Starting phenix.real_space_refine on Fri Feb 16 02:37:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dni_30784/02_2024/7dni_30784.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dni_30784/02_2024/7dni_30784.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dni_30784/02_2024/7dni_30784.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dni_30784/02_2024/7dni_30784.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dni_30784/02_2024/7dni_30784.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dni_30784/02_2024/7dni_30784.pdb" } resolution = 3.2 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= 0.005 sd= 0.074 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: 4 Type Number sf(0) Gaussians S 56 5.16 5 C 8930 2.51 5 N 2427 2.21 5 O 2664 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H GLU 16": "OE1" <-> "OE2" Residue "H ASP 32": "OD1" <-> "OD2" Residue "H ARG 42": "NH1" <-> "NH2" Residue "H ASP 52": "OD1" <-> "OD2" Residue "F GLU 51": "OE1" <-> "OE2" Residue "J ASP 39": "OD1" <-> "OD2" Residue "J ARG 42": "NH1" <-> "NH2" Residue "J TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 52": "OD1" <-> "OD2" Residue "K GLU 64": "OE1" <-> "OE2" Residue "A GLU 9": "OE1" <-> "OE2" Residue "A PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 19": "NH1" <-> "NH2" Residue "A TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 33": "OD1" <-> "OD2" Residue "A GLU 78": "OE1" <-> "OE2" Residue "A ARG 93": "NH1" <-> "NH2" Residue "A ARG 132": "NH1" <-> "NH2" Residue "A GLU 140": "OE1" <-> "OE2" Residue "A ARG 149": "NH1" <-> "NH2" Residue "A GLU 175": "OE1" <-> "OE2" Residue "B TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 93": "NH1" <-> "NH2" Residue "B ASP 101": "OD1" <-> "OD2" Residue "B ARG 149": "NH1" <-> "NH2" Residue "B GLU 161": "OE1" <-> "OE2" Residue "C TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 29": "OE1" <-> "OE2" Residue "C GLU 67": "OE1" <-> "OE2" Residue "C ARG 93": "NH1" <-> "NH2" Residue "C GLU 98": "OE1" <-> "OE2" Residue "C ASP 112": "OD1" <-> "OD2" Residue "C ASP 133": "OD1" <-> "OD2" Residue "C GLU 156": "OE1" <-> "OE2" Residue "C GLU 161": "OE1" <-> "OE2" Residue "C GLU 175": "OE1" <-> "OE2" Residue "C GLU 196": "OE1" <-> "OE2" Residue "D TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 33": "OD1" <-> "OD2" Residue "D PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 93": "NH1" <-> "NH2" Residue "D GLU 98": "OE1" <-> "OE2" Residue "D ASP 101": "OD1" <-> "OD2" Residue "D ASP 127": "OD1" <-> "OD2" Residue "D ASP 148": "OD1" <-> "OD2" Residue "D GLU 166": "OE1" <-> "OE2" Residue "E PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 51": "OE1" <-> "OE2" Residue "E TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 51": "OE1" <-> "OE2" Residue "G ASP 58": "OD1" <-> "OD2" Residue "G ARG 74": "NH1" <-> "NH2" Residue "I PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 21": "OD1" <-> "OD2" Residue "L ASP 52": "OD1" <-> "OD2" Residue "L ARG 72": "NH1" <-> "NH2" Residue "M PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 40": "OD1" <-> "OD2" Residue "M ASP 53": "OD1" <-> "OD2" Residue "M TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 87": "OE1" <-> "OE2" Residue "M TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 6": "OD1" <-> "OD2" Residue "N TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 40": "OD1" <-> "OD2" Residue "N ASP 53": "OD1" <-> "OD2" Residue "N GLU 87": "OE1" <-> "OE2" Residue "N TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 5": "OE1" <-> "OE2" Residue "O ASP 53": "OD1" <-> "OD2" Residue "O TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 38": "OD1" <-> "OD2" Residue "P ASP 53": "OD1" <-> "OD2" Residue "P ASP 83": "OD1" <-> "OD2" Residue "P ASP 86": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 14077 Number of models: 1 Model: "" Number of chains: 16 Chain: "H" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 582 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "F" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 582 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "J" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 582 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "K" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 582 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "A" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1594 Classifications: {'peptide': 199} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 191} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 1582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1582 Classifications: {'peptide': 198} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 7, 'TRANS': 190} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 1567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1567 Classifications: {'peptide': 197} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 7, 'TRANS': 189} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "D" Number of atoms: 1570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1570 Classifications: {'peptide': 197} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 7, 'TRANS': 189} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "E" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 574 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 3, 'TRANS': 68} Chain: "G" Number of atoms: 593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 593 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain: "I" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 574 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 3, 'TRANS': 68} Chain: "L" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 582 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "M" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 780 