH1" <-> "NH2" Residue "L TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 57": "NH1" <-> "NH2" Residue "M ARG 71": "NH1" <-> "NH2" Residue "N TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 29": "NH1" <-> "NH2" Residue "N TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 45": "NH1" <-> "NH2" Residue "O TYR 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 54": "NH1" <-> "NH2" Residue "O ARG 63": "NH1" <-> "NH2" Residue "O ARG 64": "NH1" <-> "NH2" Residue "P ARG 14": "NH1" <-> "NH2" Residue "P ARG 28": "NH1" <-> "NH2" Residue "P ARG 29": "NH1" <-> "NH2" Residue "P ARG 55": "NH1" <-> "NH2" Residue "Q ARG 19": "NH1" <-> "NH2" Residue "Q ARG 20": "NH1" <-> "NH2" Residue "Q ASP 30": "OD1" <-> "OD2" Residue "Q ASP 72": "OD1" <-> "OD2" Residue "Q ARG 73": "NH1" <-> "NH2" Residue "Q ARG 87": "NH1" <-> "NH2" Residue "R ARG 51": "NH1" <-> "NH2" Residue "R ARG 62": "NH1" <-> "NH2" Residue "T ARG 10": "NH1" <-> "NH2" Residue "T ARG 16": "NH1" <-> "NH2" Residue "T ARG 29": "NH1" <-> "NH2" Residue "U ARG 8": "NH1" <-> "NH2" Residue "U ARG 11": "NH1" <-> "NH2" Residue "U ARG 25": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 45157 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 29639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1379, 29639 Classifications: {'RNA': 1379} Modifications used: {'rna2p_pur': 116, 'rna2p_pyr': 90, 'rna3p_pur': 674, 'rna3p_pyr': 499} Link IDs: {'rna2p': 206, 'rna3p': 1172} Chain breaks: 16 Chain: "C" Number of atoms: 1498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1498 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 4, 'TRANS': 180} Chain breaks: 3 Chain: "D" Number of atoms: 1156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1156 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 3, 'TRANS': 134} Chain breaks: 4 Chain: "E" Number of atoms: 1147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1147 Classifications: {'peptide': 159} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 149} Chain: "F" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 530 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain breaks: 1 Chain: "G" Number of atoms: 1141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1141 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 7, 'TRANS': 136} Chain breaks: 2 Chain: "H" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 990 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain breaks: 1 Chain: "I" Number of atoms: 974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 974 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 8, 'TRANS': 115} Chain: "J" Number of atoms: 778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 778 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 7, 'TRANS': 89} Chain breaks: 1 Chain: "K" Number of atoms: 853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 853 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 8, 'TRANS': 106} Chain: "L" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 964 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 5, 'TRANS': 117} Chain: "M" Number of atoms: 868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 868 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 107} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 16 Chain: "N" Number of atoms: 477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 477 Classifications: {'peptide': 60} Link IDs: {'CIS': 2, 'PTRANS': 3, 'TRANS': 54} Chain: "O" Number of atoms: 698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 698 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "P" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 745 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 6, 'TRANS': 87} Chain breaks: 1 Chain: "Q" Number of atoms: 721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 721 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 5, 'TRANS': 85} Chain breaks: 1 Chain: "R" Number of atoms: 432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 432 Classifications: {'peptide': 55} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 52} Chain: "S" Number of atoms: 634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 634 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 4, 'TRANS': 74} Chain: "T" Number of atoms: 647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 647 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "U" Number of atoms: 217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 217 Classifications: {'peptide': 25} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 24} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 47 Unusual residues: {' MG': 47} Classifications: {'undetermined': 47} Link IDs: {None: 46} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 22.44, per 1000 atoms: 0.50 Number of scatterers: 45157 At special positions: 0 Unit cell: (154.44, 205.92, 190.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 32 16.00 P 1379 15.00 Mg 48 11.99 O 12351 8.00 N 8466 7.00 C 22881 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS N 24 " - pdb=" SG CYS N 40 " distance=1.84 Simple disulfide: pdb=" SG CYS N 27 " - pdb=" SG CYS N 40 " distance=1.83 Simple disulfide: pdb=" SG CYS N 27 " - pdb=" SG CYS N 43 " distance=1.24 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: 22.53 Conformation dependent library (CDL) restraints added in 3.3 seconds 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3632 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 19 sheets defined 41.9% alpha, 14.0% beta 329 base pairs and 743 stacking pairs defined. Time for finding SS restraints: 19.70 Creating SS restraints... Processing helix chain 'C' and resid 6 through 11 removed outlier: 3.654A pdb=" N ARG C 11 " --> pdb=" O PRO C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 42 removed outlier: 3.557A pdb=" N ALA C 37 " --> pdb=" O LYS C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 95 removed outlier: 3.542A pdb=" N ALA C 88 " --> pdb=" O ASP C 84 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS C 92 " --> pdb=" O ALA C 88 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU C 93 " --> pdb=" O ASP C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 125 removed outlier: 3.585A pdb=" N GLN C 122 " --> pdb=" O GLY C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 142 removed outlier: 3.653A pdb=" N ARG C 134 " --> pdb=" O ARG C 130 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS C 135 " --> pdb=" O ARG C 131 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ALA C 136 " --> pdb=" O ALA C 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 16 removed outlier: 4.200A pdb=" N LEU D 15 " --> pdb=" O LYS D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 61 removed outlier: 3.729A pdb=" N GLU D 52 " --> pdb=" O GLN D 48 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LYS D 53 " --> pdb=" O GLN D 49 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TYR D 60 " --> pdb=" O ALA D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 75 Processing helix chain 'D' and resid 80 through 91 removed outlier: 3.759A pdb=" N LEU D 85 " --> pdb=" O THR D 81 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU D 86 " --> pdb=" O GLY D 82 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG D 87 " --> pdb=" O ASP D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 101 Processing helix chain 'D' and resid 105 through 115 removed outlier: 3.837A pdb=" N GLN D 111 " --> pdb=" O ARG D 107 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N HIS D 115 " --> pdb=" O GLN D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 199 removed outlier: 3.690A pdb=" N TYR D 199 " --> pdb=" O ILE D 195 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 93 removed outlier: 3.814A pdb=" N ALA E 84 " --> pdb=" O GLU E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 144 removed outlier: 3.858A pdb=" N ALA E 138 " --> pdb=" O GLY E 134 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N VAL E 139 " --> pdb=" O ALA E 135 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 170 removed outlier: 3.659A pdb=" N VAL E 162 " --> pdb=" O ALA E 158 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 182 removed outlier: 3.642A pdb=" N ALA E 180 " --> pdb=" O GLU E 176 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ARG E 181 " --> pdb=" O GLU E 177 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ARG E 182 " --> pdb=" O VAL E 178 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 76 removed outlier: 3.577A pdb=" N VAL F 66 " --> pdb=" O GLU F 62 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLU F 68 " --> pdb=" O ALA F 64 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ARG F 71 " --> pdb=" O SER F 67 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU F 75 " --> pdb=" O ARG F 71 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASN F 76 " --> pdb=" O GLN F 72 " (cutoff:3.500A) Processing helix chain 'G' and resid 20 through 31 removed outlier: 3.832A pdb=" N THR G 24 " --> pdb=" O SER G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 35 through 53 removed outlier: 3.541A pdb=" N ALA G 39 " --> pdb=" O LYS G 35 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE G 42 " --> pdb=" O LEU G 38 " (cutoff:3.500A) Processing helix chain 'G' and resid 58 through 68 removed outlier: 4.130A pdb=" N LEU G 62 " --> pdb=" O PRO G 58 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASN G 68 " --> pdb=" O ARG G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 111 removed outlier: 3.940A pdb=" N THR G 97 " --> pdb=" O PRO G 93 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU G 104 " --> pdb=" O ALA G 100 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N SER G 108 " --> pdb=" O LEU G 104 " (cutoff:3.500A) Processing helix chain 'G' and resid 115 through 130 removed outlier: 3.556A pdb=" N ILE G 124 " --> pdb=" O LEU G 120 " (cutoff:3.500A) Processing helix chain 'G' and resid 132 through 147 removed outlier: 3.858A pdb=" N ARG G 138 " --> pdb=" O SER G 134 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLU G 139 " --> pdb=" O VAL G 135 " (cutoff:3.500A) Processing helix chain 'H' and resid 6 through 20 Processing helix chain 'H' and resid 30 through 43 removed outlier: 3.694A pdb=" N ALA H 37 " --> pdb=" O LYS H 33 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ILE H 39 " --> pdb=" O ASN H 35 " (cutoff:3.500A) Processing helix chain 'H' and resid 115 through 122 removed outlier: 3.651A pdb=" N ARG H 120 " --> pdb=" O ARG H 116 " (cutoff:3.500A) Processing helix chain 'I' and resid 54 through 59 Processing helix chain 'I' and resid 61 through 76 removed outlier: 3.778A pdb=" N GLN I 66 " --> pdb=" O LYS I 62 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU I 67 " --> pdb=" O VAL I 63 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS I 69 " --> pdb=" O GLN I 65 " (cutoff:3.500A) Proline residue: I 71 - end of helix removed outlier: 3.806A pdb=" N VAL I 75 " --> pdb=" O PRO I 71 " (cutoff:3.500A) Processing helix chain 'I' and resid 91 through 111 removed outlier: 3.669A pdb=" N ARG I 100 " --> pdb=" O ALA I 96 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU I 101 " --> pdb=" O GLY I 97 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ILE I 108 " --> pdb=" O ALA I 104 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU I 109 " --> pdb=" O ARG I 105 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN I 111 " --> pdb=" O LEU I 107 " (cutoff:3.500A) Processing helix chain 'I' and resid 114 through 122 removed outlier: 3.658A pdb=" N LYS I 120 " --> pdb=" O PRO I 116 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 33 removed outlier: 3.611A pdb=" N ASP J 19 " --> pdb=" O HIS J 15 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG J 23 " --> pdb=" O ASP J 19 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL J 26 " --> pdb=" O ALA J 22 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR J 28 " --> pdb=" O LYS J 24 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N THR J 32 " --> pdb=" O THR J 28 " (cutoff:3.500A) Processing helix chain 'J' and resid 80 through 90 removed outlier: 3.574A pdb=" N ASP J 85 " --> pdb=" O PRO J 81 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N MET J 88 " --> pdb=" O VAL J 84 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE J 90 " --> pdb=" O ALA J 86 " (cutoff:3.500A) Processing helix chain 'K' and resid 56 through 60 removed outlier: 4.009A pdb=" N GLY K 60 " --> pdb=" O SER K 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 56 through 60' Processing helix chain 'K' and resid 62 through 67 removed outlier: 3.679A pdb=" N ARG K 65 " --> pdb=" O LYS K 62 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS K 66 " --> pdb=" O GLY K 63 " (cutoff:3.500A) Processing helix chain 'K' and resid 68 through 81 removed outlier: 4.184A pdb=" N ALA K 72 " --> pdb=" O THR K 68 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLN K 73 " --> pdb=" O PRO K 69 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU K 77 " --> pdb=" O GLN K 73 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 87 removed outlier: 3.640A pdb=" N HIS K 86 " --> pdb=" O LYS K 82 " (cutoff:3.500A) Processing helix chain 'K' and resid 101 through 113 removed outlier: 3.853A pdb=" N ALA K 105 " --> pdb=" O GLY K 101 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 10 Processing helix chain 'M' and resid 14 through 19 removed outlier: 3.684A pdb=" N LEU M 19 " --> pdb=" O MET M 15 " (cutoff:3.500A) Processing helix chain 'M' and resid 20 through 22 No H-bonds generated for 'chain 'M' and resid 20 through 22' Processing helix chain 'M' and resid 26 through 37 Processing helix chain 'M' and resid 49 through 64 removed outlier: 3.865A pdb=" N LEU M 56 " --> pdb=" O GLN M 52 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TYR M 59 " --> pdb=" O VAL M 55 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N GLY M 62 " --> pdb=" O ASP M 58 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ASN M 63 " --> pdb=" O TYR M 59 " (cutoff:3.500A) Processing helix chain 'M' and resid 67 through 84 removed outlier: 3.546A pdb=" N GLN M 75 " --> pdb=" O ARG M 71 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU M 83 " --> pdb=" O ARG M 79 " (cutoff:3.500A) Processing helix chain 'M' and resid 86 through 91 Processing helix chain 'M' and resid 107 through 112 Processing helix chain 'N' and resid 4 through 12 removed outlier: 3.538A pdb=" N HIS N 8 " --> pdb=" O LYS N 4 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA N 10 " --> pdb=" O LEU N 6 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASN N 11 " --> pdb=" O VAL N 7 " (cutoff:3.500A) Processing helix chain 'N' and resid 41 through 50 removed outlier: 3.726A pdb=" N ARG N 45 " --> pdb=" O ARG N 41 " (cutoff:3.500A) Processing helix chain 'O' and resid 4 through 16 removed outlier: 3.927A pdb=" N LYS O 9 " --> pdb=" O ALA O 5 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU O 10 " --> pdb=" O GLU O 6 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ILE