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 91} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "N" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 780 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 91} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "O" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 773 Classifications: {'peptide': 96} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 91} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "P" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 780 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 91} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Residues with excluded nonbonded symmetry interactions: 5 residue: pdb=" N LEU H 73 " occ=0.45 ... (6 atoms not shown) pdb=" CD2 LEU H 73 " occ=0.45 residue: pdb=" N LEU F 73 " occ=0.45 ... (6 atoms not shown) pdb=" CD2 LEU F 73 " occ=0.45 residue: pdb=" N LEU J 73 " occ=0.45 ... (6 atoms not shown) pdb=" CD2 LEU J 73 " occ=0.45 residue: pdb=" N LEU G 73 " occ=0.45 ... (6 atoms not shown) pdb=" CD2 LEU G 73 " occ=0.45 residue: pdb=" N LEU L 73 " occ=0.45 ... (6 atoms not shown) pdb=" CD2 LEU L 73 " occ=0.45 Time building chain proxies: 7.46, per 1000 atoms: 0.53 Number of scatterers: 14077 At special positions: 0 Unit cell: (105.545, 117.04, 113.905, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 56 16.00 O 2664 8.00 N 2427 7.00 C 8930 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.40 Conformation dependent library (CDL) restraints added in 2.4 seconds 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3362 Finding SS restraints... Secondary structure from input PDB file: 105 helices and 8 sheets defined 66.6% alpha, 7.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.45 Creating SS restraints... Processing helix chain 'H' and resid 22 through 34 removed outlier: 3.553A pdb=" N ASP H 32 " --> pdb=" O ALA H 28 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 60 Processing helix chain 'F' and resid 22 through 34 removed outlier: 3.577A pdb=" N GLN F 31 " --> pdb=" O LYS F 27 " (cutoff:3.500A) Processing helix chain 'F' and resid 37 through 39 No H-bonds generated for 'chain 'F' and resid 37 through 39' Processing helix chain 'F' and resid 55 through 60 Processing helix chain 'J' and resid 22 through 35 Processing helix chain 'J' and resid 37 through 41 Processing helix chain 'J' and resid 55 through 60 removed outlier: 3.856A pdb=" N TYR J 59 " --> pdb=" O THR J 55 " (cutoff:3.500A) Processing helix chain 'K' and resid 22 through 35 removed outlier: 3.631A pdb=" N GLN K 31 " --> pdb=" O LYS K 27 " (cutoff:3.500A) Processing helix chain 'K' and resid 55 through 60 Processing helix chain 'A' and resid 7 through 18 removed outlier: 3.846A pdb=" N PHE A 11 " --> pdb=" O THR A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 18 through 26 removed outlier: 4.609A pdb=" N MET A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N TYR A 25 " --> pdb=" O ARG A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 32 Processing helix chain 'A' and resid 39 through 68 removed outlier: 3.547A pdb=" N ALA A 51 " --> pdb=" O GLN A 47 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N ASN A 55 " --> pdb=" O ALA A 51 " (cutoff:3.500A) removed outlier: 9.442A pdb=" N MET A 56 " --> pdb=" O THR A 52 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLN A 57 " --> pdb=" O SER A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 86 Processing helix chain 'A' and resid 88 through 94 removed outlier: 3.858A pdb=" N ALA A 92 " --> pdb=" O SER A 88 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N TYR A 94 " --> pdb=" O LEU A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 129 Proline residue: A 123 - end of helix Processing helix chain 'A' and resid 130 through 142 removed outlier: 5.128A pdb=" N ASP A 136 " --> pdb=" O ARG A 132 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LYS A 137 " --> pdb=" O ASP A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 156 removed outlier: 3.783A pdb=" N ASN A 150 " --> pdb=" O ILE A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 171 removed outlier: 3.689A pdb=" N GLY A 163 " --> pdb=" O GLY A 159 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LYS A 169 " --> pdb=" O ARG A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 174 No H-bonds generated for 'chain 'A' and resid 172 through 174' Processing helix chain 'A' and resid 176 through 187 removed outlier: 3.654A pdb=" N ASN A 183 " --> pdb=" O SER A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 199 removed outlier: 3.643A pdb=" N VAL A 194 " --> pdb=" O ASN A 190 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLN A 195 " --> pdb=" O ASN A 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 18 removed outlier: 3.829A pdb=" N PHE B 18 " --> pdb=" O LEU B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 23 removed outlier: 3.529A pdb=" N LYS B 23 " --> pdb=" O ARG B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 35 removed outlier: 3.667A pdb=" N VAL B 31 " --> pdb=" O GLN B 27 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU B 32 " --> pdb=" O VAL B 28 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N ASP B 33 " --> pdb=" O GLU B 29 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N TYR B 34 " --> pdb=" O PRO B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 54 removed outlier: 3.954A pdb=" N GLN B 45 " --> pdb=" O GLU B 41 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA B 51 " --> pdb=" O GLN B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 68 removed outlier: 3.601A pdb=" N GLU B 60 " --> pdb=" O MET B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 86 removed outlier: 3.597A pdb=" N GLU B 78 " --> pdb=" O GLY B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 96 removed outlier: 3.667A pdb=" N ALA B 92 " --> pdb=" O SER B 88 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N TYR B 94 " --> pdb=" O LEU B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 102 removed outlier: 4.280A pdb=" N ASP B 101 " --> pdb=" O GLU B 98 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU B 102 " --> pdb=" O LEU B 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 98 through 102' Processing helix chain 'B' and resid 104 through 121 Processing helix chain 'B' and resid 121 through 129 Processing helix chain 'B' and resid 134 through 142 removed outlier: 4.008A pdb=" N GLU B 140 " --> pdb=" O ASP B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 156 Processing helix chain 'B' and resid 159 through 171 removed outlier: 3.546A pdb=" N GLY B 163 " --> pdb=" O GLY B 159 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS B 169 " --> pdb=" O ARG B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 174 No H-bonds generated for 'chain 'B' and resid 172 through 174' Processing helix chain 'B' and resid 176 through 188 Processing helix chain 'B' and resid 190 through 199 removed outlier: 3.905A pdb=" N VAL B 194 " --> pdb=" O ASN B 190 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLN B 195 " --> pdb=" O ASN B 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 26 removed outlier: 3.802A pdb=" N ASN C 10 " --> pdb=" O SER C 6 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N ALA C 20 " --> pdb=" O SER C 16 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N ARG C 21 " --> pdb=" O CYS C 17 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N MET C 24 " --> pdb=" O ALA C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 32 removed outlier: 3.634A pdb=" N VAL C 31 " --> pdb=" O GLN C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 54 removed outlier: 3.879A pdb=" N GLN C 45 " --> pdb=" O GLU C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 69 removed outlier: 3.865A pdb=" N GLY C 69 " --> pdb=" O THR C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 86 removed outlier: 3.782A pdb=" N GLU C 78 " --> pdb=" O GLY C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 96 removed outlier: 3.550A pdb=" N ALA C 92 " --> pdb=" O SER C 88 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N TYR C 94 " --> pdb=" O LEU C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 121 Processing helix chain 'C' and resid 121 through 128 Processing helix chain 'C' and resid 130 through 134 Processing helix chain 'C' and resid 135 through 141 removed outlier: 3.666A pdb=" N GLU C 140 " --> pdb=" O ASP C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 156 Processing helix chain 'C' and resid 159 through 172 removed outlier: 3.980A pdb=" N VAL C 172 " --> pdb=" O LEU C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 188 Processing helix chain 'C' and resid 190 through 198 removed outlier: 3.712A pdb=" N VAL C 194 " --> pdb=" O ASN C 190 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN C 195 " --> pdb=" O ASN C 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 26 removed outlier: 5.819A pdb=" N ALA D 20 " --> pdb=" O SER D 16 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ARG D 21 " --> pdb=" O CYS D 17 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N MET D 24 " --> pdb=" O ALA D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 35 removed outlier: 3.778A pdb=" N VAL D 31 " --> pdb=" O GLN D 27 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N ASP D 33 " --> pdb=" O GLU D 29 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N TYR D 34 " --> pdb=" O PRO D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 54 removed outlier: 3.507A pdb=" N GLU D 44 " --> pdb=" O ALA D 40 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA D 51 " --> pdb=" O GLN D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 68 Processing helix chain 'D' and resid 74 through 85 removed outlier: 3.603A pdb=" N GLU D 78 " --> pdb=" O GLY D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 96 removed outlier: 3.630A pdb=" N ALA D 92 " --> pdb=" O SER D 88 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TYR D 94 " --> pdb=" O LEU D 90 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASN D 96 " --> pdb=" O ALA D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 129 removed outlier: 4.302A pdb=" N LEU D 115 " --> pdb=" O HIS D 111 " (cutoff:3.500A) Proline residue: D 123 - end of helix Processing helix chain 'D' and resid 130 through 141 removed outlier: 4.784A pdb=" N ASP D 136 " --> pdb=" O ARG D 132 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N LYS D 137 " --> pdb=" O ASP D 133 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU D 140 " --> pdb=" O ASP D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 156 Processing helix chain 'D' and resid 159 through 172 removed outlier: 3.573A pdb=" N LYS D 169 " --> pdb=" O ARG D 165 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL D 172 " --> pdb=" O LEU D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 188 removed outlier: 3.593A pdb=" N ASN D 183 " --> pdb=" O SER D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 199 Processing helix chain 'E' and resid 22 through 34 Processing helix chain 'E' and resid 55 through 60 Processing helix chain 'G' and resid 22 through 34 Processing helix chain 'G' and resid 37 through 39 No H-bonds generated for 'chain 'G' and resid 37 through 39' Processing helix chain 'G' and resid 55 through 60 removed outlier: 3.788A pdb=" N TYR G 59 " --> pdb=" O THR G 55 " (cutoff:3.500A) Processing helix chain 'I' and resid 22 through 35 Processing helix chain 'I' and resid 37 through 39 No H-bonds generated for 'chain 'I' and resid 37 through 39' Processing helix chain 'I' and resid 55 through 60 Processing helix chain 'L' and resid 22 through 32 removed outlier: 3.572A pdb=" N