O 11 " --> pdb=" O GLN O 7 " (cutoff:3.500A) Processing helix chain 'O' and resid 24 through 47 removed outlier: 3.936A pdb=" N ALA O 30 " --> pdb=" O GLU O 26 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU O 31 " --> pdb=" O ALA O 27 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLU O 41 " --> pdb=" O GLN O 37 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL O 45 " --> pdb=" O GLU O 41 " (cutoff:3.500A) Processing helix chain 'O' and resid 49 through 74 removed outlier: 3.650A pdb=" N GLY O 55 " --> pdb=" O HIS O 51 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG O 65 " --> pdb=" O GLY O 61 " (cutoff:3.500A) Processing helix chain 'O' and resid 74 through 86 removed outlier: 3.550A pdb=" N TYR O 78 " --> pdb=" O ASP O 74 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG O 84 " --> pdb=" O SER O 80 " (cutoff:3.500A) Processing helix chain 'P' and resid 52 through 63 Processing helix chain 'P' and resid 67 through 78 removed outlier: 3.527A pdb=" N ALA P 72 " --> pdb=" O GLU P 68 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU P 73 " --> pdb=" O PRO P 69 " (cutoff:3.500A) Processing helix chain 'P' and resid 78 through 85 removed outlier: 3.503A pdb=" N LYS P 82 " --> pdb=" O GLY P 78 " (cutoff:3.500A) Processing helix chain 'R' and resid 34 through 42 removed outlier: 3.746A pdb=" N LEU R 38 " --> pdb=" O ASP R 34 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N THR R 40 " --> pdb=" O ALA R 36 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TYR R 41 " --> pdb=" O LEU R 37 " (cutoff:3.500A) Processing helix chain 'R' and resid 50 through 55 Processing helix chain 'R' and resid 57 through 75 removed outlier: 3.509A pdb=" N GLU R 73 " --> pdb=" O LYS R 69 " (cutoff:3.500A) Processing helix chain 'S' and resid 12 through 26 removed outlier: 3.512A pdb=" N LEU S 16 " --> pdb=" O ASP S 12 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LYS S 18 " --> pdb=" O HIS S 14 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL S 19 " --> pdb=" O LEU S 15 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLU S 24 " --> pdb=" O ASP S 20 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS S 25 " --> pdb=" O VAL S 21 " (cutoff:3.500A) Processing helix chain 'S' and resid 63 through 67 removed outlier: 3.769A pdb=" N VAL S 67 " --> pdb=" O GLU S 64 " (cutoff:3.500A) Processing helix chain 'S' and resid 70 through 75 removed outlier: 4.047A pdb=" N PHE S 74 " --> pdb=" O LEU S 71 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA S 75 " --> pdb=" O GLY S 72 " (cutoff:3.500A) Processing helix chain 'T' and resid 6 through 41 removed outlier: 3.643A pdb=" N ARG T 12 " --> pdb=" O ILE T 8 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG T 18 " --> pdb=" O ASN T 14 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG T 36 " --> pdb=" O ILE T 32 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA T 38 " --> pdb=" O GLY T 34 " (cutoff:3.500A) Processing helix chain 'T' and resid 43 through 64 removed outlier: 3.592A pdb=" N GLU T 49 " --> pdb=" O ASP T 45 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N HIS T 52 " --> pdb=" O SER T 48 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG T 56 " --> pdb=" O HIS T 52 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASP T 59 " --> pdb=" O SER T 55 " (cutoff:3.500A) Processing helix chain 'T' and resid 68 through 85 removed outlier: 3.503A pdb=" N ALA T 78 " --> pdb=" O ASN T 74 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LYS T 85 " --> pdb=" O LEU T 81 " (cutoff:3.500A) Processing helix chain 'U' and resid 4 through 19 removed outlier: 3.544A pdb=" N MET U 12 " --> pdb=" O ARG U 8 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N SER U 13 " --> pdb=" O ARG U 9 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LYS U 14 " --> pdb=" O LYS U 10 " (cutoff:3.500A) Processing helix chain 'U' and resid 19 through 24 Processing sheet with id=AA1, first strand: chain 'C' and resid 53 through 55 removed outlier: 6.375A pdb=" N ILE C 67 " --> pdb=" O LEU C 103 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 165 through 171 removed outlier: 3.542A pdb=" N GLU C 166 " --> pdb=" O CYS C 153 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N CYS C 153 " --> pdb=" O GLU C 166 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR C 187 " --> pdb=" O VAL C 198 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 118 through 120 Processing sheet with id=AA4, first strand: chain 'E' and resid 38 through 40 Processing sheet with id=AA5, first strand: chain 'E' and resid 44 through 47 Processing sheet with id=AA6, first strand: chain 'E' and resid 110 through 114 removed outlier: 3.524A pdb=" N ALA E 114 " --> pdb=" O GLY E 117 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY E 117 " --> pdb=" O ALA E 114 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS E 151 " --> pdb=" O MET E 120 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE E 131 " --> pdb=" O ALA E 150 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N SER E 152 " --> pdb=" O ILE E 131 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 35 through 36 removed outlier: 3.552A pdb=" N LEU F 8 " --> pdb=" O ARG F 81 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 73 through 76 Processing sheet with id=AA9, first strand: chain 'H' and resid 24 through 28 removed outlier: 3.716A pdb=" N ASP H 48 " --> pdb=" O GLN H 63 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 77 through 79 Processing sheet with id=AB2, first strand: chain 'H' and resid 77 through 79 removed outlier: 5.809A pdb=" N VAL H 127 " --> pdb=" O SER H 107 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N SER H 107 " --> pdb=" O VAL H 127 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 27 through 28 removed outlier: 3.561A pdb=" N VAL I 42 " --> pdb=" O ASP I 82 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'J' and resid 45 through 51 removed outlier: 3.806A pdb=" N GLU J 45 " --> pdb=" O THR J 69 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR J 69 " --> pdb=" O GLU J 45 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN J 47 " --> pdb=" O MET J 67 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'K' and resid 50 through 55 removed outlier: 3.783A pdb=" N ALA K 52 " --> pdb=" O ILE K 43 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N VAL K 91 " --> pdb=" O GLU K 115 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 36 through 40 removed outlier: 3.700A pdb=" N ARG L 36 " --> pdb=" O ARG L 54 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'N' and resid 33 through 34 removed outlier: 3.704A pdb=" N LEU N 39 " --> pdb=" O TYR N 34 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'P' and resid 35 through 36 removed outlier: 3.572A pdb=" N GLU P 35 " --> pdb=" O VAL P 22 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N VAL P 3 " --> pdb=" O GLN P 65 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'Q' and resid 22 through 32 removed outlier: 15.522A pdb=" N THR Q 22 " --> pdb=" O ARG Q 43 " (cutoff:3.500A) removed outlier: 12.305A pdb=" N ARG Q 43 " --> pdb=" O THR Q 22 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N ILE Q 24 " --> pdb=" O GLU Q 41 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N GLU Q 41 " --> pdb=" O ILE Q 24 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL Q 37 " --> pdb=" O VAL Q 28 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N ASP Q 30 " --> pdb=" O THR Q 35 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N THR Q 35 " --> pdb=" O ASP Q 30 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYS Q 44 " --> pdb=" O ILE Q 53 " (cutoff:3.500A) removed outlier: 8.880A pdb=" N LYS Q 86 " --> pdb=" O LYS Q 58 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N LYS Q 60 " --> pdb=" O LYS Q 86 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N TRP Q 88 " --> pdb=" O LYS Q 60 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ARG Q 87 " --> pdb=" O THR Q 79 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N SER Q 75 " --> pdb=" O VAL Q 91 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N ILE Q 93 " --> pdb=" O ARG Q 73 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N ARG Q 73 " --> pdb=" O ILE Q 93 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY Q 25 " --> pdb=" O VAL Q 74 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'S' and resid 30 through 33 removed outlier: 3.534A pdb=" N ILE S 31 " --> pdb=" O THR S 48 " (cutoff:3.500A) 602 hydrogen bonds defined for protein. 1743 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 774 hydrogen bonds 1212 hydrogen bond angles 0 basepair planarities 329 basepair parallelities 743 stacking parallelities Total time for adding SS restraints: 41.05 Time building geometry restraints manager: 24.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8902 1.34 - 1.46: 18217 1.46 - 1.58: 18941 1.58 - 1.70: 2740 1.70 - 1.81: 53 Bond restraints: 48853 Sorted by residual: bond pdb=" C ALA E 190 " pdb=" N PRO E 191 " ideal model delta sigma weight residual 1.332 1.391 -0.059 1.30e-02 5.92e+03 2.09e+01 bond pdb=" C LEU M 9 " pdb=" N PRO M 10 " ideal model delta sigma weight residual 1.331 1.390 -0.059 1.31e-02 5.83e+03 2.03e+01 bond pdb=" N PRO F 63 " pdb=" CD PRO F 63 " ideal model delta sigma weight residual 1.473 1.534 -0.061 1.40e-02 5.10e+03 1.92e+01 bond pdb=" C HIS E 108 " pdb=" N PRO E 109 " ideal model delta sigma weight residual 1.332 1.390 -0.058 1.34e-02 5.57e+03 1.91e+01 bond pdb=" C1' C A1003 " pdb=" N1 C A1003 " ideal model delta sigma weight residual 1.480 1.545 -0.065 1.50e-02 4.44e+03 1.88e+01 ... (remaining 48848 not shown) Histogram of bond angle deviations from ideal: 98.64 - 106.65: 8586 106.65 - 114.66: 30947 114.66 - 122.67: 23095 122.67 - 130.68: 9778 130.68 - 138.69: 378 Bond angle restraints: 72784 Sorted by residual: angle pdb=" N HIS E 108 " pdb=" CA HIS E 108 " pdb=" C HIS E 108 " ideal model delta sigma weight residual 108.07 117.25 -9.18 8.90e-01 1.26e+00 1.06e+02 angle pdb=" N ASN M 63 " pdb=" CA ASN M 63 " pdb=" C ASN M 63 " ideal model delta sigma weight residual 111.36 122.04 -10.68 1.09e+00 8.42e-01 9.61e+01 angle pdb=" N LYS J 57 " pdb=" CA LYS J 57 " pdb=" C LYS J 57 " ideal model delta sigma weight residual 113.23 123.24 -10.01 1.22e+00 6.72e-01 6.73e+01 angle pdb=" C4' U A1456 " pdb=" C3' U A1456 " pdb=" O3' U A1456 " ideal model delta sigma weight residual 109.40 121.29 -11.89 1.50e+00 4.44e-01 6.28e+01 angle pdb=" N LYS J 59 " pdb=" CA LYS J 59 " pdb=" C LYS J 59 " ideal model delta sigma weight residual 111.28 119.77 -8.49 1.09e+00 8.42e-01 6.06e+01 ... (remaining 72779 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 27638 35.95 - 71.90: 3358 71.90 - 107.85: 439 107.85 - 143.80: 15 143.80 - 179.75: 32 Dihedral angle restraints: 31482 sinusoidal: 25861 harmonic: 5621 Sorted by residual: dihedral pdb=" C5' U A1193 " pdb=" C4' U A1193 " pdb=" C3' U A1193 " pdb=" O3' U A1193 " ideal model delta sinusoidal sigma weight residual 147.00 79.36 67.64 1 8.00e+00 1.56e-02 9.29e+01 dihedral pdb=" C4' U A1193 " pdb=" C3' U A1193 " pdb=" C2' U A1193 " pdb=" C1' U A1193 " ideal model delta sinusoidal sigma weight residual -35.00 30.85 -65.85 1 8.00e+00 1.56e-02 8.86e+01 dihedral pdb=" O4' C A1410 " pdb=" C1' C A1410 " pdb=" N1 C A1410 " pdb=" C2 C A1410 " ideal model delta sinusoidal sigma weight residual 200.00 23.75 176.25 1 1.50e+01 4.44e-03 8.52e+01 ... (remaining 31479 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.127: 7418 0.127 - 0.253: 1816 0.253 - 0.380: 25 0.380 - 0.507: 7 0.507 - 0.633: 8 Chirality restraints: 9274 Sorted by residual: chirality pdb=" C3' G A 111 " pdb=" C4' G A 111 " pdb=" O3' G A 111 " pdb=" C2' G A 111 " both_signs ideal model delta sigma weight residual False -2.74 -2.11 -0.63 2.00e-01 2.50e+01 1.00e+01 chirality pdb=" C3' G A 465 " pdb=" C4' G A 465 " pdb=" O3' G A 465 " pdb=" C2' G A 465 " both_signs ideal model delta sigma weight residual False -2.74 -2.12 -0.63 2.00e-01 2.50e+01 9.89e+00 chirality pdb=" C3' U A 942 " pdb=" C4' U A 942 " pdb=" O3' U A 942 " pdb=" C2' U A 942 " both_signs ideal model delta sigma weight residual False -2.74 -2.14 -0.60 2.00e-01 2.50e+01 9.15e+00 ... (remaining 9271 not shown) Planarity restraints: 4082 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU E 184 " 0.058 5.00e-02 4.00e+02 8.83e-02 1.25e+01 pdb=" N PRO E 185 " -0.153 5.00e-02 4.00e+02 pdb=" CA PRO E 185 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO E 185 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU F 73 " -0.012 2.00e-02 2.50e+03 2.56e-02 6.56e+00 pdb=" C LEU F 73 " 0.044 2.00e-02 2.50e+03 pdb=" O LEU F 73 " -0.017 2.00e-02 2.50e+03 pdb=" N ASN F 74 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS L 44 " 0.036 5.00e-02 4.00e+02 5.39e-02 4.66e+00 pdb=" N PRO L 45 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO L 45 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO L 45 " 0.029 5.00e-02 4.00e+02 ... (remaining 4079 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.29: 63 2.29 - 2.94: 16679 2.94 - 3.59: 67087 3.59 - 4.25: 124985 4.25 - 4.90: 178511 Nonbonded interactions: 387325 Sorted by model distance: nonbonded pdb=" O ASP F 70 " pdb=" ND2 ASN F 74 " model vdw 1.633 2.520 nonbonded pdb=" O ARG M 80 " pdb=" CG1 ILE M 84 " model vdw 1.712 3.440 nonbonded pdb=" NH1 ARG E 182 " pdb=" CZ TYR H 45 " model vdw 1.777 3.340 nonbonded pdb=" O2' U A 939 " pdb=" O5' A A 940 " model vdw 1.783 2.440 nonbonded pdb=" O LYS H 65 " pdb=" OG SER H 73 " model vdw 1.844 2.440 ... (remaining 387320 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 6.550 Check model and map are aligned: 0.570 Set scattering table: 0.350 Process input model: 149.160 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 161.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 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 : 0.006 0.065 48853 Z= 0.391 Angle : 1.041 15.147 72784 Z= 0.705 Chirality : 0.097 0.633 9274 Planarity : 0.004 0.088 4082 Dihedral : 24.532 179.748 27841 Min Nonbonded Distance : 1.633 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 2.26 % Allowed : 6.11 % Favored : 91.63 % Rotamer: Outliers : 1.66 % Allowed : 5.46 % Favored : 92.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.66 (0.15), residues: 1900 helix: -2.25 (0.14), residues: 688 sheet: -2.29 (0.24), residues: 330 loop : -2.55 (0.17), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP N 61 HIS 0.005 0.001 HIS J 56 PHE 0.014 0.001 PHE C 129 TYR 0.017 0.001 TYR H 66 ARG 0.004 0.000 ARG I 126 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 672 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 645 time to evaluate : 2.931 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: C 36 VAL cc_start: 0.8337 (t) cc_final: 0.8078 (m) REVERT: C 55 GLU cc_start: 0.7548 (mt-10) cc_final: 0.6810 (tt0) REVERT: C 99 GLN cc_start: 0.6320 (mt0) cc_final: 0.5796 (tm-30) REVERT: C 135 LYS cc_start: 0.8324 (mttt) cc_final: 0.8068 (tptp) REVERT: C 142 ARG cc_start: 0.7269 (ttp80) cc_final: 0.6991 (ttp80) REVERT: C 147 LYS cc_start: 0.7610 (tttm) cc_final: 0.7349 (mppt) REVERT: C 188 GLU cc_start: 0.8079 (mt-10) cc_final: 0.7818 (mt-10) REVERT: D 10 ARG cc_start: 0.7517 (ptt-90) cc_final: 0.6285 (tpt170) REVERT: D 17 VAL cc_start: 0.7872 (m) cc_final: 0.7659 (p) REVERT: D 48 GLN cc_start: 0.7257 (tp-100) cc_final: 0.6890 (pm20) REVERT: D 54 GLN cc_start: 0.7877 (tp40) cc_final: 0.7435 (tp40) REVERT: D 91 SER cc_start: 0.8900 (m) cc_final: 0.8628 (p) REVERT: D 99 ARG cc_start: 0.7269 (OUTLIER) cc_final: 0.6818 (tpt170) REVERT: D 102 LEU cc_start: 0.7914 (tt) cc_final: 0.7708 (mp) REVERT: D 118 PHE cc_start: 0.8004 (OUTLIER) cc_final: 0.7146 (m-80) REVERT: D 125 VAL cc_start: 0.8982 (t) cc_final: 0.8745 (m) REVERT: D 174 ARG cc_start: 0.6651 (ptm160) cc_final: 0.6349 (mmt-90) REVERT: D 177 VAL cc_start: 0.9003 (t) cc_final: 0.8726 (m) REVERT: E 36 TYR cc_start: 0.7058 (p90) cc_final: 0.6726 (p90) REVERT: E 39 ARG cc_start: 0.7460 (ttm110) cc_final: 0.7208 (ttm110) REVERT: E 75 TYR cc_start: 0.8299 (t80) cc_final: 0.7825 (t80) REVERT: E 91 GLU cc_start: 0.7761 (tp30) cc_final: 0.7317 (tp30) REVERT: E 111 GLN cc_start: 0.8959 (tt0) cc_final: 0.8710 (tt0) REVERT: E 125 SER cc_start: 0.7386 (m) cc_final: 0.7155 (p) REVERT: E 147 ASP cc_start: 0.7764 (m-30) cc_final: 0.7363 (m-30) REVERT: G 9 LYS cc_start: 0.8258 (ttmt) cc_final: 0.7425 (tmtt) REVERT: G 10 ARG cc_start: 0.7297 (mmt-90) cc_final: 0.6743 (mmt180) REVERT: G 58 PRO cc_start: 0.7763 (Cg_endo) cc_final: 0.6781 (Cg_exo) REVERT: G 71 PRO cc_start: 0.8578 (Cg_endo) cc_final: 0.8357 (Cg_exo) REVERT: G 126 ASP cc_start: 0.7951 (m-30) cc_final: 0.7567 (m-30) REVERT: G 136 LYS cc_start: 0.8504 (ttmt) cc_final: 0.7910 (tptt) REVERT: G 140 ASP cc_start: 0.7848 (m-30) cc_final: 0.7273 (m-30) REVERT: H 3 MET cc_start: 0.8307 (mmm) cc_final: 0.8051 (tpp) REVERT: H 31 LYS cc_start: 0.8906 (tptm) cc_final: 0.8582 (ttpt) REVERT: H 38 GLU cc_start: 0.8355 (mm-30) cc_final: 0.8136 (mm-30) REVERT: H 78 ARG cc_start: 0.7825 (ptm160) cc_final: 0.7509 (ptm-80) REVERT: H 115 ASP cc_start: 0.8710 (p0) cc_final: 0.7962 (p0) REVERT: I 61 ASN cc_start: 0.8331 (t0) cc_final: 0.8070 (t0) REVERT: I 115 ARG cc_start: 0.7703 (ttm170) cc_final: 0.7176 (tmt170) REVERT: J 11 LYS cc_start: 0.7532 (mttt) cc_final: 0.7065 (mtpp) REVERT: J 45 GLU cc_start: 0.8106 (mt-10) cc_final: 0.7455 (mt-10) REVERT: J 46 LYS cc_start: 0.8388 (mtmm) cc_final: 0.7533 (ttpt) REVERT: J 47 ASN cc_start: 0.8049 (m-40) cc_final: 0.7721 (m-40) REVERT: J 53 ARG cc_start: 0.7105 (mtt180) cc_final: 0.6855 (mtt180) REVERT: J 71 LYS cc_start: 0.7880 (mtmt) cc_final: 0.7535 (mttm) REVERT: K 32 ILE cc_start: 0.8511 (mp) cc_final: 0.8270 (pt) REVERT: K 41 VAL cc_start: 0.8287 (t) cc_final: 0.7993 (m) REVERT: K 82 LYS cc_start: 0.7869 (mmtp) cc_final: 0.7618 (mttt) REVERT: K 114 LEU cc_start: 0.7090 (OUTLIER) cc_final: 0.6663 (pp) REVERT: L 3 THR cc_start: 0.8718 (p) cc_final: 0.8470 (p) REVERT: L 6 GLN cc_start: 0.8869 (tt0) cc_final: 0.8569 (tt0) REVERT: L 77 HIS cc_start: 0.8304 (m-70) cc_final: 0.7671 (m90) REVERT: L 87 VAL cc_start: 0.8597 (t) cc_final: 0.8393 (p) REVERT: L 102 LEU cc_start: 0.7007 (OUTLIER) cc_final: 0.6778 (tt) REVERT: L 105 GLN cc_start: 0.8089 (mt0) cc_final: 0.7791 (mp10) REVERT: L 107 VAL cc_start: 0.8456 (t) cc_final: 0.8187 (m) REVERT: M 16 GLU cc_start: 0.7300 (tt0) cc_final: 0.7069 (tt0) REVERT: M 65 LYS cc_start: 0.7333 (mptt) cc_final: 0.6771 (mmmt) REVERT: M 80 ARG cc_start: 0.7594 (ptt90) cc_final: 0.7377 (tmm-80) REVERT: M 83 GLU cc_start: 0.7371 (mt-10) cc_final: 0.7155 (tp30) REVERT: M 108 ARG cc_start: 0.5762 (mmt180) cc_final: 0.5374 (mmp-170) REVERT: N 4 LYS cc_start: 0.7333 (mmtt) cc_final: 0.7006 (mtpt) REVERT: N 26 LYS cc_start: 0.7673 (tttp) cc_final: 0.7456 (tttm) REVERT: O 44 LYS cc_start: 0.8671 (mtpt) cc_final: 0.8411 (mtpp) REVERT: O 53 ARG cc_start: 0.8019 (ttm110) cc_final: 0.7629 (mtm-85) REVERT: P 17 GLN cc_start: 0.7687 (mp10) cc_final: 0.6863 (mm-40) REVERT: P 44 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.7866 (mm-30) REVERT: P 50 GLN cc_start: 0.7656 (mt0) cc_final: 0.6601 (tm-30) REVERT: P 84 LYS cc_start: 0.8514 (tptt) cc_final: 0.8135 (tppt) REVERT: Q 54 ARG cc_start: 0.8698 (ttp80) cc_final: 0.8159 (ttp80) REVERT: Q 77 MET cc_start: 0.8369 (ttm) cc_final: 0.8067 (ttt) REVERT: Q 96 LYS cc_start: 0.8797 (mttm) cc_final: 0.8492 (mmmt) REVERT: R 39 ARG cc_start: 0.8483 (mmt90) cc_final: 0.7931 (mmm-85) REVERT: R 48 ILE cc_start: 0.8452 (mt) cc_final: 0.8130 (mp) REVERT: R 66 VAL cc_start: 0.8709 (t) cc_final: 0.8389 (p) REVERT: S 33 THR cc_start: 0.7922 (m) cc_final: 0.7625 (m) REVERT: T 49 GLU cc_start: 0.8950 (tt0) cc_final: 0.8257 (mt-10) outliers start: 27 outliers final: 10 residues processed: 657 average time/residue: 0.7166 time to fit residues: 714.1108 Evaluate side-chains 516 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 501 time to evaluate : 2.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain D residue 99 ARG Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 118 PHE Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 186 ILE Chi-restraints excluded: chain J residue 56 HIS Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain K residue 114 LEU Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain M residue 60 ILE Chi-restraints excluded: chain M residue 64 LEU Chi-restraints excluded: chain P residue 44 GLU Chi-restraints excluded: chain S residue 29 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 273 optimal weight: 3.9990 chunk 245 optimal weight: 9.9990 chunk 136 optimal weight: 4.9990 chunk 83 optimal weight: 5.9990 chunk 165 optimal weight: 5.9990 chunk 131 optimal weight: 10.0000 chunk 253 optimal weight: 4.9990 chunk 98 optimal weight: 8.9990 chunk 154 optimal weight: 7.9990 chunk 189 optimal weight: 3.9990 chunk 294 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 HIS C 125 ASN C 176 HIS ** D 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 49 HIS ** F 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 25 GLN H 93 ASN K 31 HIS K 49 ASN ** K 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 31 ASN M 75 GLN M 101 GLN O 7 GLN O 37 GLN O 51 HIS P 15 ASN Q 62 HIS Q 65 ASN ** R 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 60 HIS ** S 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 68 HIS T 70 ASN T 71 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.084 48853 Z= 0.505 Angle : 0.890 11.184 72784 Z= 0.447 Chirality : 0.049 0.375 9274 Planarity : 0.007 0.072 4082 Dihedral : 25.270 178.535 23958 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 1.42 % Allowed : 6.37 % Favored : 92.21 % Rotamer: Outliers : 6.01 % Allowed : 13.19 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.17), residues: 1900 helix: -0.77 (0.17), residues: 744 sheet: -1.67 (0.26), residues: 339 loop : -2.36 (0.19), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 18 HIS 0.017 0.002 HIS S 52 PHE 0.026 0.002 PHE H 10 TYR 0.024 0.003 TYR Q 49 ARG 0.016 0.001 ARG E 182 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 632 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 534 time to evaluate : 2.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 55 GLU cc_start: 0.7678 (mt-10) cc_final: 0.6973 (tt0) REVERT: C 68 HIS cc_start: 0.5988 (OUTLIER) cc_final: 0.5323 (m90) REVERT: C 71 ARG cc_start: 0.5384 (ptp-170) cc_final: 0.5059 (ptt-90) REVERT: C 93 LEU cc_start: 0.7497 (mp) cc_final: 0.7219 (tp) REVERT: C 106 LYS cc_start: 0.8332 (mttp) cc_final: 0.7414 (mmmt) REVERT: C 161 GLU cc_start: 0.7136 (tp30) cc_final: 0.6642 (pm20) REVERT: D 10 ARG cc_start: 0.7548 (ptt-90) cc_final: 0.6209 (tpt170) REVERT: D 17 VAL cc_start: 0.7238 (m) cc_final: 0.6995 (p) REVERT: D 54 GLN cc_start: 0.8090 (tp40) cc_final: 0.7763 (tp40) REVERT: D 99 ARG cc_start: 0.7316 (OUTLIER) cc_final: 0.6883 (tpt170) REVERT: D 174 ARG cc_start: 0.6784 (ptm160) cc_final: 0.6540 (mmt-90) REVERT: D 177 VAL cc_start: 0.9036 (t) cc_final: 0.8773 (m) REVERT: E 63 ILE cc_start: 0.8426 (mt) cc_final: 0.8208 (mp) REVERT: E 66 ASP cc_start: 0.8729 (OUTLIER) cc_final: 0.7839 (p0) REVERT: E 147 ASP cc_start: 0.8112 (m-30) cc_final: 0.7604 (m-30) REVERT: F 1 MET cc_start: 0.5628 (mmt) cc_final: 0.5359 (mmt) REVERT: F 44 TYR cc_start: 0.7686 (p90) cc_final: 0.7425 (p90) REVERT: F 45 GLU cc_start: 0.7037 (mt-10) cc_final: 0.6755 (mm-30) REVERT: F 49 HIS cc_start: 0.7761 (m90) cc_final: 0.7270 (m-70) REVERT: F 54 TYR cc_start: 0.5663 (m-80) cc_final: 0.5392 (m-80) REVERT: G 10 ARG cc_start: 0.7594 (mmt-90) cc_final: 0.7336 (mmt-90) REVERT: G 52 GLU cc_start: 0.7925 (mt-10) cc_final: 0.7517 (mt-10) REVERT: G 58 PRO cc_start: 0.7955 (Cg_endo) cc_final: 0.7632 (Cg_exo) REVERT: G 104 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8553 (tt) REVERT: G 118 GLU cc_start: 0.8165 (mt-10) cc_final: 0.7955 (mt-10) REVERT: G 151 PHE cc_start: 0.7356 (m-80) cc_final: 0.7040 (m-80) REVERT: H 18 ASN cc_start: 0.8323 (t0) cc_final: 0.8078 (t0) REVERT: H 27 LEU cc_start: 0.7956 (OUTLIER) cc_final: 0.7674 (mt) REVERT: H 31 LYS cc_start: 0.8791 (tptm) cc_final: 0.8429 (ttpt) REVERT: H 43 GLU cc_start: 0.7902 (mm-30) cc_final: 0.7203 (mm-30) REVERT: H 52 GLU cc_start: 0.8112 (tp30) cc_final: 0.7457 (tp30) REVERT: H 63 GLN cc_start: 0.6845 (OUTLIER) cc_final: 0.6069 (mp10) REVERT: H 78 ARG cc_start: 0.7755 (ptm160) cc_final: 0.7470 (ptm-80) REVERT: H 115 ASP cc_start: 0.8587 (p0) cc_final: 0.8057 (p0) REVERT: H 126 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.8105 (tt0) REVERT: I 61 ASN cc_start: 0.8077 (t0) cc_final: 0.6832 (t0) REVERT: I 115 ARG cc_start: 0.7412 (ttm170) cc_final: 0.6822 (tmt170) REVERT: I 127 ASP cc_start: 0.8243 (m-30) cc_final: 0.7754 (p0) REVERT: J 11 LYS cc_start: 0.7549 (mttt) cc_final: 0.6868 (mttm) REVERT: J 45 GLU cc_start: 0.7625 (mt-10) cc_final: 0.6949 (mt-10) REVERT: J 46 LYS cc_start: 0.8534 (mtmm) cc_final: 0.7890 (ttpt) REVERT: J 71 LYS cc_start: 0.7701 (mtmt) cc_final: 0.7378 (mttm) REVERT: J 82 LYS cc_start: 0.8228 (OUTLIER) cc_final: 0.7841 (tttt) REVERT: K 82 LYS cc_start: 0.8148 (mmtp) cc_final: 0.7812 (mtmt) REVERT: K 128 ASN cc_start: 0.6758 (m-40) cc_final: 0.6461 (m-40) REVERT: L 76 GLU cc_start: 0.8011 (mm-30) cc_final: 0.7779 (mm-30) REVERT: L 77 HIS cc_start: 0.8182 (m-70) cc_final: 0.7779 (m90) REVERT: L 86 ARG cc_start: 0.7442 (mtp180) cc_final: 0.7242 (mmt180) REVERT: L 87 VAL cc_start: 0.8568 (t) cc_final: 0.8329 (p) REVERT: L 89 ASP cc_start: 0.8030 (OUTLIER) cc_final: 0.7475 (p0) REVERT: L 105 GLN cc_start: 0.8166 (mt0) cc_final: 0.7671 (mt0) REVERT: M 15 MET cc_start: 0.8042 (tpt) cc_final: 0.7614 (mmm) REVERT: M 16 GLU cc_start: 0.7758 (tt0) cc_final: 0.7316 (tt0) REVERT: M 31 ASN cc_start: 0.8057 (m-40) cc_final: 0.7836 (m110) REVERT: M 32 GLU cc_start: 0.8611 (tm-30) cc_final: 0.8209 (tm-30) REVERT: M 65 LYS cc_start: 0.6998 (mptt) cc_final: 0.6261 (mmmt) REVERT: M 67 GLU cc_start: 0.7474 (tp30) cc_final: 0.7107 (tp30) REVERT: M 83 GLU cc_start: 0.7732 (mt-10) cc_final: 0.6852 (tp30) REVERT: M 108 ARG cc_start: 0.6309 (mmt180) cc_final: 0.5625 (mmp-170) REVERT: N 4 LYS cc_start: 0.7751 (mmtt) cc_final: 0.7339 (mtpt) REVERT: N 26 LYS cc_start: 0.8042 (tttp) cc_final: 0.7817 (tttm) REVERT: N 36 LYS cc_start: 0.8275 (tttp) cc_final: 0.7918 (tttp) REVERT: O 14 GLN cc_start: 0.7837 (tt0) cc_final: 0.7632 (tt0) REVERT: O 53 ARG cc_start: 0.8163 (ttm110) cc_final: 0.7925 (ttp-170) REVERT: O 74 ASP cc_start: 0.7277 (m-30) cc_final: 0.6789 (p0) REVERT: O 77 ARG cc_start: 0.7443 (mtp180) cc_final: 0.6818 (mtm-85) REVERT: P 17 GLN cc_start: 0.7982 (mp10) cc_final: 0.6271 (tp40) REVERT: P 44 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.8040 (mm-30) REVERT: P 50 GLN cc_start: 0.7687 (mt0) cc_final: 0.6520 (tm-30) REVERT: P 68 GLU cc_start: 0.8363 (tt0) cc_final: 0.8120 (tp30) REVERT: P 84 LYS cc_start: 0.8403 (tptt) cc_final: 0.8171 (tppt) REVERT: Q 65 ASN cc_start: 0.7300 (OUTLIER) cc_final: 0.7027 (t0) REVERT: Q 77 MET cc_start: 0.8260 (ttm) cc_final: 0.8034 (ttt) REVERT: Q 96 LYS cc_start: 0.8929 (mttm) cc_final: 0.8600 (mmmt) REVERT: R 32 TYR cc_start: 0.8440 (p90) cc_final: 0.7908 (p90) REVERT: R 39 ARG cc_start: 0.8213 (mmt90) cc_final: 0.7636 (mmm-85) REVERT: R 49 ARG cc_start: 0.8062 (mtt-85) cc_final: 0.7110 (ttm110) REVERT: R 62 ARG cc_start: 0.8397 (tpm170) cc_final: 0.8179 (tpm170) REVERT: S 17 LYS cc_start: 0.7249 (tttt) cc_final: 0.6929 (tppt) REVERT: T 49 GLU cc_start: 0.8740 (tt0) cc_final: 0.8286 (mt-10) outliers start: 98 outliers final: 64 residues processed: 593 average time/residue: 0.6645 time to fit residues: 613.6283 Evaluate side-chains 567 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 492 time to evaluate : 2.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 68 HIS Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 99 ARG Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 129 SER Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 66 ASP Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 152 SER Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 3 ILE Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 77 GLU Chi-restraints excluded: chain F residue 80 LEU Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain H residue 27 LEU Chi-restraints excluded: chain H residue 63 GLN Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 107 SER Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 126 GLU Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 87 LEU Chi-restraints excluded: chain J residue 6 ILE Chi-restraints excluded: chain J residue 56 HIS Chi-restraints excluded: chain J residue 82 LYS Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain K residue 34 SER Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain K residue 114 LEU Chi-restraints excluded: chain K residue 116 VAL Chi-restraints excluded: chain K residue 120 SER Chi-restraints excluded: chain L residue 16 ILE Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 34 CYS Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 89 ASP Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain M residue 49 THR Chi-restraints excluded: chain M residue 60 ILE Chi-restraints excluded: chain M residue 64 LEU Chi-restraints excluded: chain N residue 27 CYS Chi-restraints excluded: chain O residue 11 ILE Chi-restraints excluded: chain O residue 39 LEU Chi-restraints excluded: chain P residue 44 GLU Chi-restraints excluded: chain P residue 92 THR Chi-restraints excluded: chain Q residue 65 ASN Chi-restraints excluded: chain Q residue 79 THR Chi-restraints excluded: chain Q residue 90 LEU Chi-restraints excluded: chain R residue 40 THR Chi-restraints excluded: chain R residue 56 ASN Chi-restraints excluded: chain S residue 29 GLN Chi-restraints excluded: chain S residue 30 VAL Chi-restraints excluded: chain S residue 35 SER Chi-restraints excluded: chain S residue 49 PHE Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain T residue 26 SER Chi-restraints excluded: chain T residue 57 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 163 optimal weight: 6.9990 chunk 91 optimal weight: 9.9990 chunk 244 optimal weight: 1.9990 chunk 200 optimal weight: 0.8980 chunk 81 optimal weight: 3.9990 chunk 294 optimal weight: 0.9980 chunk 318 optimal weight: 0.9980 chunk 262 optimal weight: 6.9990 chunk 292 optimal weight: 5.9990 chunk 100 optimal weight: 10.0000 chunk 236 optimal weight: 0.9980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 8 HIS F 74 ASN I 64 HIS J 56 HIS ** K 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 7 GLN R 59 GLN ** S 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.3291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 48853 Z= 0.165 Angle : 0.625 10.022 72784 Z= 0.318 Chirality : 0.036 0.355 9274 Planarity : 0.004 0.055 4082 Dihedral : 24.923 179.810 23952 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.95 % Allowed : 6.32 % Favored : 92.74 % Rotamer: Outliers : 4.79 % Allowed : 17.42 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.18), residues: 1900 helix: 0.41 (0.18), residues: 743 sheet: -1.26 (0.27), residues: 330 loop : -2.08 (0.20), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 18 HIS 0.026 0.001 HIS C 68 PHE 0.014 0.002 PHE I 48 TYR 0.016 0.001 TYR M 59 ARG 0.006 0.001 ARG Q 54 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 619 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 541 time to evaluate : 2.