VAL L 26 " --> pdb=" O THR L 22 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE L 30 " --> pdb=" O VAL L 26 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLN L 31 " --> pdb=" O LYS L 27 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ASP L 32 " --> pdb=" O ALA L 28 " (cutoff:3.500A) Processing helix chain 'L' and resid 56 through 60 Processing helix chain 'M' and resid 3 through 15 Processing helix chain 'M' and resid 16 through 20 removed outlier: 3.577A pdb=" N CYS M 20 " --> pdb=" O SER M 17 " (cutoff:3.500A) Processing helix chain 'M' and resid 23 through 31 removed outlier: 4.533A pdb=" N LEU M 28 " --> pdb=" O VAL M 25 " (cutoff:3.500A) Proline residue: M 29 - end of helix Processing helix chain 'M' and resid 35 through 49 removed outlier: 3.600A pdb=" N ARG M 43 " --> pdb=" O GLN M 39 " (cutoff:3.500A) Processing helix chain 'M' and resid 51 through 63 removed outlier: 4.567A pdb=" N TRP M 56 " --> pdb=" O ARG M 52 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N HIS M 57 " --> pdb=" O ASP M 53 " (cutoff:3.500A) Processing helix chain 'M' and resid 67 through 79 removed outlier: 4.194A pdb=" N TYR M 71 " --> pdb=" O GLY M 67 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA M 74 " --> pdb=" O GLU M 70 " (cutoff:3.500A) Processing helix chain 'M' and resid 81 through 96 removed outlier: 3.610A pdb=" N TYR M 95 " --> pdb=" O VAL M 91 " (cutoff:3.500A) Processing helix chain 'N' and resid 3 through 15 Processing helix chain 'N' and resid 16 through 22 removed outlier: 3.713A pdb=" N CYS N 20 " --> pdb=" O SER N 17 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ASN N 21 " --> pdb=" O ASN N 18 " (cutoff:3.500A) Processing helix chain 'N' and resid 23 through 31 removed outlier: 4.345A pdb=" N LEU N 28 " --> pdb=" O VAL N 25 " (cutoff:3.500A) Proline residue: N 29 - end of helix Processing helix chain 'N' and resid 35 through 49 Processing helix chain 'N' and resid 54 through 63 Processing helix chain 'N' and resid 67 through 79 removed outlier: 3.644A pdb=" N TYR N 71 " --> pdb=" O GLY N 67 " (cutoff:3.500A) Processing helix chain 'N' and resid 81 through 93 removed outlier: 4.117A pdb=" N GLU N 87 " --> pdb=" O ASP N 83 " (cutoff:3.500A) Processing helix chain 'O' and resid 3 through 15 Processing helix chain 'O' and resid 16 through 22 removed outlier: 4.269A pdb=" N ASN O 21 " --> pdb=" O ASN O 18 " (cutoff:3.500A) Processing helix chain 'O' and resid 23 through 31 removed outlier: 4.468A pdb=" N LEU O 28 " --> pdb=" O VAL O 25 " (cutoff:3.500A) Proline residue: O 29 - end of helix Processing helix chain 'O' and resid 35 through 49 Processing helix chain 'O' and resid 51 through 63 removed outlier: 4.543A pdb=" N TRP O 56 " --> pdb=" O ARG O 52 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N HIS O 57 " --> pdb=" O ASP O 53 " (cutoff:3.500A) Processing helix chain 'O' and resid 67 through 79 removed outlier: 3.540A pdb=" N TYR O 71 " --> pdb=" O GLY O 67 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA O 74 " --> pdb=" O GLU O 70 " (cutoff:3.500A) Processing helix chain 'O' and resid 81 through 93 removed outlier: 3.630A pdb=" N ALA O 85 " --> pdb=" O LEU O 81 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLU O 87 " --> pdb=" O ASP O 83 " (cutoff:3.500A) Processing helix chain 'O' and resid 94 through 96 No H-bonds generated for 'chain 'O' and resid 94 through 96' Processing helix chain 'P' and resid 3 through 15 Processing helix chain 'P' and resid 16 through 22 removed outlier: 4.066A pdb=" N CYS P 20 " --> pdb=" O SER P 17 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASN P 21 " --> pdb=" O ASN P 18 " (cutoff:3.500A) Processing helix chain 'P' and resid 23 through 31 removed outlier: 4.244A pdb=" N LEU P 28 " --> pdb=" O VAL P 25 " (cutoff:3.500A) Proline residue: P 29 - end of helix Processing helix chain 'P' and resid 35 through 49 removed outlier: 3.637A pdb=" N ASP P 40 " --> pdb=" O ALA P 36 " (cutoff:3.500A) Processing helix chain 'P' and resid 51 through 63 removed outlier: 4.169A pdb=" N TRP P 56 " --> pdb=" O ARG P 52 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N HIS P 57 " --> pdb=" O ASP P 53 " (cutoff:3.500A) Processing helix chain 'P' and resid 67 through 77 removed outlier: 3.634A pdb=" N TYR P 71 " --> pdb=" O GLY P 67 " (cutoff:3.500A) Processing helix chain 'P' and resid 78 through 80 No H-bonds generated for 'chain 'P' and resid 78 through 80' Processing helix chain 'P' and resid 81 through 94 removed outlier: 4.432A pdb=" N GLU P 87 " --> pdb=" O ASP P 83 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL P 88 " --> pdb=" O LEU P 84 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER P 94 " --> pdb=" O SER P 90 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 12 through 16 removed outlier: 7.457A pdb=" N GLN H 2 " --> pdb=" O SER H 65 " (cutoff:3.500A) removed outlier: 8.476A pdb=" N LEU H 67 " --> pdb=" O GLN H 2 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N PHE H 4 " --> pdb=" O LEU H 67 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LEU H 69 " --> pdb=" O PHE H 4 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N LYS H 6 " --> pdb=" O LEU H 69 " (cutoff:3.500A) removed outlier: 8.515A pdb=" N LEU H 71 " --> pdb=" O LYS H 6 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 12 through 16 removed outlier: 3.660A pdb=" N ILE F 13 " --> pdb=" O VAL F 5 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N LEU F 67 " --> pdb=" O GLN F 2 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N PHE F 4 " --> pdb=" O LEU F 67 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N LEU F 69 " --> pdb=" O PHE F 4 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LYS F 6 " --> pdb=" O LEU F 69 " (cutoff:3.500A) removed outlier: 8.943A pdb=" N LEU F 71 " --> pdb=" O LYS F 6 