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 71 ARG cc_start: 0.4992 (ptp-170) cc_final: 0.4689 (ptt-90) REVERT: C 93 LEU cc_start: 0.7514 (mp) cc_final: 0.7237 (tp) REVERT: C 99 GLN cc_start: 0.5745 (mt0) cc_final: 0.5200 (tm-30) REVERT: C 106 LYS cc_start: 0.8298 (mttp) cc_final: 0.7428 (mmmt) REVERT: C 161 GLU cc_start: 0.7248 (tp30) cc_final: 0.6683 (pm20) REVERT: D 10 ARG cc_start: 0.7333 (ptt-90) cc_final: 0.6070 (tpt170) REVERT: D 54 GLN cc_start: 0.8031 (tp40) cc_final: 0.7423 (tp40) REVERT: D 99 ARG cc_start: 0.7273 (ttm-80) cc_final: 0.6840 (tpt170) REVERT: D 104 ARG cc_start: 0.5878 (ttm-80) cc_final: 0.5641 (ttt90) REVERT: D 126 ASP cc_start: 0.7479 (OUTLIER) cc_final: 0.6289 (p0) REVERT: D 174 ARG cc_start: 0.6471 (ptm160) cc_final: 0.6093 (mmt-90) REVERT: D 177 VAL cc_start: 0.9033 (t) cc_final: 0.8792 (m) REVERT: E 36 TYR cc_start: 0.7403 (p90) cc_final: 0.7086 (p90) REVERT: E 66 ASP cc_start: 0.8700 (m-30) cc_final: 0.8248 (p0) REVERT: E 70 MET cc_start: 0.7658 (mmm) cc_final: 0.7336 (mmp) REVERT: E 91 GLU cc_start: 0.7546 (tp30) cc_final: 0.7135 (tp30) REVERT: E 120 MET cc_start: 0.7840 (OUTLIER) cc_final: 0.7435 (ttp) REVERT: E 147 ASP cc_start: 0.7969 (m-30) cc_final: 0.7575 (m-30) REVERT: E 176 GLU cc_start: 0.6563 (mp0) cc_final: 0.6285 (mp0) REVERT: F 1 MET cc_start: 0.5480 (mmt) cc_final: 0.5215 (mmt) REVERT: G 52 GLU cc_start: 0.7337 (mt-10) cc_final: 0.6996 (mt-10) REVERT: G 149 ARG cc_start: 0.6781 (mmt90) cc_final: 0.6482 (mmm-85) REVERT: H 3 MET cc_start: 0.8469 (mmm) cc_final: 0.8188 (mmm) REVERT: H 5 ASP cc_start: 0.7371 (OUTLIER) cc_final: 0.7135 (t0) REVERT: H 31 LYS cc_start: 0.8697 (tptm) cc_final: 0.8481 (ttpp) REVERT: H 38 GLU cc_start: 0.8538 (mm-30) cc_final: 0.8182 (mm-30) REVERT: H 52 GLU cc_start: 0.7754 (tp30) cc_final: 0.7215 (tp30) REVERT: H 63 GLN cc_start: 0.6925 (OUTLIER) cc_final: 0.6182 (mp10) REVERT: H 78 ARG cc_start: 0.7355 (ptm160) cc_final: 0.7121 (ptm-80) REVERT: H 115 ASP cc_start: 0.8376 (p0) cc_final: 0.7880 (p0) REVERT: H 117 GLN cc_start: 0.8479 (tt0) cc_final: 0.8115 (tt0) REVERT: H 126 GLU cc_start: 0.7921 (pt0) cc_final: 0.7604 (tt0) REVERT: I 61 ASN cc_start: 0.8000 (t0) cc_final: 0.7167 (t0) REVERT: I 65 GLN cc_start: 0.8030 (mt0) cc_final: 0.7782 (mp10) REVERT: I 115 ARG cc_start: 0.7262 (ttm170) cc_final: 0.6617 (tmt170) REVERT: I 127 ASP cc_start: 0.8270 (m-30) cc_final: 0.7782 (p0) REVERT: J 11 LYS cc_start: 0.7720 (mttt) cc_final: 0.7066 (mtpp) REVERT: J 45 GLU cc_start: 0.7625 (mt-10) cc_final: 0.6982 (mt-10) REVERT: J 46 LYS cc_start: 0.8482 (mtmm) cc_final: 0.7927 (ttpt) REVERT: J 71 LYS cc_start: 0.7743 (mtmt) cc_final: 0.7389 (mttm) REVERT: K 82 LYS cc_start: 0.8106 (mmtp) cc_final: 0.7883 (mtmm) REVERT: K 128 ASN cc_start: 0.6714 (m-40) cc_final: 0.6427 (m-40) REVERT: L 76 GLU cc_start: 0.7891 (mm-30) cc_final: 0.7638 (mm-30) REVERT: L 77 HIS cc_start: 0.8154 (m-70) cc_final: 0.7741 (m90) REVERT: L 87 VAL cc_start: 0.8540 (t) cc_final: 0.8245 (p) REVERT: L 89 ASP cc_start: 0.7965 (OUTLIER) cc_final: 0.7380 (p0) REVERT: L 103 ASP cc_start: 0.7342 (m-30) cc_final: 0.7023 (m-30) REVERT: L 107 VAL cc_start: 0.8538 (t) cc_final: 0.8282 (m) REVERT: M 15 MET cc_start: 0.7720 (tpt) cc_final: 0.7367 (mmm) REVERT: M 16 GLU cc_start: 0.7681 (tt0) cc_final: 0.7197 (tt0) REVERT: M 32 GLU cc_start: 0.8518 (tm-30) cc_final: 0.8088 (tm-30) REVERT: M 60 ILE cc_start: 0.7715 (OUTLIER) cc_final: 0.7371 (mt) REVERT: M 65 LYS cc_start: 0.6275 (mptt) cc_final: 0.5629 (mmmt) REVERT: M 108 ARG cc_start: 0.6364 (mmt180) cc_final: 0.5645 (mmp-170) REVERT: N 4 LYS cc_start: 0.7460 (mmtt) cc_final: 0.6991 (mtpt) REVERT: N 26 LYS cc_start: 0.7933 (tttp) cc_final: 0.7710 (tttm) REVERT: N 47 MET cc_start: 0.7479 (mmt) cc_final: 0.7030 (mmt) REVERT: N 52 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.8090 (mm-30) REVERT: O 53 ARG cc_start: 0.8123 (ttm110) cc_final: 0.7860 (ttp-170) REVERT: P 17 GLN cc_start: 0.7951 (mp10) cc_final: 0.6633 (tp40) REVERT: P 39 ARG cc_start: 0.8289 (ptp90) cc_final: 0.7737 (ptp90) REVERT: P 44 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.7699 (mt-10) REVERT: P 50 GLN cc_start: 0.7765 (mt0) cc_final: 0.6576 (tm-30) REVERT: P 84 LYS cc_start: 0.8470 (tptt) cc_final: 0.8242 (tppt) REVERT: Q 19 ARG cc_start: 0.8097 (mtp85) cc_final: 0.7745 (mtp85) REVERT: Q 96 LYS cc_start: 0.8897 (mttm) cc_final: 0.8576 (mmmt) REVERT: R 32 TYR cc_start: 0.8303 (p90) cc_final: 0.7986 (p90) REVERT: R 33 LYS cc_start: 0.7117 (mmmt) cc_final: 0.6911 (mmmt) REVERT: R 39 ARG cc_start: 0.8215 (mmt90) cc_final: 0.7731 (mmm-85) REVERT: R 49 ARG cc_start: 0.7997 (mtt-85) cc_final: 0.7226 (ttm-80) REVERT: S 16 LEU cc_start: 0.8353 (tp) cc_final: 0.7828 (pp) REVERT: S 17 LYS cc_start: 0.7135 (tttt) cc_final: 0.6703 (tppt) REVERT: S 55 ARG cc_start: 0.5833 (ttt-90) cc_final: 0.5546 (ttp80) REVERT: T 19 LEU cc_start: 0.8232 (mm) cc_final: 0.7988 (mm) REVERT: T 49 GLU cc_start: 0.8965 (tt0) cc_final: 0.8525 (mt-10) REVERT: T 54 THR cc_start: 0.8414 (m) cc_final: 0.8004 (p) outliers start: 78 outliers final: 48 residues processed: 582 average time/residue: 0.6770 time to fit residues: 615.5972 Evaluate side-chains 559 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 503 time to evaluate : 2.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 126 ASP Chi-restraints excluded: chain D residue 129 SER Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 152 SER Chi-restraints excluded: chain F residue 3 ILE Chi-restraints excluded: chain F residue 77 GLU Chi-restraints excluded: chain F residue 80 LEU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain H residue 5 ASP Chi-restraints excluded: chain H residue 23 ASP Chi-restraints excluded: chain H residue 63 GLN Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 87 LEU Chi-restraints excluded: chain I residue 125 THR Chi-restraints excluded: chain J residue 6 ILE Chi-restraints excluded: chain J residue 19 ASP Chi-restraints excluded: chain J residue 82 LYS Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain K residue 114 LEU Chi-restraints excluded: chain L residue 89 ASP Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 115 SER Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 49 THR Chi-restraints excluded: chain M residue 60 ILE Chi-restraints excluded: chain M residue 64 LEU Chi-restraints excluded: chain M residue 69 ASP Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain N residue 52 GLU Chi-restraints excluded: chain O residue 11 ILE Chi-restraints excluded: chain P residue 44 GLU Chi-restraints excluded: chain P residue 92 THR Chi-restraints excluded: chain Q residue 10 THR Chi-restraints excluded: chain Q residue 45 SER Chi-restraints excluded: chain Q residue 79 THR Chi-restraints excluded: chain Q residue 90 LEU Chi-restraints excluded: chain R residue 63 ASP Chi-restraints excluded: chain S residue 29 GLN Chi-restraints excluded: chain S residue 30 VAL Chi-restraints excluded: chain S residue 35 SER Chi-restraints excluded: chain S residue 49 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 291 optimal weight: 0.9990 chunk 221 optimal weight: 9.9990 chunk 152 optimal weight: 0.7980 chunk 32 optimal weight: 6.9990 chunk 140 optimal weight: 9.9990 chunk 197 optimal weight: 0.0870 chunk 295 optimal weight: 2.9990 chunk 313 optimal weight: 6.9990 chunk 154 optimal weight: 8.9990 chunk 280 optimal weight: 6.9990 chunk 84 optimal weight: 5.9990 overall best weight: 2.1764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 68 HIS D 54 GLN K 78 ASN K 110 GLN ** K 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 31 ASN M 75 GLN O 7 GLN ** S 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 74 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.3538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 48853 Z= 0.246 Angle : 0.648 10.018 72784 Z= 0.328 Chirality : 0.037 0.327 9274 Planarity : 0.005 0.076 4082 Dihedral : 24.825 179.789 23942 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.95 % Allowed : 6.89 % Favored : 92.16 % Rotamer: Outliers : 5.58 % Allowed : 19.94 % Favored : 74.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.19), residues: 1900 helix: 0.64 (0.19), residues: 755 sheet: -0.91 (0.27), residues: 335 loop : -2.09 (0.20), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 18 HIS 0.007 0.001 HIS O 46 PHE 0.017 0.002 PHE H 10 TYR 0.014 0.002 TYR Q 49 ARG 0.006 0.001 ARG G 10 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 603 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 512 time to evaluate : 2.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 71 ARG cc_start: 0.5072 (ptp-170) cc_final: 0.4838 (ptt-90) REVERT: C 93 LEU cc_start: 0.7646 (mp) cc_final: 0.7387 (tp) REVERT: C 99 GLN cc_start: 0.5671 (mt0) cc_final: 0.5144 (tm-30) REVERT: C 106 LYS cc_start: 0.8285 (mttp) cc_final: 0.7401 (mmmt) REVERT: C 133 MET cc_start: 0.8680 (mmm) cc_final: 0.8453 (mtm) REVERT: C 161 GLU cc_start: 0.7249 (tp30) cc_final: 0.6675 (pm20) REVERT: C 187 TYR cc_start: 0.8125 (t80) cc_final: 0.7775 (t80) REVERT: D 10 ARG cc_start: 0.7488 (ptt-90) cc_final: 0.6210 (tpt170) REVERT: D 48 GLN cc_start: 0.7283 (tp-100) cc_final: 0.6829 (pm20) REVERT: D 54 GLN cc_start: 0.7892 (OUTLIER) cc_final: 0.7635 (mm-40) REVERT: D 99 ARG cc_start: 0.7342 (ttm-80) cc_final: 0.6899 (tpt170) REVERT: D 126 ASP cc_start: 0.7590 (OUTLIER) cc_final: 0.6434 (p0) REVERT: D 177 VAL cc_start: 0.9023 (t) cc_final: 0.8754 (m) REVERT: E 36 TYR cc_start: 0.7320 (p90) cc_final: 0.7085 (p90) REVERT: E 66 ASP cc_start: 0.8696 (m-30) cc_final: 0.8056 (p0) REVERT: E 91 GLU cc_start: 0.7849 (tp30) cc_final: 0.7389 (tp30) REVERT: E 147 ASP cc_start: 0.8125 (m-30) cc_final: 0.7811 (m-30) REVERT: G 37 SER cc_start: 0.8369 (t) cc_final: 0.8046 (t) REVERT: G 52 GLU cc_start: 0.7882 (mt-10) cc_final: 0.7078 (tp30) REVERT: G 58 PRO cc_start: 0.7790 (Cg_endo) cc_final: 0.7493 (Cg_exo) REVERT: H 3 MET cc_start: 0.8437 (mmm) cc_final: 0.8215 (mmm) REVERT: H 38 GLU cc_start: 0.8545 (mm-30) cc_final: 0.8110 (mm-30) REVERT: H 43 GLU cc_start: 0.7899 (mm-30) cc_final: 0.7234 (mm-30) REVERT: H 52 GLU cc_start: 0.7790 (tp30) cc_final: 0.7232 (tp30) REVERT: H 78 ARG cc_start: 0.7452 (ptm160) cc_final: 0.7249 (ptm-80) REVERT: H 115 ASP cc_start: 0.8643 (p0) cc_final: 0.8153 (p0) REVERT: H 121 GLN cc_start: 0.7585 (tp40) cc_final: 0.7255 (tm-30) REVERT: H 126 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7699 (tt0) REVERT: I 61 ASN cc_start: 0.8106 (t0) cc_final: 0.7402 (t0) REVERT: I 115 ARG cc_start: 0.7172 (ttm170) cc_final: 0.6503 (tmt170) REVERT: I 127 ASP cc_start: 0.8380 (m-30) cc_final: 0.7842 (p0) REVERT: J 11 LYS cc_start: 0.7762 (mttt) cc_final: 0.7204 (mtpp) REVERT: J 45 GLU cc_start: 0.7839 (mt-10) cc_final: 0.7074 (mt-10) REVERT: J 46 LYS cc_start: 0.8509 (mtmm) cc_final: 0.7899 (ttpt) REVERT: J 71 LYS cc_start: 0.7542 (mtmt) cc_final: 0.7339 (mttm) REVERT: K 128 ASN cc_start: 0.6722 (m-40) cc_final: 0.6476 (m-40) REVERT: L 31 ARG cc_start: 0.7769 (OUTLIER) cc_final: 0.7367 (ptt-90) REVERT: L 76 GLU cc_start: 0.7935 (mm-30) cc_final: 0.7706 (mm-30) REVERT: L 77 HIS cc_start: 0.8162 (m-70) cc_final: 0.7778 (m90) REVERT: L 87 VAL cc_start: 0.8307 (t) cc_final: 0.7882 (p) REVERT: L 89 ASP cc_start: 0.7558 (OUTLIER) cc_final: 0.7322 (p0) REVERT: L 105 GLN cc_start: 0.8125 (mt0) cc_final: 0.7667 (mt0) REVERT: M 15 MET cc_start: 0.7920 (tpt) cc_final: 0.7639 (mmm) REVERT: M 32 GLU cc_start: 0.8539 (tm-30) cc_final: 0.8122 (tm-30) REVERT: M 60 ILE cc_start: 0.7785 (OUTLIER) cc_final: 0.7568 (mt) REVERT: M 65 LYS cc_start: 0.6265 (mptt) cc_final: 0.5608 (mmtt) REVERT: M 80 ARG cc_start: 0.8092 (ptt90) cc_final: 0.7627 (tmm160) REVERT: M 83 GLU cc_start: 0.8233 (mp0) cc_final: 0.8032 (mp0) REVERT: M 90 LEU cc_start: 0.7727 (OUTLIER) cc_final: 0.7493 (mp) REVERT: M 108 ARG cc_start: 0.6408 (mmt180) cc_final: 0.5666 (mmp-170) REVERT: N 4 LYS cc_start: 0.7518 (mmtt) cc_final: 0.7041 (mtpt) REVERT: N 21 TYR cc_start: 0.8421 (p90) cc_final: 0.7833 (p90) REVERT: N 26 LYS cc_start: 0.7953 (tttp) cc_final: 0.7745 (tttm) REVERT: N 47 MET cc_start: 0.7556 (mmt) cc_final: 0.6995 (mmt) REVERT: N 52 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.7240 (mp0) REVERT: O 53 ARG cc_start: 0.8207 (ttm110) cc_final: 0.7976 (ttp-170) REVERT: P 17 GLN cc_start: 0.8024 (mp10) cc_final: 0.6555 (tp40) REVERT: P 44 GLU cc_start: 0.8686 (OUTLIER) cc_final: 0.7999 (mm-30) REVERT: P 50 GLN cc_start: 0.7779 (mt0) cc_final: 0.6604 (tm-30) REVERT: P 68 GLU cc_start: 0.8356 (tt0) cc_final: 0.8083 (tp30) REVERT: P 73 LEU cc_start: 0.8856 (mp) cc_final: 0.8635 (mp) REVERT: P 84 LYS cc_start: 0.8418 (tptt) cc_final: 0.8185 (tppt) REVERT: Q 77 MET cc_start: 0.7837 (ttp) cc_final: 0.7596 (ttp) REVERT: Q 96 LYS cc_start: 0.8956 (mttm) cc_final: 0.8636 (mmmt) REVERT: R 32 TYR cc_start: 0.8285 (p90) cc_final: 0.7834 (p90) REVERT: R 33 LYS cc_start: 0.7021 (mmmt) cc_final: 0.6751 (mmmt) REVERT: R 39 ARG cc_start: 0.8205 (mmt90) cc_final: 0.7681 (mmm-85) REVERT: R 49 ARG cc_start: 0.7989 (mtt-85) cc_final: 0.7173 (ttm110) REVERT: S 16 LEU cc_start: 0.8319 (tp) cc_final: 0.7764 (pp) REVERT: S 17 LYS cc_start: 0.6916 (tttt) cc_final: 0.6258 (tppt) REVERT: S 21 VAL cc_start: 0.7367 (OUTLIER) cc_final: 0.7051 (m) REVERT: S 25 LYS cc_start: 0.6623 (mmmt) cc_final: 0.6409 (mptt) REVERT: S 55 ARG cc_start: 0.5798 (ttt-90) cc_final: 0.5549 (ttp80) REVERT: T 19 LEU cc_start: 0.8192 (mm) cc_final: 0.7893 (mm) REVERT: T 46 LYS cc_start: 0.7673 (ttpp) cc_final: 0.7408 (mtmt) REVERT: T 49 GLU cc_start: 0.8927 (tt0) cc_final: 0.8568 (mt-10) REVERT: T 54 THR cc_start: 0.8361 (m) cc_final: 0.7979 (p) outliers start: 91 outliers final: 62 residues processed: 559 average time/residue: 0.6696 time to fit residues: 585.3171 Evaluate side-chains 564 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 492 time to evaluate : 3.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain D residue 54 GLN Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 126 ASP Chi-restraints excluded: chain D residue 129 SER Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 152 SER Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 3 ILE Chi-restraints excluded: chain F residue 8 LEU Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 77 GLU Chi-restraints excluded: chain F residue 80 LEU Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain G residue 149 ARG Chi-restraints excluded: chain H residue 107 SER Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 126 GLU Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 87 LEU Chi-restraints excluded: chain I residue 125 THR Chi-restraints excluded: chain J residue 19 ASP Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 82 LYS Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain K residue 78 ASN Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 114 LEU Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 31 ARG Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 89 ASP Chi-restraints excluded: chain L residue 115 SER Chi-restraints excluded: chain M residue 49 THR Chi-restraints excluded: chain M residue 60 ILE Chi-restraints excluded: chain M residue 64 LEU Chi-restraints excluded: chain M residue 69 ASP Chi-restraints excluded: chain M residue 90 LEU Chi-restraints excluded: chain N residue 27 CYS Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain N residue 52 GLU Chi-restraints excluded: chain O residue 11 ILE Chi-restraints excluded: chain P residue 44 GLU Chi-restraints excluded: chain P residue 92 THR Chi-restraints excluded: chain Q residue 10 THR Chi-restraints excluded: chain Q residue 45 SER Chi-restraints excluded: chain Q residue 79 THR Chi-restraints excluded: chain Q residue 90 LEU Chi-restraints excluded: chain Q residue 93 ILE Chi-restraints excluded: chain R residue 63 ASP Chi-restraints excluded: chain R residue 66 VAL Chi-restraints excluded: chain S residue 21 VAL Chi-restraints excluded: chain S residue 29 GLN Chi-restraints excluded: chain S residue 35 SER Chi-restraints excluded: chain S residue 38 SER Chi-restraints excluded: chain S residue 49 PHE Chi-restraints excluded: chain S residue 66 MET Chi-restraints excluded: chain T residue 57 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 260 optimal weight: 8.9990 chunk 177 optimal weight: 0.9980 chunk 4 optimal weight: 6.9990 chunk 233 optimal weight: 8.9990 chunk 129 optimal weight: 10.0000 chunk 267 optimal weight: 5.9990 chunk 216 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 159 optimal weight: 0.6980 chunk 281 optimal weight: 0.8980 chunk 79 optimal weight: 5.9990 overall best weight: 2.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 68 HIS D 54 GLN D 66 GLN D 173 GLN G 142 HIS I 64 HIS K 110 GLN ** K 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 109 ASN ** O 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 65 ASN ** R 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.3733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 48853 Z= 0.271 Angle : 0.656 12.221 72784 Z= 0.332 Chirality : 0.038 0.295 9274 Planarity : 0.005 0.061 4082 Dihedral : 24.770 177.111 23940 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.84 % Allowed : 7.53 % Favored : 91.63 % Rotamer: Outliers : 6.44 % Allowed : 20.86 % Favored : 72.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % 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: -0.99 (0.19), residues: 1900 helix: 0.82 (0.19), residues: 740 sheet: -0.91 (0.27), residues: 349 loop : -1.96 (0.20), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 18 HIS 0.007 0.001 HIS J 56 PHE 0.015 0.002 PHE H 10 TYR 0.015 0.002 TYR Q 9 ARG 0.008 0.001 ARG J 62 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 607 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 502 time to evaluate : 2.748 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: C 71 ARG cc_start: 0.5086 (OUTLIER) cc_final: 0.4868 (ptt-90) REVERT: C 93 LEU cc_start: 0.7650 (mp) cc_final: 0.7399 (tp) REVERT: C 99 GLN cc_start: 0.5578 (mt0) cc_final: 0.5050 (tm-30) REVERT: C 106 LYS cc_start: 0.8284 (mttp) cc_final: 0.7404 (mmmt) REVERT: C 133 MET cc_start: 0.8645 (mmm) cc_final: 0.8392 (mtm) REVERT: C 161 GLU cc_start: 0.7259 (tp30) cc_final: 0.6644 (pm20) REVERT: C 187 TYR cc_start: 0.8119 (t80) cc_final: 0.7793 (t80) REVERT: D 10 ARG cc_start: 0.7577 (ptt-90) cc_final: 0.6302 (tpt170) REVERT: D 54 GLN cc_start: 0.7712 (OUTLIER) cc_final: 0.7255 (tt0) REVERT: D 99 ARG cc_start: 0.7380 (ttm-80) cc_final: 0.6938 (tpt170) REVERT: D 112 LEU cc_start: 0.7673 (mt) cc_final: 0.7467 (mt) REVERT: D 113 VAL cc_start: 0.7607 (t) cc_final: 0.7373 (t) REVERT: D 126 ASP cc_start: 0.7622 (OUTLIER) cc_final: 0.6447 (p0) REVERT: D 177 VAL cc_start: 0.8998 (t) cc_final: 0.8709 (m) REVERT: E 36 TYR cc_start: 0.7279 (p90) cc_final: 0.7021 (p90) REVERT: E 66 ASP cc_start: 0.8651 (OUTLIER) cc_final: 0.8030 (p0) REVERT: E 91 GLU cc_start: 0.7990 (tp30) cc_final: 0.7531 (tp30) REVERT: E 142 CYS cc_start: 0.8184 (m) cc_final: 0.7917 (m) REVERT: E 147 ASP cc_start: 0.8138 (m-30) cc_final: 0.7818 (m-30) REVERT: E 176 GLU cc_start: 0.6646 (mp0) cc_final: 0.6421 (mp0) REVERT: G 52 GLU cc_start: 0.7878 (mt-10) cc_final: 0.7613 (mt-10) REVERT: G 104 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8420 (tt) REVERT: H 5 ASP cc_start: 0.7135 (t0) cc_final: 0.6847 (t70) REVERT: H 38 GLU cc_start: 0.8573 (mm-30) cc_final: 0.8182 (mm-30) REVERT: H 43 GLU cc_start: 0.7892 (mm-30) cc_final: 0.7145 (mm-30) REVERT: H 48 ASP cc_start: 0.8031 (t70) cc_final: 0.7808 (t70) REVERT: H 52 GLU cc_start: 0.7818 (tp30) cc_final: 0.7319 (tp30) REVERT: H 78 ARG cc_start: 0.7463 (ptm160) cc_final: 0.7256 (ptm-80) REVERT: H 115 ASP cc_start: 0.8650 (p0) cc_final: 0.8148 (p0) REVERT: H 121 GLN cc_start: 0.7610 (tp40) cc_final: 0.7254 (tm-30) REVERT: H 126 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7714 (tt0) REVERT: I 61 ASN cc_start: 0.8342 (t0) cc_final: 0.7763 (m-40) REVERT: I 65 GLN cc_start: 0.8105 (mt0) cc_final: 0.7843 (mp10) REVERT: I 115 ARG cc_start: 0.7072 (ttm170) cc_final: 0.6457 (tmt170) REVERT: I 127 ASP cc_start: 0.8233 (OUTLIER) cc_final: 0.7742 (p0) REVERT: J 11 LYS cc_start: 0.7800 (mttt) cc_final: 0.7231 (mtpp) REVERT: J 45 GLU cc_start: 0.7866 (mt-10) cc_final: 0.7093 (mt-10) REVERT: J 46 LYS cc_start: 0.8530 (mtmm) cc_final: 0.7961 (ttpt) REVERT: J 82 LYS cc_start: 0.8030 (OUTLIER) cc_final: 0.7803 (tttt) REVERT: K 128 ASN cc_start: 0.6634 (m-40) cc_final: 0.6433 (m-40) REVERT: L 31 ARG cc_start: 0.7811 (OUTLIER) cc_final: 0.7227 (ptt-90) REVERT: L 76 GLU cc_start: 0.7900 (mm-30) cc_final: 0.7683 (mm-30) REVERT: L 77 HIS cc_start: 0.8262 (m-70) cc_final: 0.7906 (m90) REVERT: L 87 VAL cc_start: 0.8392 (t) cc_final: 0.8089 (p) REVERT: L 89 ASP cc_start: 0.7581 (m-30) cc_final: 0.7364 (p0) REVERT: M 15 MET cc_start: 0.7900 (tpt) cc_final: 0.7641 (mmm) REVERT: M 16 GLU cc_start: 0.7598 (tt0) cc_final: 0.7314 (tt0) REVERT: M 32 GLU cc_start: 0.8503 (tm-30) cc_final: 0.8007 (tm-30) REVERT: M 59 TYR cc_start: 0.8096 (t80) cc_final: 0.7781 (t80) REVERT: M 65 LYS cc_start: 0.6078 (mptt) cc_final: 0.5672 (mmtt) REVERT: M 80 ARG cc_start: 0.7993 (ptt90) cc_final: 0.7431 (ppt170) REVERT: M 90 LEU cc_start: 0.7877 (OUTLIER) cc_final: 0.7631 (mp) REVERT: M 108 ARG cc_start: 0.6465 (mmt180) cc_final: 0.5706 (mmp-170) REVERT: N 4 LYS cc_start: 0.7435 (mmtt) cc_final: 0.6964 (mtpt) REVERT: N 21 TYR cc_start: 0.8398 (p90) cc_final: 0.7599 (p90) REVERT: N 47 MET cc_start: 0.7568 (mmt) cc_final: 0.6999 (mmt) REVERT: N 52 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.7173 (mp0) REVERT: O 10 GLU cc_start: 0.7964 (mm-30) cc_final: 0.7757 (mm-30) REVERT: O 14 GLN cc_start: 0.7821 (tt0) cc_final: 0.7575 (tt0) REVERT: O 53 ARG cc_start: 0.8267 (ttm110) cc_final: 0.8063 (ttp-170) REVERT: O 79 ARG cc_start: 0.7631 (mmm-85) cc_final: 0.7336 (mpp80) REVERT: P 17 GLN cc_start: 0.7970 (mp10) cc_final: 0.6396 (tp40) REVERT: P 21 ILE cc_start: 0.8807 (mt) cc_final: 0.8600 (mt) REVERT: P 44 GLU cc_start: 0.8639 (OUTLIER) cc_final: 0.7886 (mm-30) REVERT: P 50 GLN cc_start: 0.7852 (mt0) cc_final: 0.6714 (tm-30) REVERT: P 68 GLU cc_start: 0.8319 (tt0) cc_final: 0.8048 (tp30) REVERT: P 84 LYS cc_start: 0.8364 (tptt) cc_final: 0.8153 (tppt) REVERT: P 90 GLU cc_start: 0.6846 (OUTLIER) cc_final: 0.6571 (pm20) REVERT: Q 28 VAL cc_start: 0.7126 (t) cc_final: 0.6916 (m) REVERT: Q 43 ARG cc_start: 0.8566 (mtt90) cc_final: 0.8292 (mtt90) REVERT: Q 77 MET cc_start: 0.7983 (ttp) cc_final: 0.7704 (ttp) REVERT: Q 96 LYS cc_start: 0.8965 (mttm) cc_final: 0.8635 (mmmt) REVERT: R 33 LYS cc_start: 0.7003 (mmmt) cc_final: 0.6710 (mmmt) REVERT: R 39 ARG cc_start: 0.8213 (mmt90) cc_final: 0.7692 (mmm-85) REVERT: R 49 ARG cc_start: 0.8026 (mtt-85) cc_final: 0.7219 (ttm110) REVERT: R 59 GLN cc_start: 0.7440 (mt0) cc_final: 0.7035 (mt0) REVERT: S 16 LEU cc_start: 0.8312 (tp) cc_final: 0.7723 (pp) REVERT: S 17 LYS cc_start: 0.6849 (tttt) cc_final: 0.6216 (tppt) REVERT: S 21 VAL cc_start: 0.7248 (OUTLIER) cc_final: 0.6922 (m) REVERT: S 25 LYS cc_start: 0.6784 (mmmt) cc_final: 0.6513 (mptt) REVERT: S 28 LYS cc_start: 0.7245 (OUTLIER) cc_final: 0.7020 (pptt) REVERT: S 47 HIS cc_start: 0.7885 (t70) cc_final: 0.6654 (m-70) REVERT: T 19 LEU cc_start: 0.8285 (mm) cc_final: 0.7937 (mm) REVERT: T 49 GLU cc_start: 0.8918 (tt0) cc_final: 0.8550 (mt-10) REVERT: T 54 THR cc_start: 0.8337 (m) cc_final: 0.7955 (p) REVERT: U 12 MET cc_start: 0.6513 (mmm) cc_final: 0.6097 (mmm) outliers start: 105 outliers final: 74 residues processed: 557 average time/residue: 0.6630 time to fit residues: 577.7818 Evaluate side-chains 583 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 494 time to evaluate : 2.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 71 ARG Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain D residue 54 GLN Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 126 ASP Chi-restraints excluded: chain D residue 129 SER Chi-restraints excluded: chain D residue 173 GLN Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 66 ASP Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 152 SER Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 3 ILE Chi-restraints excluded: chain F residue 8 LEU Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 77 GLU Chi-restraints excluded: chain F residue 80 LEU Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain G residue 149 ARG Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 107 SER Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 126 GLU Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 87 LEU Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain I residue 125 THR Chi-restraints excluded: chain I residue 127 ASP Chi-restraints excluded: chain J residue 19 ASP Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 66 GLU Chi-restraints excluded: chain J residue 82 LYS Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 114 LEU Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 31 ARG Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain L residue 115 SER Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 49 THR Chi-restraints excluded: chain M residue 64 LEU Chi-restraints excluded: chain M residue 69 ASP Chi-restraints excluded: chain M residue 90 LEU Chi-restraints excluded: chain N residue 27 CYS Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain N residue 52 GLU Chi-restraints excluded: chain O residue 11 ILE Chi-restraints excluded: chain P residue 44 GLU Chi-restraints excluded: chain P residue 90 GLU Chi-restraints excluded: chain P residue 92 THR Chi-restraints excluded: chain Q residue 45 SER Chi-restraints excluded: chain Q residue 65 ASN Chi-restraints excluded: chain Q residue 79 THR Chi-restraints excluded: chain Q residue 90 LEU Chi-restraints excluded: chain R residue 40 THR Chi-restraints excluded: chain R residue 56 ASN Chi-restraints excluded: chain R residue 63 ASP Chi-restraints excluded: chain S residue 11 VAL Chi-restraints excluded: chain S residue 21 VAL Chi-restraints excluded: chain S residue 28 LYS Chi-restraints excluded: chain S residue 29 GLN Chi-restraints excluded: chain S residue 35 SER Chi-restraints excluded: chain S residue 38 SER Chi-restraints excluded: chain S residue 49 PHE Chi-restraints excluded: chain S residue 60 VAL Chi-restraints excluded: chain S residue 66 MET Chi-restraints excluded: chain T residue 26 SER Chi-restraints excluded: chain T residue 28 LEU Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain T residue 57 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 105 optimal weight: 6.9990 chunk 282 optimal weight: 4.9990 chunk 61 optimal weight: 10.0000 chunk 183 optimal weight: 2.9990 chunk 77 optimal weight: 8.9990 chunk 313 optimal weight: 0.8980 chunk 260 optimal weight: 6.9990 chunk 145 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 103 optimal weight: 9.9990 chunk 164 optimal weight: 4.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 68 HIS D 54 GLN D 173 GLN H 29 HIS I 57 ASN I 64 HIS K 110 GLN ** K 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 57 GLN ** R 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 60 HIS ** S 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.3798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 48853 Z= 0.405 Angle : 0.756 13.330 72784 Z= 0.380 Chirality : 0.042 0.337 9274 Planarity : 0.005 0.058 4082 Dihedral : 24.849 179.651 23938 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.84 % Allowed : 7.89 % Favored : 91.26 % Rotamer: Outliers : 7.18 % Allowed : 21.17 % Favored : 71.