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL F 70 " --> pdb=" O ARG F 42 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'J' and resid 12 through 16 removed outlier: 7.255A pdb=" N GLN J 2 " --> pdb=" O SER J 65 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N LEU J 67 " --> pdb=" O GLN J 2 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N PHE J 4 " --> pdb=" O LEU J 67 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N LEU J 69 " --> pdb=" O PHE J 4 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N LYS J 6 " --> pdb=" O LEU J 69 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'K' and resid 13 through 16 removed outlier: 3.744A pdb=" N SER K 65 " --> pdb=" O GLN K 2 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 12 through 16 Processing sheet with id=AA6, first strand: chain 'G' and resid 12 through 15 removed outlier: 3.729A pdb=" N VAL G 70 " --> pdb=" O ARG G 42 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'I' and resid 14 through 16 removed outlier: 3.624A pdb=" N VAL I 70 " --> pdb=" O ARG I 42 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 12 through 16 removed outlier: 3.535A pdb=" N VAL L 70 " --> pdb=" O ARG L 42 " (cutoff:3.500A) 728 hydrogen bonds defined for protein. 2061 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.66 Time building geometry restraints manager: 5.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2428 1.32 - 1.44: 3518 1.44 - 1.56: 8282 1.56 - 1.69: 0 1.69 - 1.81: 84 Bond restraints: 14312 Sorted by residual: bond pdb=" C PRO L 37 " pdb=" O PRO L 37 " ideal model delta sigma weight residual 1.243 1.200 0.044 8.50e-03 1.38e+04 2.63e+01 bond pdb=" C PRO E 19 " pdb=" O PRO E 19 " ideal model delta sigma weight residual 1.237 1.196 0.042 1.28e-02 6.10e+03 1.06e+01 bond pdb=" C PRO L 38 " pdb=" O PRO L 38 " ideal model delta sigma weight residual 1.238 1.197 0.041 1.33e-02 5.65e+03 9.48e+00 bond pdb=" N GLU D 166 " pdb=" CA GLU D 166 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.27e-02 6.20e+03 6.21e+00 bond pdb=" CA ALA H 46 " pdb=" CB ALA H 46 " ideal model delta sigma weight residual 1.527 1.485 0.042 1.70e-02 3.46e+03 6.08e+00 ... (remaining 14307 not shown) Histogram of bond angle deviations from ideal: 97.69 - 104.95: 209 104.95 - 112.21: 7308 112.21 - 119.47: 4920 119.47 - 126.74: 6810 126.74 - 134.00: 148 Bond angle restraints: 19395 Sorted by residual: angle pdb=" N PRO L 37 " pdb=" CA PRO L 37 " pdb=" CB PRO L 37 " ideal model delta sigma weight residual 103.22 106.69 -3.47 5.20e-01 3.70e+00 4.47e+01 angle pdb=" C LYS F 48 " pdb=" CA LYS F 48 " pdb=" CB LYS F 48 " ideal model delta sigma weight residual 110.34 102.57 7.77 1.40e+00 5.10e-01 3.08e+01 angle pdb=" C THR D 124 " pdb=" CA THR D 124 " pdb=" CB THR D 124 " ideal model delta sigma weight residual 110.90 102.79 8.11 1.58e+00 4.01e-01 2.64e+01 angle pdb=" N PRO E 19 " pdb=" CA PRO E 19 " pdb=" C PRO E 19 " ideal model delta sigma weight residual 113.86 107.77 6.09 1.25e+00 6.40e-01 2.37e+01 angle pdb=" N GLY F 35 " pdb=" CA GLY F 35 " pdb=" C GLY F 35 " ideal model delta sigma weight residual 113.18 123.45 -10.27 2.37e+00 1.78e-01 1.88e+01 ... (remaining 19390 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 7886 17.66 - 35.32: 699 35.32 - 52.98: 131 52.98 - 70.64: 21 70.64 - 88.30: 18 Dihedral angle restraints: 8755 sinusoidal: 3592 harmonic: 5163 Sorted by residual: dihedral pdb=" CA GLN E 41 " pdb=" C GLN E 41 " pdb=" N ARG E 42 " pdb=" CA ARG E 42 " ideal model delta harmonic sigma weight residual 180.00 158.23 21.77 0 5.00e+00 4.00e-02 1.90e+01 dihedral pdb=" CA GLU J 34 " pdb=" C GLU J 34 " pdb=" N GLY J 35 " pdb=" CA GLY J 35 " ideal model delta harmonic sigma weight residual 180.00 158.42 21.58 0 5.00e+00 4.00e-02 1.86e+01 dihedral pdb=" C LYS F 48 " pdb=" N LYS F 48 " pdb=" CA LYS F 48 " pdb=" CB LYS F 48 " ideal model delta harmonic sigma weight residual -122.60 -112.24 -10.36 0 2.50e+00 1.60e-01 1.72e+01 ... (remaining 8752 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1717 0.057 - 0.114: 468 0.114 - 0.171: 62 0.171 - 0.228: 6 0.228 - 0.285: 2 Chirality restraints: 2255 Sorted by residual: chirality pdb=" CA LYS F 48 " pdb=" N LYS F 48 " pdb=" C LYS F 48 " pdb=" CB LYS F 48 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.28 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" CA GLU E 51 " pdb=" N GLU E 51 " pdb=" C GLU E 51 " pdb=" CB GLU E 51 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" CA LYS H 48 " pdb=" N LYS H 48 " pdb=" C LYS H 48 " pdb=" CB LYS H 48 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 2252 not shown) Planarity restraints: 2497 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP P 86 " 0.021 2.00e-02 2.50e+03 4.33e-02 1.87e+01 pdb=" C ASP P 86 " -0.075 2.00e-02 2.50e+03 pdb=" O ASP P 86 " 0.028 2.00e-02 2.50e+03 pdb=" N GLU P 87 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO K 37 " 0.060 5.00e-02 4.00e+02 8.95e-02 1.28e+01 pdb=" N PRO K 38 " -0.155 5.00e-02 4.00e+02 pdb=" CA PRO K 38 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO K 38 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU L 18 " 0.051 5.00e-02 4.00e+02 7.75e-02 9.62e+00 pdb=" N PRO L 19 " -0.134 5.00e-02 4.00e+02 pdb=" CA PRO L 19 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO L 19 " 0.043 5.00e-02 4.00e+02 ... (remaining 2494 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1898 2.74 - 3.28: 15246 3.28 - 3.82: 23496 3.82 - 4.36: 29405 4.36 - 4.90: 49030 Nonbonded interactions: 119075 Sorted by model distance: nonbonded pdb=" NE2 GLN G 2 " pdb=" OG1 THR G 14 " model vdw 2.196 2.520 nonbonded pdb=" NH1 ARG B 12 " pdb=" O GLU B 67 " model vdw 2.202 2.520 nonbonded pdb=" OG1 THR E 22 " pdb=" O GLY E 53 " model vdw 2.203 2.440 nonbonded pdb=" N MET E 1 " pdb=" O VAL E 17 " model vdw 2.213 2.520 nonbonded