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.19), residues: 1900 helix: 0.61 (0.19), residues: 740 sheet: -1.03 (0.27), residues: 354 loop : -2.11 (0.20), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 22 HIS 0.007 0.001 HIS Q 62 PHE 0.018 0.002 PHE H 10 TYR 0.021 0.002 TYR Q 49 ARG 0.007 0.001 ARG D 174 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 603 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 486 time to evaluate : 2.652 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: C 93 LEU cc_start: 0.7662 (mp) cc_final: 0.7307 (tp) REVERT: C 106 LYS cc_start: 0.8305 (mttp) cc_final: 0.7434 (mmmt) REVERT: C 133 MET cc_start: 0.8666 (mmm) cc_final: 0.8416 (mtm) REVERT: C 138 GLN cc_start: 0.8372 (tt0) cc_final: 0.7720 (pt0) REVERT: C 161 GLU cc_start: 0.7266 (tp30) cc_final: 0.6634 (pm20) REVERT: D 10 ARG cc_start: 0.7791 (ptt-90) cc_final: 0.6454 (tpt170) REVERT: D 18 ASP cc_start: 0.2555 (OUTLIER) cc_final: 0.2332 (m-30) REVERT: D 48 GLN cc_start: 0.7217 (tp-100) cc_final: 0.6863 (pm20) REVERT: D 99 ARG cc_start: 0.7414 (ttm-80) cc_final: 0.6944 (tpt170) REVERT: D 126 ASP cc_start: 0.7740 (OUTLIER) cc_final: 0.6499 (p0) REVERT: E 36 TYR cc_start: 0.7304 (p90) cc_final: 0.7037 (p90) REVERT: E 66 ASP cc_start: 0.8603 (OUTLIER) cc_final: 0.7935 (p0) REVERT: E 91 GLU cc_start: 0.8131 (tp30) cc_final: 0.7659 (tp30) REVERT: E 142 CYS cc_start: 0.8204 (m) cc_final: 0.7977 (m) REVERT: E 147 ASP cc_start: 0.8069 (m-30) cc_final: 0.7756 (m-30) REVERT: G 52 GLU cc_start: 0.7886 (mt-10) cc_final: 0.7618 (mt-10) REVERT: G 90 GLU cc_start: 0.7618 (pm20) cc_final: 0.7313 (pm20) REVERT: G 104 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8526 (tt) REVERT: G 149 ARG cc_start: 0.6681 (OUTLIER) cc_final: 0.5563 (mmt90) REVERT: H 5 ASP cc_start: 0.7149 (t0) cc_final: 0.6886 (t70) REVERT: H 38 GLU cc_start: 0.8642 (mm-30) cc_final: 0.8168 (mm-30) REVERT: H 43 GLU cc_start: 0.7948 (mm-30) cc_final: 0.7445 (mm-30) REVERT: H 48 ASP cc_start: 0.8164 (t70) cc_final: 0.7293 (t0) REVERT: H 52 GLU cc_start: 0.7888 (tp30) cc_final: 0.7338 (tp30) REVERT: H 63 GLN cc_start: 0.6694 (OUTLIER) cc_final: 0.5586 (mp10) REVERT: H 115 ASP cc_start: 0.8698 (p0) cc_final: 0.8176 (p0) REVERT: H 121 GLN cc_start: 0.7657 (tp40) cc_final: 0.7362 (tm-30) REVERT: I 61 ASN cc_start: 0.8386 (t0) cc_final: 0.7606 (m-40) REVERT: I 65 GLN cc_start: 0.8165 (mt0) cc_final: 0.7812 (mp10) REVERT: I 115 ARG cc_start: 0.7097 (ttm170) cc_final: 0.6530 (tmt170) REVERT: I 127 ASP cc_start: 0.8484 (OUTLIER) cc_final: 0.7750 (p0) REVERT: J 11 LYS cc_start: 0.7633 (mttt) cc_final: 0.7001 (mtpp) REVERT: J 42 LEU cc_start: 0.7207 (OUTLIER) cc_final: 0.6804 (tp) REVERT: J 46 LYS cc_start: 0.8516 (mtmm) cc_final: 0.7865 (ttpt) REVERT: K 82 LYS cc_start: 0.7833 (mtmm) cc_final: 0.7626 (mtmm) REVERT: L 31 ARG cc_start: 0.7989 (OUTLIER) cc_final: 0.7533 (ptt180) REVERT: L 76 GLU cc_start: 0.7867 (mm-30) cc_final: 0.7454 (mm-30) REVERT: L 77 HIS cc_start: 0.8242 (m-70) cc_final: 0.7760 (m90) REVERT: L 87 VAL cc_start: 0.8402 (t) cc_final: 0.8082 (p) REVERT: M 15 MET cc_start: 0.8035 (tpt) cc_final: 0.7817 (mmm) REVERT: M 16 GLU cc_start: 0.7664 (tt0) cc_final: 0.7426 (tt0) REVERT: M 32 GLU cc_start: 0.8520 (tm-30) cc_final: 0.8076 (tm-30) REVERT: M 42 ASN cc_start: 0.7980 (m-40) cc_final: 0.7378 (t0) REVERT: M 65 LYS cc_start: 0.6433 (mptt) cc_final: 0.6029 (mttt) REVERT: M 70 LEU cc_start: 0.7374 (OUTLIER) cc_final: 0.7160 (mp) REVERT: M 80 ARG cc_start: 0.8053 (ptt90) cc_final: 0.7441 (ppt170) REVERT: M 90 LEU cc_start: 0.7877 (OUTLIER) cc_final: 0.7624 (mp) REVERT: M 108 ARG cc_start: 0.6308 (mmt180) cc_final: 0.5577 (mmp-170) REVERT: N 4 LYS cc_start: 0.7497 (mmtt) cc_final: 0.7044 (mtpt) REVERT: N 21 TYR cc_start: 0.8360 (p90) cc_final: 0.7458 (p90) REVERT: N 47 MET cc_start: 0.7743 (mmt) cc_final: 0.7137 (mmt) REVERT: N 52 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.7350 (mp0) REVERT: O 14 GLN cc_start: 0.7814 (tt0) cc_final: 0.7500 (tt0) REVERT: O 75 VAL cc_start: 0.6929 (OUTLIER) cc_final: 0.6554 (p) REVERT: O 79 ARG cc_start: 0.7675 (mmm-85) cc_final: 0.7458 (mpp80) REVERT: P 17 GLN cc_start: 0.8069 (mp10) cc_final: 0.6373 (tp40) REVERT: P 44 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.7869 (mm-30) REVERT: Q 28 VAL cc_start: 0.7186 (t) cc_final: 0.6891 (m) REVERT: Q 96 LYS cc_start: 0.9047 (mttm) cc_final: 0.8645 (mmmt) REVERT: R 33 LYS cc_start: 0.6868 (mmmt) cc_final: 0.6561 (mmmt) REVERT: R 39 ARG cc_start: 0.8226 (mmt90) cc_final: 0.7658 (mmm-85) REVERT: R 49 ARG cc_start: 0.8078 (mtt-85) cc_final: 0.7246 (ttm110) REVERT: R 59 GLN cc_start: 0.7580 (mt0) cc_final: 0.7161 (mt0) REVERT: S 16 LEU cc_start: 0.8307 (tp) cc_final: 0.7713 (pp) REVERT: S 17 LYS cc_start: 0.7139 (tttt) cc_final: 0.6524 (tppt) REVERT: S 21 VAL cc_start: 0.7334 (OUTLIER) cc_final: 0.7022 (m) REVERT: S 25 LYS cc_start: 0.6681 (mmmt) cc_final: 0.6376 (mptt) REVERT: S 43 ASP cc_start: 0.8271 (m-30) cc_final: 0.8039 (m-30) REVERT: T 19 LEU cc_start: 0.8307 (mm) cc_final: 0.7939 (mm) REVERT: T 49 GLU cc_start: 0.8883 (tt0) cc_final: 0.8489 (mt-10) REVERT: T 54 THR cc_start: 0.8335 (m) cc_final: 0.7956 (p) REVERT: U 12 MET cc_start: 0.7352 (mmm) cc_final: 0.6493 (mmt) outliers start: 117 outliers final: 87 residues processed: 551 average time/residue: 0.6434 time to fit residues: 556.0239 Evaluate side-chains 576 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 474 time to evaluate : 2.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 126 ASP Chi-restraints excluded: chain D residue 129 SER Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 66 ASP Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 152 SER Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 3 ILE Chi-restraints excluded: chain F residue 8 LEU Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 77 GLU Chi-restraints excluded: chain F residue 80 LEU Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 94 ASP Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain G residue 149 ARG Chi-restraints excluded: chain H residue 63 GLN Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 107 SER Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 126 GLU Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 87 LEU Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain I residue 125 THR Chi-restraints excluded: chain I residue 127 ASP Chi-restraints excluded: chain J residue 6 ILE Chi-restraints excluded: chain J residue 18 ILE Chi-restraints excluded: chain J residue 19 ASP Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 66 GLU Chi-restraints excluded: chain J residue 82 LYS Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 114 LEU Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 31 ARG Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 97 ILE Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain L residue 115 SER Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 49 THR Chi-restraints excluded: chain M residue 64 LEU Chi-restraints excluded: chain M residue 69 ASP Chi-restraints excluded: chain M residue 70 LEU Chi-restraints excluded: chain M residue 90 LEU Chi-restraints excluded: chain N residue 15 LYS Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain N residue 52 GLU Chi-restraints excluded: chain O residue 11 ILE Chi-restraints excluded: chain O residue 73 VAL Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain P residue 24 ASP Chi-restraints excluded: chain P residue 44 GLU Chi-restraints excluded: chain P residue 76 ILE Chi-restraints excluded: chain P residue 92 THR Chi-restraints excluded: chain Q residue 45 SER Chi-restraints excluded: chain Q residue 65 ASN Chi-restraints excluded: chain Q residue 79 THR Chi-restraints excluded: chain Q residue 90 LEU Chi-restraints excluded: chain R residue 40 THR Chi-restraints excluded: chain R residue 56 ASN Chi-restraints excluded: chain R residue 63 ASP Chi-restraints excluded: chain R residue 66 VAL Chi-restraints excluded: chain S residue 11 VAL Chi-restraints excluded: chain S residue 21 VAL Chi-restraints excluded: chain S residue 29 GLN Chi-restraints excluded: chain S residue 35 SER Chi-restraints excluded: chain S residue 38 SER Chi-restraints excluded: chain S residue 49 PHE Chi-restraints excluded: chain S residue 60 VAL Chi-restraints excluded: chain S residue 66 MET Chi-restraints excluded: chain S residue 77 THR Chi-restraints excluded: chain T residue 26 SER Chi-restraints excluded: chain T residue 28 LEU Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain T residue 57 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 302 optimal weight: 7.9990 chunk 35 optimal weight: 5.9990 chunk 178 optimal weight: 0.8980 chunk 228 optimal weight: 4.9990 chunk 177 optimal weight: 4.9990 chunk 263 optimal weight: 0.0970 chunk 175 optimal weight: 2.9990 chunk 312 optimal weight: 10.0000 chunk 195 optimal weight: 0.7980 chunk 190 optimal weight: 0.6980 chunk 144 optimal weight: 3.9990 overall best weight: 1.0980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 68 HIS I 64 HIS I 146 GLN K 110 GLN ** L 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 75 GLN ** N 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 37 GLN ** R 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 60 HIS S 52 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.4106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 48853 Z= 0.157 Angle : 0.590 11.953 72784 Z= 0.298 Chirality : 0.034 0.244 9274 Planarity : 0.004 0.056 4082 Dihedral : 24.624 179.648 23938 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.79 % Allowed : 6.58 % Favored : 92.63 % Rotamer: Outliers : 5.52 % Allowed : 22.94 % Favored : 71.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % 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: -0.67 (0.19), residues: 1900 helix: 1.22 (0.19), residues: 746 sheet: -0.75 (0.29), residues: 329 loop : -1.93 (0.20), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 18 HIS 0.008 0.001 HIS J 56 PHE 0.025 0.002 PHE C 167 TYR 0.022 0.001 TYR Q 9 ARG 0.005 0.000 ARG F 41 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 605 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 515 time to evaluate : 2.623 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: C 17 GLU cc_start: 0.6829 (OUTLIER) cc_final: 0.6301 (pm20) REVERT: C 93 LEU cc_start: 0.7687 (mp) cc_final: 0.7322 (tp) REVERT: C 99 GLN cc_start: 0.5550 (mt0) cc_final: 0.4941 (tm-30) REVERT: C 106 LYS cc_start: 0.8297 (mttp) cc_final: 0.7425 (mmmt) REVERT: C 133 MET cc_start: 0.8629 (mmm) cc_final: 0.8303 (mtt) REVERT: C 138 GLN cc_start: 0.8376 (tt0) cc_final: 0.7800 (pt0) REVERT: C 161 GLU cc_start: 0.7353 (tp30) cc_final: 0.6649 (pm20) REVERT: C 167 PHE cc_start: 0.8908 (p90) cc_final: 0.8577 (p90) REVERT: C 187 TYR cc_start: 0.7916 (t80) cc_final: 0.7522 (t80) REVERT: D 10 ARG cc_start: 0.7602 (ptt-90) cc_final: 0.6287 (tpt170) REVERT: D 99 ARG cc_start: 0.7322 (ttm-80) cc_final: 0.6870 (tpt170) REVERT: D 104 ARG cc_start: 0.6222 (ttm-80) cc_final: 0.5970 (ttt-90) REVERT: D 112 LEU cc_start: 0.7795 (mt) cc_final: 0.7590 (mt) REVERT: D 113 VAL cc_start: 0.7439 (t) cc_final: 0.7190 (t) REVERT: D 126 ASP cc_start: 0.7815 (OUTLIER) cc_final: 0.6692 (p0) REVERT: D 177 VAL cc_start: 0.8806 (t) cc_final: 0.8491 (m) REVERT: E 36 TYR cc_start: 0.7294 (p90) cc_final: 0.7006 (p90) REVERT: E 66 ASP cc_start: 0.8720 (OUTLIER) cc_final: 0.8086 (p0) REVERT: E 70 MET cc_start: 0.7877 (mmm) cc_final: 0.7417 (mmp) REVERT: E 79 LYS cc_start: 0.7436 (mttm) cc_final: 0.6899 (tppt) REVERT: E 91 GLU cc_start: 0.7873 (tp30) cc_final: 0.7345 (tp30) REVERT: E 142 CYS cc_start: 0.8094 (m) cc_final: 0.7825 (m) REVERT: E 147 ASP cc_start: 0.7981 (m-30) cc_final: 0.7638 (m-30) REVERT: E 176 GLU cc_start: 0.6743 (mp0) cc_final: 0.6529 (mp0) REVERT: F 40 ARG cc_start: 0.8051 (mtp85) cc_final: 0.7421 (mtm180) REVERT: H 31 LYS cc_start: 0.8458 (OUTLIER) cc_final: 0.8073 (ptmt) REVERT: H 38 GLU cc_start: 0.8572 (mm-30) cc_final: 0.8129 (mm-30) REVERT: H 43 GLU cc_start: 0.8034 (mm-30) cc_final: 0.7251 (mm-30) REVERT: H 48 ASP cc_start: 0.8117 (t70) cc_final: 0.7887 (t0) REVERT: H 52 GLU cc_start: 0.7757 (tp30) cc_final: 0.7422 (tp30) REVERT: H 117 GLN cc_start: 0.8599 (tt0) cc_final: 0.8215 (tt0) REVERT: H 121 GLN cc_start: 0.7710 (tp40) cc_final: 0.7419 (tm-30) REVERT: I 26 ILE cc_start: 0.6681 (mm) cc_final: 0.6379 (tp) REVERT: I 61 ASN cc_start: 0.8383 (t0) cc_final: 0.8054 (m-40) REVERT: I 65 GLN cc_start: 0.8342 (mt0) cc_final: 0.8024 (mp10) REVERT: I 66 GLN cc_start: 0.8261 (OUTLIER) cc_final: 0.8012 (pp30) REVERT: I 87 LEU cc_start: 0.7198 (OUTLIER) cc_final: 0.6782 (mt) REVERT: I 115 ARG cc_start: 0.6968 (ttm170) cc_final: 0.6268 (tmt170) REVERT: I 127 ASP cc_start: 0.8220 (m-30) cc_final: 0.7775 (p0) REVERT: J 10 LEU cc_start: 0.8219 (mp) cc_final: 0.7902 (mm) REVERT: J 11 LYS cc_start: 0.7524 (mttt) cc_final: 0.7089 (mtpp) REVERT: J 46 LYS cc_start: 0.8446 (mtmm) cc_final: 0.7816 (ttpt) REVERT: K 82 LYS cc_start: 0.7800 (mtmm) cc_final: 0.7559 (mtmm) REVERT: L 31 ARG cc_start: 0.7961 (OUTLIER) cc_final: 0.7286 (ptt-90) REVERT: L 76 GLU cc_start: 0.7981 (mm-30) cc_final: 0.7768 (mm-30) REVERT: L 77 HIS cc_start: 0.8325 (m-70) cc_final: 0.7952 (m90) REVERT: L 87 VAL cc_start: 0.8267 (t) cc_final: 0.7960 (p) REVERT: L 105 GLN cc_start: 0.7775 (mt0) cc_final: 0.7461 (mt0) REVERT: L 107 VAL cc_start: 0.8609 (t) cc_final: 0.8368 (m) REVERT: M 16 GLU cc_start: 0.7749 (tt0) cc_final: 0.7428 (tt0) REVERT: M 31 ASN cc_start: 0.8066 (m110) cc_final: 0.7790 (m-40) REVERT: M 32 GLU cc_start: 0.8482 (tm-30) cc_final: 0.8174 (tm-30) REVERT: M 59 TYR cc_start: 0.7783 (t80) cc_final: 0.7490 (t80) REVERT: M 65 LYS cc_start: 0.6198 (mptt) cc_final: 0.5886 (mttt) REVERT: M 80 ARG cc_start: 0.7940 (ptt90) cc_final: 0.7321 (ppt170) REVERT: M 90 LEU cc_start: 0.7738 (mp) cc_final: 0.7492 (mp) REVERT: M 108 ARG cc_start: 0.6368 (mmt180) cc_final: 0.5622 (mmp-170) REVERT: N 4 LYS cc_start: 0.7301 (mmtt) cc_final: 0.6792 (mtpt) REVERT: N 21 TYR cc_start: 0.8430 (p90) cc_final: 0.7539 (p90) REVERT: N 47 MET cc_start: 0.7540 (mmt) cc_final: 0.6944 (mmt) REVERT: N 52 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.7074 (mp0) REVERT: O 14 GLN cc_start: 0.7798 (tt0) cc_final: 0.7531 (tt0) REVERT: P 17 GLN cc_start: 0.8036 (mp10) cc_final: 0.6732 (tp40) REVERT: P 44 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.7877 (mm-30) REVERT: P 50 GLN cc_start: 0.7682 (mt0) cc_final: 0.6632 (tm-30) REVERT: P 90 GLU cc_start: 0.6827 (OUTLIER) cc_final: 0.6561 (pm20) REVERT: Q 8 LYS cc_start: 0.8051 (ttmm) cc_final: 0.7821 (tppt) REVERT: Q 43 ARG cc_start: 0.8545 (mtt90) cc_final: 0.8257 (mtt90) REVERT: Q 96 LYS cc_start: 0.8998 (mttm) cc_final: 0.8668 (mmmt) REVERT: R 39 ARG cc_start: 0.8182 (mmt90) cc_final: 0.7660 (mmm-85) REVERT: R 48 ILE cc_start: 0.8762 (mt) cc_final: 0.8487 (mp) REVERT: R 49 ARG cc_start: 0.8033 (mtt-85) cc_final: 0.7254 (ttm110) REVERT: S 16 LEU cc_start: 0.8269 (tp) cc_final: 0.7707 (pp) REVERT: S 17 LYS cc_start: 0.6816 (tttt) cc_final: 0.6085 (tmtt) REVERT: S 21 VAL cc_start: 0.7383 (OUTLIER) cc_final: 0.7016 (m) REVERT: S 25 LYS cc_start: 0.6903 (mmmt) cc_final: 0.6486 (mptt) REVERT: T 19 LEU cc_start: 0.8234 (mm) cc_final: 0.7857 (mm) REVERT: T 49 GLU cc_start: 0.8859 (tt0) cc_final: 0.8536 (mt-10) REVERT: T 54 THR cc_start: 0.8282 (m) cc_final: 0.7931 (p) REVERT: U 12 MET cc_start: 0.7307 (mmm) cc_final: 0.6520 (mmt) outliers start: 90 outliers final: 60 residues processed: 561 average time/residue: 0.6560 time to fit residues: 572.5528 Evaluate side-chains 560 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 489 time to evaluate : 2.