pdb=" OG1 THR L 22 " pdb=" OE1 GLU L 24 " model vdw 2.213 2.440 ... (remaining 119070 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 4 through 100 or (resid 101 and (name N or name CA or name \ C or name O or name CB )) or resid 102 through 131 or (resid 132 and (name N or \ name CA or name C or name O or name CB )) or resid 133 through 186 or (resid 18 \ 7 and (name N or name CA or name C or name O or name CB )) or resid 188 through \ 200)) selection = (chain 'B' and (resid 4 through 100 or (resid 101 and (name N or name CA or name \ C or name O or name CB )) or resid 102 through 186 or (resid 187 and (name N or \ name CA or name C or name O or name CB )) or resid 188 through 200)) selection = chain 'C' selection = (chain 'D' and (resid 4 through 100 or (resid 101 and (name N or name CA or name \ C or name O or name CB )) or resid 102 through 200)) } ncs_group { reference = chain 'E' selection = (chain 'F' and resid 1 through 72) selection = (chain 'G' and resid 1 through 72) selection = (chain 'H' and resid 1 through 72) selection = chain 'I' selection = (chain 'J' and resid 1 through 72) selection = (chain 'K' and resid 1 through 72) selection = (chain 'L' and resid 1 through 72) } ncs_group { reference = (chain 'M' and resid 1 through 96) selection = (chain 'N' and resid 1 through 96) selection = chain 'O' selection = (chain 'P' and resid 1 through 96) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.45 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: 0.840 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: 0.010 Extract box with map and model: 3.500 Check model and map are aligned: 0.180 Set scattering table: 0.120 Process input model: 37.210 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 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 : 0.009 0.079 14312 Z= 0.580 Angle : 0.842 10.266 19395 Z= 0.482 Chirality : 0.052 0.285 2255 Planarity : 0.005 0.090 2497 Dihedral : 14.309 88.302 5393 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 0.90 % Allowed : 0.71 % Favored : 98.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.20), residues: 1729 helix: -1.57 (0.15), residues: 999 sheet: -1.66 (0.36), residues: 198 loop : 0.67 (0.29), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 177 HIS 0.008 0.002 HIS A 111 PHE 0.016 0.002 PHE C 107 TYR 0.034 0.002 TYR O 95 ARG 0.007 0.001 ARG E 42 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 405 time to evaluate : 1.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 1 MET cc_start: 0.7599 (ttp) cc_final: 0.7180 (ttm) REVERT: H 18 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.8072 (tm-30) REVERT: H 20 SER cc_start: 0.9156 (p) cc_final: 0.8795 (p) REVERT: H 31 GLN cc_start: 0.8631 (tp40) cc_final: 0.8357 (tp40) REVERT: F 41 GLN cc_start: 0.7577 (mt0) cc_final: 0.7157 (mt0) REVERT: F 63 LYS cc_start: 0.9276 (ptpt) cc_final: 0.9058 (pttp) REVERT: F 65 SER cc_start: 0.8503 (m) cc_final: 0.8206 (m) REVERT: J 1 MET cc_start: 0.8498 (ttp) cc_final: 0.8246 (ttp) REVERT: J 30 ILE cc_start: 0.9625 (mp) cc_final: 0.9425 (mp) REVERT: J 31 GLN cc_start: 0.8902 (tm-30) cc_final: 0.8503 (tm-30) REVERT: K 2 GLN cc_start: 0.8176 (pt0) cc_final: 0.7924 (pt0) REVERT: K 4 PHE cc_start: 0.7893 (m-10) cc_final: 0.7461 (m-10) REVERT: K 34 GLU cc_start: 0.8345 (mm-30) cc_final: 0.7897 (mp0) REVERT: A 24 MET cc_start: 0.8960 (mtm) cc_final: 0.8737 (mtp) REVERT: A 136 ASP cc_start: 0.7832 (t0) cc_final: 0.7208 (t0) REVERT: B 8 ASP cc_start: 0.8162 (t70) cc_final: 0.7805 (t0) REVERT: B 60 GLU cc_start: 0.8382 (tp30) cc_final: 0.8151 (tm-30) REVERT: B 101 ASP cc_start: 0.8299 (t0) cc_final: 0.7913 (t0) REVERT: B 127 ASP cc_start: 0.8324 (m-30) cc_final: 0.7945 (m-30) REVERT: C 166 GLU cc_start: 0.8782 (tp30) cc_final: 0.8385 (tp30) REVERT: D 41 GLU cc_start: 0.8559 (tm-30) cc_final: 0.8343 (tm-30) REVERT: D 112 ASP cc_start: 0.8548 (t0) cc_final: 0.8287 (t0) REVERT: D 137 LYS cc_start: 0.9015 (tppp) cc_final: 0.8751 (tppt) REVERT: E 48 LYS cc_start: 0.8590 (tttp) cc_final: 0.8115 (tptt) REVERT: G 24 GLU cc_start: 0.8960 (mm-30) cc_final: 0.8466 (mm-30) REVERT: G 31 GLN cc_start: 0.9509 (tt0) cc_final: 0.9302 (tt0) REVERT: G 32 ASP cc_start: 0.8476 (m-30) cc_final: 0.8135 (m-30) REVERT: G 34 GLU cc_start: 0.7937 (mm-30) cc_final: 0.7695 (mm-30) REVERT: G 52 ASP cc_start: 0.8715 (m-30) cc_final: 0.8358 (m-30) REVERT: I 2 GLN cc_start: 0.7511 (tp-100) cc_final: 0.7210 (tp40) REVERT: L 18 GLU cc_start: 0.8816 (tm-30) cc_final: 0.8576 (tm-30) REVERT: L 31 GLN cc_start: 0.8096 (OUTLIER) cc_final: 0.7780 (mp10) REVERT: L 51 GLU cc_start: 0.6369 (mp0) cc_final: 0.5845 (mp0) REVERT: M 6 ASP cc_start: 0.8750 (t70) cc_final: 0.8512 (t0) REVERT: M 82 VAL cc_start: 0.9051 (t) cc_final: 0.8670 (t) REVERT: N 86 ASP cc_start: 0.8584 (p0) cc_final: 0.8338 (p0) REVERT: N 90 SER cc_start: 0.9018 (m) cc_final: 0.8816 (m) REVERT: N 93 GLN cc_start: 0.8732 (pm20) cc_final: 0.8473 (pm20) REVERT: O 15 ASN cc_start: 0.8908 (m-40) cc_final: 0.8600 (m-40) REVERT: O 93 GLN cc_start: 0.9158 (pp30) cc_final: 0.8948 (pp30) REVERT: O 95 TYR cc_start: 0.7587 (t80) cc_final: 0.6800 (t80) REVERT: P 6 ASP cc_start: 0.8370 (t0) cc_final: 0.8133 (t0) REVERT: P 38 ASP cc_start: 0.7855 (OUTLIER) cc_final: 0.7524 (m-30) REVERT: P 65 ARG cc_start: 0.8387 (mmt-90) cc_final: 0.8074 (mpt180) REVERT: P 95 TYR cc_start: 0.7145 (t80) cc_final: 0.6790 (t80) outliers start: 14 outliers final: 2 residues processed: 408 average time/residue: 0.2977 time to fit residues: 168.2866 Evaluate side-chains 344 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 339 time to evaluate : 1.