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 126 ASP Chi-restraints excluded: chain D residue 129 SER Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 66 ASP Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 152 SER Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 3 ILE Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 77 GLU Chi-restraints excluded: chain F residue 80 LEU Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain G residue 149 ARG Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 107 SER Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 126 GLU Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 66 GLN Chi-restraints excluded: chain I residue 87 LEU Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain I residue 125 THR Chi-restraints excluded: chain J residue 18 ILE Chi-restraints excluded: chain J residue 19 ASP Chi-restraints excluded: chain J residue 66 GLU Chi-restraints excluded: chain J residue 82 LYS Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 114 LEU Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 31 ARG Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 94 ARG Chi-restraints excluded: chain L residue 115 SER Chi-restraints excluded: chain M residue 64 LEU Chi-restraints excluded: chain M residue 69 ASP Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain N residue 52 GLU Chi-restraints excluded: chain O residue 11 ILE Chi-restraints excluded: chain P residue 24 ASP Chi-restraints excluded: chain P residue 44 GLU Chi-restraints excluded: chain P residue 76 ILE Chi-restraints excluded: chain P residue 90 GLU Chi-restraints excluded: chain P residue 92 THR Chi-restraints excluded: chain Q residue 79 THR Chi-restraints excluded: chain Q residue 90 LEU Chi-restraints excluded: chain R residue 63 ASP Chi-restraints excluded: chain S residue 11 VAL Chi-restraints excluded: chain S residue 21 VAL Chi-restraints excluded: chain S residue 29 GLN Chi-restraints excluded: chain S residue 35 SER Chi-restraints excluded: chain S residue 49 PHE Chi-restraints excluded: chain S residue 66 MET Chi-restraints excluded: chain T residue 28 LEU Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain T residue 57 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 193 optimal weight: 0.1980 chunk 124 optimal weight: 6.9990 chunk 186 optimal weight: 5.9990 chunk 94 optimal weight: 6.9990 chunk 61 optimal weight: 10.0000 chunk 60 optimal weight: 10.0000 chunk 198 optimal weight: 0.5980 chunk 212 optimal weight: 0.2980 chunk 154 optimal weight: 6.9990 chunk 29 optimal weight: 6.9990 chunk 245 optimal weight: 8.9990 overall best weight: 2.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 68 HIS ** D 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 106 ASN I 64 HIS J 64 HIS K 110 GLN ** L 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 37 GLN ** R 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 60 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.4051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 48853 Z= 0.297 Angle : 0.664 12.604 72784 Z= 0.335 Chirality : 0.038 0.305 9274 Planarity : 0.005 0.054 4082 Dihedral : 24.678 178.722 23938 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.79 % Allowed : 7.84 % Favored : 91.37 % Rotamer: Outliers : 6.01 % Allowed : 23.19 % Favored : 70.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % 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: -0.80 (0.19), residues: 1900 helix: 1.08 (0.19), residues: 745 sheet: -0.79 (0.28), residues: 353 loop : -1.99 (0.21), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP P 80 HIS 0.007 0.001 HIS J 56 PHE 0.023 0.002 PHE C 167 TYR 0.018 0.002 TYR Q 9 ARG 0.005 0.001 ARG J 62 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 593 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 495 time to evaluate : 3.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 93 LEU cc_start: 0.7620 (mp) cc_final: 0.7271 (tp) REVERT: C 99 GLN cc_start: 0.5227 (mt0) cc_final: 0.4621 (tm-30) REVERT: C 106 LYS cc_start: 0.8295 (mttp) cc_final: 0.7434 (mmmt) REVERT: C 133 MET cc_start: 0.8643 (mmm) cc_final: 0.8280 (mtm) REVERT: C 138 GLN cc_start: 0.8357 (tt0) cc_final: 0.7749 (pt0) REVERT: C 161 GLU cc_start: 0.7306 (tp30) cc_final: 0.6661 (pm20) REVERT: C 167 PHE cc_start: 0.8880 (p90) cc_final: 0.8445 (p90) REVERT: D 10 ARG cc_start: 0.7845 (ptt-90) cc_final: 0.6385 (tpt170) REVERT: D 99 ARG cc_start: 0.7429 (ttm-80) cc_final: 0.6885 (tpt170) REVERT: D 112 LEU cc_start: 0.7659 (mt) cc_final: 0.7432 (mt) REVERT: D 113 VAL cc_start: 0.7607 (t) cc_final: 0.7385 (t) REVERT: D 126 ASP cc_start: 0.7733 (OUTLIER) cc_final: 0.6552 (p0) REVERT: D 177 VAL cc_start: 0.8830 (t) cc_final: 0.8403 (p) REVERT: E 36 TYR cc_start: 0.7262 (p90) cc_final: 0.6949 (p90) REVERT: E 66 ASP cc_start: 0.8695 (OUTLIER) cc_final: 0.8061 (p0) REVERT: E 91 GLU cc_start: 0.7998 (tp30) cc_final: 0.7460 (tp30) REVERT: E 142 CYS cc_start: 0.8222 (m) cc_final: 0.7999 (m) REVERT: E 147 ASP cc_start: 0.7968 (m-30) cc_final: 0.7678 (m-30) REVERT: E 176 GLU cc_start: 0.6676 (mp0) cc_final: 0.6407 (mp0) REVERT: F 40 ARG cc_start: 0.8071 (mtp85) cc_final: 0.7071 (mtm180) REVERT: G 52 GLU cc_start: 0.7880 (mt-10) cc_final: 0.7607 (mt-10) REVERT: H 43 GLU cc_start: 0.8058 (mm-30) cc_final: 0.7288 (mm-30) REVERT: H 48 ASP cc_start: 0.8191 (t70) cc_final: 0.7888 (t0) REVERT: H 52 GLU cc_start: 0.7824 (tp30) cc_final: 0.7459 (tp30) REVERT: H 126 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7610 (tt0) REVERT: I 61 ASN cc_start: 0.8261 (t0) cc_final: 0.7661 (m-40) REVERT: I 65 GLN cc_start: 0.8430 (mt0) cc_final: 0.8165 (mp10) REVERT: I 66 GLN cc_start: 0.8241 (OUTLIER) cc_final: 0.7993 (pp30) REVERT: I 115 ARG cc_start: 0.7119 (ttm170) cc_final: 0.6504 (tmt170) REVERT: I 127 ASP cc_start: 0.8411 (OUTLIER) cc_final: 0.7740 (p0) REVERT: J 11 LYS cc_start: 0.7803 (mttt) cc_final: 0.7177 (mtpp) REVERT: J 42 LEU cc_start: 0.7322 (OUTLIER) cc_final: 0.6854 (tp) REVERT: J 45 GLU cc_start: 0.7463 (mt-10) cc_final: 0.7195 (mt-10) REVERT: J 46 LYS cc_start: 0.8527 (mtmm) cc_final: 0.7870 (ttpt) REVERT: J 82 LYS cc_start: 0.7966 (OUTLIER) cc_final: 0.7759 (tttt) REVERT: K 82 LYS cc_start: 0.7743 (mtmm) cc_final: 0.7523 (mtmm) REVERT: L 31 ARG cc_start: 0.7915 (OUTLIER) cc_final: 0.7333 (ptt-90) REVERT: L 76 GLU cc_start: 0.7921 (mm-30) cc_final: 0.7525 (mm-30) REVERT: L 77 HIS cc_start: 0.8245 (m-70) cc_final: 0.7760 (m90) REVERT: M 16 GLU cc_start: 0.7747 (tt0) cc_final: 0.7455 (tt0) REVERT: M 31 ASN cc_start: 0.8044 (m110) cc_final: 0.7793 (m-40) REVERT: M 32 GLU cc_start: 0.8471 (tm-30) cc_final: 0.8187 (tm-30) REVERT: M 65 LYS cc_start: 0.6336 (mptt) cc_final: 0.5993 (mttt) REVERT: M 80 ARG cc_start: 0.7927 (ptt90) cc_final: 0.7262 (ppt170) REVERT: M 90 LEU cc_start: 0.7754 (OUTLIER) cc_final: 0.7494 (mp) REVERT: M 108 ARG cc_start: 0.6414 (mmt180) cc_final: 0.5669 (mmp-170) REVERT: N 4 LYS cc_start: 0.7481 (mmtt) cc_final: 0.7018 (mtpt) REVERT: N 21 TYR cc_start: 0.8358 (p90) cc_final: 0.7435 (p90) REVERT: N 47 MET cc_start: 0.7524 (mmt) cc_final: 0.6912 (mmt) REVERT: N 52 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.7131 (mp0) REVERT: O 14 GLN cc_start: 0.7838 (tt0) cc_final: 0.7575 (tt0) REVERT: P 17 GLN cc_start: 0.8140 (mp10) cc_final: 0.6705 (tp40) REVERT: P 44 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.8094 (mm-30) REVERT: P 90 GLU cc_start: 0.7176 (OUTLIER) cc_final: 0.6772 (pm20) REVERT: Q 43 ARG cc_start: 0.8633 (mtt90) cc_final: 0.8339 (mtt90) REVERT: Q 96 LYS cc_start: 0.9046 (mttm) cc_final: 0.8639 (mmmt) REVERT: R 39 ARG cc_start: 0.8154 (mmt90) cc_final: 0.7625 (mmm-85) REVERT: R 49 ARG cc_start: 0.8077 (mtt-85) cc_final: 0.7258 (ttm110) REVERT: R 59 GLN cc_start: 0.7492 (mt0) cc_final: 0.7065 (mt0) REVERT: S 16 LEU cc_start: 0.8119 (tp) cc_final: 0.7530 (pp) REVERT: S 17 LYS cc_start: 0.6851 (tttt) cc_final: 0.6122 (tmtt) REVERT: S 21 VAL cc_start: 0.7362 (OUTLIER) cc_final: 0.6961 (m) REVERT: S 25 LYS cc_start: 0.6887 (mmmt) cc_final: 0.6455 (mptt) REVERT: T 19 LEU cc_start: 0.8280 (mm) cc_final: 0.7898 (mm) REVERT: T 54 THR cc_start: 0.8390 (m) cc_final: 0.8047 (p) REVERT: U 12 MET cc_start: 0.7579 (mmm) cc_final: 0.6721 (mmt) outliers start: 98 outliers final: 72 residues processed: 548 average time/residue: 0.6528 time to fit residues: 560.8267 Evaluate side-chains 573 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 488 time to evaluate : 2.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 126 ASP Chi-restraints excluded: chain D residue 129 SER Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 66 ASP Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 152 SER Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 3 ILE Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 70 ASP Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 80 LEU Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 48 GLU Chi-restraints excluded: chain G residue 94 ASP Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain G residue 149 ARG Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 107 SER Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 126 GLU Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 66 GLN Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain I residue 125 THR Chi-restraints excluded: chain I residue 127 ASP Chi-restraints excluded: chain J residue 15 HIS Chi-restraints excluded: chain J residue 18 ILE Chi-restraints excluded: chain J residue 19 ASP Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 66 GLU Chi-restraints excluded: chain J residue 82 LYS Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 114 LEU Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 31 ARG Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain L residue 115 SER Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 49 THR Chi-restraints excluded: chain M residue 64 LEU Chi-restraints excluded: chain M residue 69 ASP Chi-restraints excluded: chain M residue 90 LEU Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain N residue 52 GLU Chi-restraints excluded: chain O residue 11 ILE Chi-restraints excluded: chain O residue 73 VAL Chi-restraints excluded: chain P residue 24 ASP Chi-restraints excluded: chain P residue 44 GLU Chi-restraints excluded: chain P residue 90 GLU Chi-restraints excluded: chain P residue 92 THR Chi-restraints excluded: chain Q residue 45 SER Chi-restraints excluded: chain Q residue 79 THR Chi-restraints excluded: chain Q residue 90 LEU Chi-restraints excluded: chain R residue 40 THR Chi-restraints excluded: chain R residue 63 ASP Chi-restraints excluded: chain S residue 11 VAL Chi-restraints excluded: chain S residue 21 VAL Chi-restraints excluded: chain S residue 29 GLN Chi-restraints excluded: chain S residue 35 SER Chi-restraints excluded: chain S residue 38 SER Chi-restraints excluded: chain S residue 49 PHE Chi-restraints excluded: chain S residue 66 MET Chi-restraints excluded: chain T residue 26 SER Chi-restraints excluded: chain T residue 28 LEU Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain T residue 57 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 284 optimal weight: 0.7980 chunk 299 optimal weight: 0.9980 chunk 272 optimal weight: 1.9990 chunk 291 optimal weight: 1.9990 chunk 175 optimal weight: 3.9990 chunk 126 optimal weight: 6.9990 chunk 228 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 262 optimal weight: 0.7980 chunk 275 optimal weight: 1.9990 chunk 289 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 68 HIS ** D 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 106 ASN K 110 GLN ** L 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 7 GLN O 37 GLN P 50 GLN Q 65 ASN ** R 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 60 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.4123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 48853 Z= 0.172 Angle : 0.616 13.677 72784 Z= 0.312 Chirality : 0.035 0.271 9274 Planarity : 0.004 0.054 4082 Dihedral : 24.684 178.716 23938 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.84 % Allowed : 6.53 % Favored : 92.63 % Rotamer: Outliers : 4.79 % Allowed : 24.66 % Favored : 70.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % 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: -0.73 (0.19), residues: 1900 helix: 1.12 (0.19), residues: 743 sheet: -0.76 (0.28), residues: 352 loop : -1.92 (0.21), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP P 80 HIS 0.007 0.001 HIS S 52 PHE 0.023 0.002 PHE C 167 TYR 0.025 0.002 TYR Q 9 ARG 0.007 0.000 ARG O 84 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 565 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 487 time to evaluate : 2.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 93 LEU cc_start: 0.7683 (mp) cc_final: 0.7338 (tp) REVERT: C 99 GLN cc_start: 0.5379 (mt0) cc_final: 0.4784 (tm-30) REVERT: C 106 LYS cc_start: 0.8283 (mttp) cc_final: 0.7428 (mmmt) REVERT: C 133 MET cc_start: 0.8594 (mmm) cc_final: 0.8366 (mtm) REVERT: C 138 GLN cc_start: 0.8375 (tt0) cc_final: 0.7748 (pt0) REVERT: C 161 GLU cc_start: 0.7207 (tp30) cc_final: 0.6598 (pm20) REVERT: C 167 PHE cc_start: 0.8860 (p90) cc_final: 0.8410 (p90) REVERT: C 187 TYR cc_start: 0.8063 (t80) cc_final: 0.7741 (t80) REVERT: D 10 ARG cc_start: 0.7786 (ptt-90) cc_final: 0.6371 (tpt170) REVERT: D 99 ARG cc_start: 0.7413 (ttm-80) cc_final: 0.6882 (tpt170) REVERT: D 112 LEU cc_start: 0.7653 (mt) cc_final: 0.7425 (mt) REVERT: D 113 VAL cc_start: 0.7591 (t) cc_final: 0.7348 (t) REVERT: D 126 ASP cc_start: 0.7703 (OUTLIER) cc_final: 0.6527 (p0) REVERT: D 177 VAL cc_start: 0.8788 (t) cc_final: 0.8388 (p) REVERT: E 36 TYR cc_start: 0.7293 (p90) cc_final: 0.6956 (p90) REVERT: E 66 ASP cc_start: 0.8695 (OUTLIER) cc_final: 0.8129 (p0) REVERT: E 70 MET cc_start: 0.7954 (mmm) cc_final: 0.7519 (mmp) REVERT: E 91 GLU cc_start: 0.8072 (tp30) cc_final: 0.7479 (tp30) REVERT: E 142 CYS cc_start: 0.8175 (m) cc_final: 0.7937 (m) REVERT: E 147 ASP cc_start: 0.7914 (m-30) cc_final: 0.7595 (m-30) REVERT: E 176 GLU cc_start: 0.6683 (mp0) cc_final: 0.6431 (mp0) REVERT: F 40 ARG cc_start: 0.8068 (mtp85) cc_final: 0.7034 (mtm180) REVERT: G 37 SER cc_start: 0.8505 (t) cc_final: 0.8287 (m) REVERT: G 104 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8464 (tt) REVERT: H 31 LYS cc_start: 0.8453 (ttpt) cc_final: 0.7987 (ptmt) REVERT: H 38 GLU cc_start: 0.8491 (mm-30) cc_final: 0.7908 (mm-30) REVERT: H 43 GLU cc_start: 0.8053 (mm-30) cc_final: 0.7292 (mm-30) REVERT: H 48 ASP cc_start: 0.8177 (t70) cc_final: 0.7848 (t0) REVERT: H 52 GLU cc_start: 0.7778 (tp30) cc_final: 0.7435 (tp30) REVERT: H 126 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7546 (tt0) REVERT: I 61 ASN cc_start: 0.8241 (t0) cc_final: 0.7679 (m-40) REVERT: I 65 GLN cc_start: 0.8439 (mt0) cc_final: 0.8170 (mp10) REVERT: I 66 GLN cc_start: 0.8220 (OUTLIER) cc_final: 0.7974 (pp30) REVERT: I 115 ARG cc_start: 0.7159 (ttm170) cc_final: 0.6546 (tmt170) REVERT: I 127 ASP cc_start: 0.8368 (OUTLIER) cc_final: 0.7698 (p0) REVERT: J 10 LEU cc_start: 0.8317 (mp) cc_final: 0.8018 (mm) REVERT: J 11 LYS cc_start: 0.7527 (mttt) cc_final: 0.7074 (mtpp) REVERT: J 42 LEU cc_start: 0.7361 (OUTLIER) cc_final: 0.6910 (tp) REVERT: J 46 LYS cc_start: 0.8504 (mtmm) cc_final: 0.7860 (ttpt) REVERT: J 62 ARG cc_start: 0.7613 (mmt90) cc_final: 0.7322 (mpt180) REVERT: K 82 LYS cc_start: 0.7763 (mtmm) cc_final: 0.7526 (mtmm) REVERT: L 31 ARG cc_start: 0.7828 (OUTLIER) cc_final: 0.7421 (ptt-90) REVERT: L 76 GLU cc_start: 0.7948 (mm-30) cc_final: 0.7489 (mm-30) REVERT: L 77 HIS cc_start: 0.8256 (m-70) cc_final: 0.7757 (m90) REVERT: L 107 VAL cc_start: 0.8616 (t) cc_final: 0.8393 (m) REVERT: M 16 GLU cc_start: 0.7723 (tt0) cc_final: 0.7402 (tt0) REVERT: M 31 ASN cc_start: 0.8023 (m110) cc_final: 0.7714 (m-40) REVERT: M 32 GLU cc_start: 0.8476 (tm-30) cc_final: 0.8236 (tm-30) REVERT: M 65 LYS cc_start: 0.6119 (mptt) cc_final: 0.5845 (mttt) REVERT: M 80 ARG cc_start: 0.7879 (ptt90) cc_final: 0.7245 (ppt170) REVERT: M 90 LEU cc_start: 0.7761 (OUTLIER) cc_final: 0.7511 (mp) REVERT: M 108 ARG cc_start: 0.6375 (mmt180) cc_final: 0.5632 (mmp-170) REVERT: N 4 LYS cc_start: 0.7412 (mmtt) cc_final: 0.6967 (mtpt) REVERT: N 21 TYR cc_start: 0.8383 (p90) cc_final: 0.7536 (p90) REVERT: N 47 MET cc_start: 0.7571 (mmt) cc_final: 0.6946 (mmt) REVERT: N 52 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.7163 (mp0) REVERT: O 14 GLN cc_start: 0.7758 (tt0) cc_final: 0.7471 (tt0) REVERT: P 17 GLN cc_start: 0.8085 (mp10) cc_final: 0.6636 (tp40) REVERT: P 44 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.7899 (mm-30) REVERT: P 90 GLU cc_start: 0.7161 (OUTLIER) cc_final: 0.6845 (pm20) REVERT: Q 43 ARG cc_start: 0.8533 (mtt90) cc_final: 0.8239 (mtt90) REVERT: Q 96 LYS cc_start: 0.9025 (mttm) cc_final: 0.8663 (mmmt) REVERT: R 39 ARG cc_start: 0.8148 (mmt90) cc_final: 0.7620 (mmm-85) REVERT: R 48 ILE cc_start: 0.8798 (mt) cc_final: 0.8532 (mp) REVERT: R 49 ARG cc_start: 0.8047 (mtt-85) cc_final: 0.7266 (ttm110) REVERT: R 59 GLN cc_start: 0.7468 (mt0) cc_final: 0.7066 (mt0) REVERT: S 16 LEU cc_start: 0.8187 (tp) cc_final: 0.7608 (pp) REVERT: S 17 LYS cc_start: 0.6835 (tttt) cc_final: 0.6097 (tmtt) REVERT: S 21 VAL cc_start: 0.7366 (OUTLIER) cc_final: 0.7013 (m) REVERT: S 25 LYS cc_start: 0.6899 (mmmt) cc_final: 0.6500 (mptt) REVERT: S 47 HIS cc_start: 0.7937 (t70) cc_final: 0.6792 (m-70) REVERT: T 19 LEU cc_start: 0.8259 (mm) cc_final: 0.7886 (mm) REVERT: T 54 THR cc_start: 0.8280 (m) cc_final: 0.7922 (p) REVERT: U 12 MET cc_start: 0.7556 (mmm) cc_final: 0.6729 (mmt) outliers start: 78 outliers final: 59 residues processed: 526 average time/residue: 0.6579 time to fit residues: 542.8320 Evaluate side-chains 558 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 486 time to evaluate : 2.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 126 ASP Chi-restraints excluded: chain D residue 129 SER Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 66 ASP Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 152 SER Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 3 ILE Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 80 LEU Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 94 ASP Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 149 ARG Chi-restraints excluded: chain H residue 42 ARG Chi-restraints excluded: chain H residue 107 SER Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 126 GLU Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 66 GLN Chi-restraints excluded: chain I residue 127 ASP Chi-restraints excluded: chain J residue 15 HIS Chi-restraints excluded: chain J residue 18 ILE Chi-restraints excluded: chain J residue 19 ASP Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 66 GLU Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 114 LEU Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 31 ARG Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 79 MET Chi-restraints excluded: chain L residue 94 ARG Chi-restraints excluded: chain L residue 115 SER Chi-restraints excluded: chain M residue 64 LEU Chi-restraints excluded: chain M residue 69 ASP Chi-restraints excluded: chain M residue 90 LEU Chi-restraints excluded: chain N residue 15 LYS Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain N residue 52 GLU Chi-restraints excluded: chain O residue 11 ILE Chi-restraints excluded: chain O residue 73 VAL Chi-restraints excluded: chain P residue 24 ASP Chi-restraints excluded: chain P residue 44 GLU Chi-restraints excluded: chain P residue 90 GLU Chi-restraints excluded: chain P residue 92 THR Chi-restraints excluded: chain Q residue 65 ASN Chi-restraints excluded: chain Q residue 79 THR Chi-restraints excluded: chain Q residue 90 LEU Chi-restraints excluded: chain R residue 63 ASP Chi-restraints excluded: chain S residue 21 VAL Chi-restraints excluded: chain S residue 29 GLN Chi-restraints excluded: chain S residue 35 SER Chi-restraints excluded: chain S residue 49 PHE Chi-restraints excluded: chain S residue 66 MET Chi-restraints excluded: chain T residue 26 SER Chi-restraints excluded: chain T residue 57 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 191 optimal weight: 1.9990 chunk 307 optimal weight: 0.0270 chunk 187 optimal weight: 2.9990 chunk 145 optimal weight: 9.9990 chunk 213 optimal weight: 0.9980 chunk 322 optimal weight: 1.9990 chunk 297 optimal weight: 0.9990 chunk 257 optimal weight: 0.2980 chunk 26 optimal weight: 5.9990 chunk 198 optimal weight: 0.9980 chunk 157 optimal weight: 6.9990 overall best weight: 0.6640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 68 HIS D 54 GLN G 106 ASN K 110 GLN ** L 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 37 GLN ** Q 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 59 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.4487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 48853 Z= 0.130 Angle : 0.563 12.903 72784 Z= 0.284 Chirality : 0.032 0.256 9274 Planarity : 0.004 0.054 4082 Dihedral : 24.509 179.799 23938 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.79 % Allowed : 6.37 % Favored : 92.84 % Rotamer: Outliers : 4.17 % Allowed : 25.40 % Favored : 70.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % 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: -0.42 (0.20), residues: 1900 helix: 1.42 (0.19), residues: 750 sheet: -0.62 (0.29), residues: 334 loop : -1.81 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 18 HIS 0.006 0.001 HIS J 56 PHE 0.021 0.001 PHE C 167 TYR 0.021 0.001 TYR Q 9 ARG 0.005 0.000 ARG R 51 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 505 time to evaluate : 2.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 17 GLU cc_start: 0.6609 (OUTLIER) cc_final: 0.6065 (pm20) REVERT: C 93 LEU cc_start: 0.7665 (mp) cc_final: 0.7392 (tp) REVERT: C 99 GLN cc_start: 0.5424 (mt0) cc_final: 0.4802 (tm-30) REVERT: C 106 LYS cc_start: 0.8168 (mttp) cc_final: 0.7293 (mmmt) REVERT: C 133 MET cc_start: 0.8604 (mmm) cc_final: 0.8302 (mtt) REVERT: C 138 GLN cc_start: 0.8328 (tt0) cc_final: 0.7729 (pt0) REVERT: C 161 GLU cc_start: 0.7391 (tp30) cc_final: 0.6781 (pm20) REVERT: C 167 PHE cc_start: 0.8690 (p90) cc_final: 0.8310 (p90) REVERT: C 170 GLU cc_start: 0.6800 (tt0) cc_final: 0.6532 (mt-10) REVERT: C 187 TYR cc_start: 0.7964 (t80) cc_final: 0.7699 (t80) REVERT: D 10 ARG cc_start: 0.7494 (ptt-90) cc_final: 0.6082 (tpt170) REVERT: D 99 ARG cc_start: 0.7199 (ttm-80) cc_final: 0.6772 (tpt170) REVERT: D 108 MET cc_start: 0.7307 (ttt) cc_final: 0.7012 (ttp) REVERT: D 113 VAL cc_start: 0.7428 (t) cc_final: 0.7190 (t) REVERT: D 126 ASP cc_start: 0.7675 (OUTLIER) cc_final: 0.6725 (p0) REVERT: D 177 VAL cc_start: 0.8744 (t) cc_final: 0.8389 (p) REVERT: E 36 TYR cc_start: 0.7250 (p90) cc_final: 0.6900 (p90) REVERT: E 66 ASP cc_start: 0.8674 (OUTLIER) cc_final: 0.8076 (p0) REVERT: E 91 GLU cc_start: 0.7891 (tp30) cc_final: 0.7308 (tp30) REVERT: E 111 GLN cc_start: 0.9219 (tt0) cc_final: 0.9013 (tt0) REVERT: E 120 MET cc_start: 0.7639 (OUTLIER) cc_final: 0.7382 (ttp) REVERT: E 142 CYS cc_start: 0.8071 (m) cc_final: 0.7815 (m) REVERT: E 147 ASP cc_start: 0.7917 (m-30) cc_final: 0.7601 (m-30) REVERT: E 176 GLU cc_start: 0.6558 (mp0) cc_final: 0.6305 (mp0) REVERT: E 187 GLU cc_start: 0.6830 (tp30) cc_final: 0.6373 (pp20) REVERT: F 1 MET cc_start: 0.5248 (mmt) cc_final: 0.4752 (mmm) REVERT: F 40 ARG cc_start: 0.8125 (mtp85) cc_final: 0.7071 (mtm180) REVERT: F 44 TYR cc_start: 0.7399 (p90) cc_final: 0.6898 (p90) REVERT: G 90 GLU cc_start: 0.7424 (tp30) cc_final: 0.7157 (pm20) REVERT: H 31 LYS cc_start: 0.8352 (ttpt) cc_final: 0.8056 (ptmt) REVERT: H 38 GLU cc_start: 0.8483 (mm-30) cc_final: 0.8220 (tp30) REVERT: H 43 GLU cc_start: 0.8017 (mm-30) cc_final: 0.7411 (tp30) REVERT: H 48 ASP cc_start: 0.8068 (t70) cc_final: 0.7790 (t0) REVERT: H 52 GLU cc_start: 0.7618 (tp30) cc_final: 0.7291 (tp30) REVERT: I 61 ASN cc_start: 0.8310 (t0) cc_final: 0.7760 (m-40) REVERT: I 65 GLN cc_start: 0.8420 (mt0) cc_final: 0.8118 (mp10) REVERT: I 115 ARG cc_start: 0.7003 (ttm170) cc_final: 0.6333 (tmt170) REVERT: I 127 ASP cc_start: 0.8268 (OUTLIER) cc_final: 0.7820 (p0) REVERT: J 10 LEU cc_start: 0.8406 (mp) cc_final: 0.8104 (mm) REVERT: J 11 LYS cc_start: 0.7351 (mttt) cc_final: 0.7076 (mtpp) REVERT: J 42 LEU cc_start: 0.7414 (OUTLIER) cc_final: 0.6932 (tp) REVERT: J 46 LYS cc_start: 0.8404 (mtmm) cc_final: 0.7835 (ttpt) REVERT: K 82 LYS cc_start: 0.7929 (mtmm) cc_final: 0.7676 (mtmm) REVERT: L 73 ASN cc_start: 0.7355 (p0) cc_final: 0.7001 (p0) REVERT: L 77 HIS cc_start: 0.8325 (m-70) cc_final: 0.8005 (m90) REVERT: L 105 GLN cc_start: 0.7760 (mt0) cc_final: 0.7391 (mt0) REVERT: L 107 VAL cc_start: 0.8596 (t) cc_final: 0.8343 (m) REVERT: M 32 GLU cc_start: 0.8397 (tm-30) cc_final: 0.8151 (tm-30) REVERT: M 80 ARG cc_start: 0.8154 (ptt90) cc_final: 0.7460 (ppt170) REVERT: M 90 LEU cc_start: 0.7813 (OUTLIER) cc_final: 0.7571 (mp) REVERT: M 108 ARG cc_start: 0.6436 (mmt180) cc_final: 0.5614 (mmp-170) REVERT: N 4 LYS cc_start: 0.7564 (mmtt) cc_final: 0.7101 (mtpt) REVERT: N 21 TYR cc_start: 0.8427 (p90) cc_final: 0.7634 (p90) REVERT: N 36 LYS cc_start: 0.8405 (ptmt) cc_final: 0.8046 (ptmm) REVERT: N 47 MET cc_start: 0.7557 (mmt) cc_final: 0.7006 (mmt) REVERT: N 52 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.6671 (mp0) REVERT: O 14 GLN cc_start: 0.7798 (tt0) cc_final: 0.7503 (tt0) REVERT: O 17 LEU cc_start: 0.7932 (mt) cc_final: 0.7547 (pt) REVERT: P 7 LEU cc_start: 0.8258 (mp) cc_final: 0.7929 (mm) REVERT: P 17 GLN cc_start: 0.8040 (mp10) cc_final: 0.6793 (tp40) REVERT: P 39 ARG cc_start: 0.8414 (ptp90) cc_final: 0.8083 (ptp90) REVERT: P 44 GLU cc_start: 0.8660 (OUTLIER) cc_final: 0.8323 (mt-10) REVERT: P 50 GLN cc_start: 0.7751 (mt0) cc_final: 0.6624 (tm-30) REVERT: P 90 GLU cc_start: 0.6813 (OUTLIER) cc_final: 0.6559 (pm20) REVERT: Q 19 ARG cc_start: 0.8115 (mtp85) cc_final: 0.7836 (mtp85) REVERT: Q 96 LYS cc_start: 0.8987 (mttm) cc_final: 0.8656 (mmmt) REVERT: R 39 ARG cc_start: 0.7941 (mmt90) cc_final: 0.7533 (mmm-85) REVERT: R 48 ILE cc_start: 0.8789 (mt) cc_final: 0.8496 (mp) REVERT: R 49 ARG cc_start: 0.8021 (mtt-85) cc_final: 0.7246 (ttm110) REVERT: S 16 LEU cc_start: 0.8149 (tp) cc_final: 0.7494 (pp) REVERT: S 17 LYS cc_start: 0.6774 (tttt) cc_final: 0.6279 (tppt) REVERT: S 25 LYS cc_start: 0.7043 (mmmt) cc_final: 0.6660 (mptt) REVERT: S 47 HIS cc_start: 0.8033 (t70) cc_final: 0.7091 (m-70) REVERT: T 5 LYS cc_start: 0.6659 (ptpp) cc_final: 0.6425 (mtmm) REVERT: T 19 LEU cc_start: 0.8205 (mm) cc_final: 0.7832 (mm) REVERT: T 54 THR cc_start: 0.8187 (m) cc_final: 0.7864 (p) REVERT: U 12 MET cc_start: 0.7549 (mmm) cc_final: 0.6715 (mmt) outliers start: 68 outliers final: 45 residues processed: 536 average time/residue: 0.6433 time to fit residues: 537.9862 Evaluate side-chains 537 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 482 time to evaluate : 2.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain D residue 54 GLN Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 126 ASP Chi-restraints excluded: chain D residue 129 SER Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 66 ASP Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 152 SER Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 3 ILE Chi-restraints excluded: chain F residue 80 LEU Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 94 ASP Chi-restraints excluded: chain G residue 149 ARG Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 127 ASP Chi-restraints excluded: chain J residue 19 ASP Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 66 GLU Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain K residue 32 ILE Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain K residue 114 LEU Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 94 ARG Chi-restraints excluded: chain L residue 115 SER Chi-restraints excluded: chain M residue 49 THR Chi-restraints excluded: chain M residue 64 LEU Chi-restraints excluded: chain M residue 69 ASP Chi-restraints excluded: chain M residue 70 LEU Chi-restraints excluded: chain M residue 90 LEU Chi-restraints excluded: chain N residue 52 GLU Chi-restraints excluded: chain O residue 11 ILE Chi-restraints excluded: chain O residue 73 VAL Chi-restraints excluded: chain P residue 44 GLU Chi-restraints excluded: chain P residue 80 TRP Chi-restraints excluded: chain P residue 90 GLU Chi-restraints excluded: chain P residue 92 THR Chi-restraints excluded: chain Q residue 79 THR Chi-restraints excluded: chain S residue 29 GLN Chi-restraints excluded: chain S residue 35 SER Chi-restraints excluded: chain S residue 49 PHE Chi-restraints excluded: chain S residue 66 MET Chi-restraints excluded: chain T residue 26 SER Chi-restraints excluded: chain T residue 57 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 204 optimal weight: 4.9990 chunk 273 optimal weight: 0.9990 chunk 78 optimal weight: 5.9990 chunk 237 optimal weight: 0.0070 chunk 37 optimal weight: 9.9990 chunk 71 optimal weight: 5.9990 chunk 257 optimal weight: 10.0000 chunk 107 optimal weight: 8.9990 chunk 264 optimal weight: 6.9990 chunk 32 optimal weight: 6.9990 chunk 47 optimal weight: 8.9990 overall best weight: 3.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 68 HIS F 49 HIS G 106 ASN K 110 GLN ** L 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 77 HIS ** M 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 37 GLN ** Q 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 56 ASN ** R 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.128694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.107392 restraints weight = 85266.055| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 1.05 r_work: 0.3143 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.4499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.400 48853 Z= 0.277 Angle : 0.643 65.886 72784 Z= 0.344 Chirality : 0.035 0.258 9274 Planarity : 0.005 0.243 4082 Dihedral : 24.508 179.886 23938 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.79 % Allowed : 6.37 % Favored : 92.84 % Rotamer: Outliers : 3.87 % Allowed : 25.83 % Favored : 70.31 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % 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: -0.44 (0.20), residues: 1900 helix: 1.40 (0.19), residues: 750 sheet: -0.61 (0.29), residues: 334 loop : -1.81 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 18 HIS 0.006 0.001 HIS J 56 PHE 0.019 0.002 PHE C 167 TYR 0.018 0.001 TYR Q 9 ARG 0.004 0.000 ARG R 51 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10674.04 seconds wall clock time: 196 minutes 16.20 seconds (11776.20 seconds total)