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 GLU Chi-restraints excluded: chain C residue 158 ASN Chi-restraints excluded: chain L residue 14 THR Chi-restraints excluded: chain L residue 31 GLN Chi-restraints excluded: chain P residue 38 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 0.9980 chunk 127 optimal weight: 4.9990 chunk 70 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 85 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 131 optimal weight: 0.5980 chunk 50 optimal weight: 0.9980 chunk 80 optimal weight: 0.7980 chunk 98 optimal weight: 2.9990 chunk 152 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 40 GLN ** F 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 GLN C 183 ASN D 10 ASN ** E 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 40 GLN G 2 GLN G 49 GLN L 25 ASN P 15 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14312 Z= 0.207 Angle : 0.648 9.610 19395 Z= 0.340 Chirality : 0.043 0.210 2255 Planarity : 0.005 0.056 2497 Dihedral : 5.464 57.254 1922 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.35 % Allowed : 11.83 % Favored : 86.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.20), residues: 1729 helix: -0.58 (0.15), residues: 1048 sheet: -1.59 (0.36), residues: 193 loop : 0.70 (0.30), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP O 56 HIS 0.004 0.001 HIS A 72 PHE 0.018 0.001 PHE A 107 TYR 0.016 0.001 TYR B 13 ARG 0.008 0.001 ARG O 52 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 398 time to evaluate : 1.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 1 MET cc_start: 0.7489 (ttp) cc_final: 0.7165 (ttm) REVERT: H 18 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.7794 (tm-30) REVERT: H 21 ASP cc_start: 0.8045 (m-30) cc_final: 0.7560 (m-30) REVERT: H 31 GLN cc_start: 0.8683 (tp40) cc_final: 0.8103 (tp40) REVERT: H 58 ASP cc_start: 0.8776 (t0) cc_final: 0.8551 (t0) REVERT: H 60 ASN cc_start: 0.8870 (t0) cc_final: 0.8482 (p0) REVERT: F 25 ASN cc_start: 0.8594 (t0) cc_final: 0.8322 (t0) REVERT: F 41 GLN cc_start: 0.7162 (mt0) cc_final: 0.6908 (mt0) REVERT: F 63 LYS cc_start: 0.9184 (ptpt) cc_final: 0.8935 (pttp) REVERT: F 65 SER cc_start: 0.8581 (m) cc_final: 0.8356 (m) REVERT: J 18 GLU cc_start: 0.8598 (mp0) cc_final: 0.8276 (mp0) REVERT: J 31 GLN cc_start: 0.8812 (tm-30) cc_final: 0.8464 (tm-30) REVERT: K 4 PHE cc_start: 0.8008 (m-10) cc_final: 0.7758 (m-80) REVERT: K 62 GLN cc_start: 0.7291 (pp30) cc_final: 0.7075 (pp30) REVERT: A 166 GLU cc_start: 0.7745 (tm-30) cc_final: 0.7360 (tm-30) REVERT: B 8 ASP cc_start: 0.7941 (t70) cc_final: 0.7583 (t0) REVERT: B 23 LYS cc_start: 0.8922 (ptmt) cc_final: 0.8536 (ptpp) REVERT: B 101 ASP cc_start: 0.8282 (t0) cc_final: 0.7678 (t0) REVERT: B 127 ASP cc_start: 0.8283 (m-30) cc_final: 0.7892 (m-30) REVERT: C 166 GLU cc_start: 0.8354 (tp30) cc_final: 0.5899 (mm-30) REVERT: C 170 ARG cc_start: 0.7117 (mpt90) cc_final: 0.5597 (mpt90) REVERT: D 41 GLU cc_start: 0.8219 (tm-30) cc_final: 0.7875 (tm-30) REVERT: D 112 ASP cc_start: 0.8532 (t0) cc_final: 0.8191 (t0) REVERT: E 4 PHE cc_start: 0.7676 (m-80) cc_final: 0.7347 (m-10) REVERT: E 48 LYS cc_start: 0.8592 (tttp) cc_final: 0.8157 (tptt) REVERT: G 24 GLU cc_start: 0.8967 (mm-30) cc_final: 0.8617 (mm-30) REVERT: G 32 ASP cc_start: 0.8321 (m-30) cc_final: 0.8100 (m-30) REVERT: G 34 GLU cc_start: 0.7790 (mm-30) cc_final: 0.7455 (mm-30) REVERT: G 42 ARG cc_start: 0.8159 (OUTLIER) cc_final: 0.7021 (mtm180) REVERT: L 18 GLU cc_start: 0.8772 (tm-30) cc_final: 0.8440 (tm-30) REVERT: L 31 GLN cc_start: 0.8027 (OUTLIER) cc_final: 0.7751 (mp10) REVERT: L 51 GLU cc_start: 0.6553 (mp0) cc_final: 0.6049 (mp0) REVERT: L 64 GLU cc_start: 0.8443 (tm-30) cc_final: 0.8017 (tm-30) REVERT: N 86 ASP cc_start: 0.8363 (p0) cc_final: 0.8111 (p0) REVERT: O 3 PHE cc_start: 0.7690 (t80) cc_final: 0.7427 (t80) REVERT: O 93 GLN cc_start: 0.9129 (pp30) cc_final: 0.8879 (pp30) REVERT: P 6 ASP cc_start: 0.8167 (t0) cc_final: 0.7852 (t0) REVERT: P 18 ASN cc_start: 0.9070 (m110) cc_final: 0.8825 (m110) REVERT: P 95 TYR cc_start: 0.6801 (t80) cc_final: 0.6513 (t80) outliers start: 21 outliers final: 12 residues processed: 408 average time/residue: 0.2716 time to fit residues: 158.0280 Evaluate side-chains 358 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 343 time to evaluate : 1.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 GLU Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain J residue 54 ARG Chi-restraints excluded: chain A residue 138 CYS Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain G residue 42 ARG Chi-restraints excluded: chain I residue 39 ASP Chi-restraints excluded: chain L residue 31 GLN Chi-restraints excluded: chain M residue 83 ASP Chi-restraints excluded: chain N residue 82 VAL Chi-restraints excluded: chain P residue 10 LYS Chi-restraints excluded: chain P residue 22 VAL Chi-restraints excluded: chain P residue 88 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 84 optimal weight: 5.9990 chunk 47 optimal weight: 7.9990 chunk 126 optimal weight: 10.0000 chunk 103 optimal weight: 0.2980 chunk 42 optimal weight: 0.9980 chunk 152 optimal weight: 0.6980 chunk 165 optimal weight: 5.9990 chunk 136 optimal weight: 3.9990 chunk 151 optimal weight: 4.9990 chunk 52 optimal weight: 7.9990 chunk 122 optimal weight: 8.9990 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 41 GLN J 49 GLN A 150 ASN ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 ASN E 49 GLN ** G 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 2 GLN L 68 HIS M 21 ASN ** M 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 18 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 14312 Z= 0.299 Angle : 0.614 8.046 19395 Z= 0.315 Chirality : 0.044 0.198 2255 Planarity : 0.004 0.051 2497 Dihedral : 5.125 58.542 1917 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.09 % Allowed : 14.47 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.20), residues: 1729 helix: -0.19 (0.16), residues: 1030 sheet: -1.50 (0.36), residues: 193 loop : 0.68 (0.29), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP O 56 HIS 0.007 0.001 HIS A 111 PHE 0.016 0.001 PHE C 107 TYR 0.027 0.001 TYR M 95 ARG 0.005 0.000 ARG H 54 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 357 time to evaluate : 1.793 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: H 1 MET cc_start: 0.7479 (ttp) cc_final: 0.7119 (ttm) REVERT: H 18 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.7680 (tm-30) REVERT: H 21 ASP cc_start: 0.8133 (m-30) cc_final: 0.7347 (m-30) REVERT: H 31 GLN cc_start: 0.8669 (tp40) cc_final: 0.8118 (tp40) REVERT: H 60 ASN cc_start: 0.8860 (t0) cc_final: 0.8344 (p0) REVERT: F 41 GLN cc_start: 0.7273 (mt0) cc_final: 0.7039 (mt0) REVERT: F 59 TYR cc_start: 0.8246 (m-80) cc_final: 0.7985 (m-80) REVERT: F 63 LYS cc_start: 0.9155 (ptpt) cc_final: 0.8893 (pttp) REVERT: F 65 SER cc_start: 0.8526 (m) cc_final: 0.8286 (m) REVERT: J 18 GLU cc_start: 0.8704 (mp0) cc_final: 0.8203 (mp0) REVERT: J 31 GLN cc_start: 0.8864 (tm-30) cc_final: 0.8501 (tm-30) REVERT: K 4 PHE cc_start: 0.8073 (m-10) cc_final: 0.7856 (m-80) REVERT: B 8 ASP cc_start: 0.7951 (t70) cc_final: 0.7582 (t0) REVERT: B 23 LYS cc_start: 0.9002 (ptmt) cc_final: 0.8726 (ptpp) REVERT: B 101 ASP cc_start: 0.8358 (t0) cc_final: 0.7755 (t0) REVERT: B 118 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8107 (tt) REVERT: B 127 ASP cc_start: 0.8287 (m-30) cc_final: 0.7919 (m-30) REVERT: C 166 GLU cc_start: 0.8417 (tp30) cc_final: 0.7526 (mm-30) REVERT: D 41 GLU cc_start: 0.8213 (tm-30) cc_final: 0.7852 (tm-30) REVERT: D 112 ASP cc_start: 0.8543 (t0) cc_final: 0.8224 (t0) REVERT: D 137 LYS cc_start: 0.8794 (tppp) cc_final: 0.8490 (tppt) REVERT: E 4 PHE cc_start: 0.7705 (m-80) cc_final: 0.7369 (m-10) REVERT: E 11 LYS cc_start: 0.8355 (pptt) cc_final: 0.8091 (ptpp) REVERT: E 48 LYS cc_start: 0.8621 (tttp) cc_final: 0.8206 (tptt) REVERT: G 32 ASP cc_start: 0.8368 (m-30) cc_final: 0.8148 (m-30) REVERT: G 34 GLU cc_start: 0.7697 (mm-30) cc_final: 0.7481 (mm-30) REVERT: G 72 ARG cc_start: 0.7558 (ttm-80) cc_final: 0.6557 (mtp85) REVERT: I 41 GLN cc_start: 0.7555 (OUTLIER) cc_final: 0.6712 (pm20) REVERT: L 2 GLN cc_start: 0.7115 (OUTLIER) cc_final: 0.6270 (tm-30) REVERT: L 51 GLU cc_start: 0.6404 (mp0) cc_final: 0.5841 (mp0) REVERT: L 64 GLU cc_start: 0.8478 (tm-30) cc_final: 0.7827 (tm-30) REVERT: M 14 ARG cc_start: 0.8051 (mtm110) cc_final: 0.7826 (ttp-110) REVERT: N 11 TYR cc_start: 0.8452 (t80) cc_final: 0.8204 (t80) REVERT: N 86 ASP cc_start: 0.8344 (p0) cc_final: 0.8091 (p0) REVERT: P 6 ASP cc_start: 0.8208 (t0) cc_final: 0.8007 (t0) REVERT: P 49 SER cc_start: 0.9117 (m) cc_final: 0.8481 (p) REVERT: P 95 TYR cc_start: 0.6924 (t80) cc_final: 0.6550 (t80) outliers start: 48 outliers final: 26 residues processed: 386 average time/residue: 0.2691 time to fit residues: 148.8934 Evaluate side-chains 368 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 338 time to evaluate : 1.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 GLU Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain J residue 54 ARG Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 138 CYS Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 24 MET Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain G residue 9 THR Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain I residue 39 ASP Chi-restraints excluded: chain I residue 41 GLN Chi-restraints excluded: chain L residue 2 GLN Chi-restraints excluded: chain L residue 12 THR Chi-restraints excluded: chain M residue 82 VAL Chi-restraints excluded: chain M residue 83 ASP Chi-restraints excluded: chain N residue 82 VAL Chi-restraints excluded: chain P residue 10 LYS Chi-restraints excluded: chain P residue 15 ASN Chi-restraints excluded: chain P residue 17 SER Chi-restraints excluded: chain P residue 88 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 151 optimal weight: 4.9990 chunk 114 optimal weight: 0.0040 chunk 79 optimal weight: 0.6980 chunk 16 optimal weight: 4.9990 chunk 72 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 153 optimal weight: 5.9990 chunk 162 optimal weight: 8.9990 chunk 80 optimal weight: 2.9990 chunk 145 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 overall best weight: 2.3398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 47 GLN ** G 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 49 GLN L 2 GLN L 68 HIS M 21 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 14312 Z= 0.313 Angle : 0.607 7.851 19395 Z= 0.314 Chirality : 0.044 0.206 2255 Planarity : 0.004 0.048 2497 Dihedral : 4.824 47.245 1914 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.89 % Allowed : 16.85 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.21), residues: 1729 helix: 0.03 (0.16), residues: 1027 sheet: -1.44 (0.36), residues: 193 loop : 0.62 (0.30), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP O 56 HIS 0.007 0.001 HIS A 111 PHE 0.016 0.001 PHE C 107 TYR 0.024 0.001 TYR M 95 ARG 0.006 0.000 ARG G 72 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 355 time to evaluate : 1.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 1 MET cc_start: 0.7431 (ttp) cc_final: 0.7098 (ttm) REVERT: H 21 ASP cc_start: 0.8195 (m-30) cc_final: 0.7736 (m-30) REVERT: F 41 GLN cc_start: 0.7179 (mt0) cc_final: 0.6952 (mt0) REVERT: F 59 TYR cc_start: 0.8204 (m-80) cc_final: 0.7913 (m-80) REVERT: F 63 LYS cc_start: 0.9133 (ptpt) cc_final: 0.8877 (pttp) REVERT: F 65 SER cc_start: 0.8566 (m) cc_final: 0.8331 (m) REVERT: J 18 GLU cc_start: 0.8766 (mp0) cc_final: 0.8306 (mp0) REVERT: J 31 GLN cc_start: 0.8827 (tm-30) cc_final: 0.8496 (tm-30) REVERT: J 54 ARG cc_start: 0.7568 (OUTLIER) cc_final: 0.7245 (mtt-85) REVERT: B 8 ASP cc_start: 0.8010 (t70) cc_final: 0.7648 (t0) REVERT: B 23 LYS cc_start: 0.9040 (ptmt) cc_final: 0.8761 (ptpp) REVERT: B 101 ASP cc_start: 0.8347 (t0) cc_final: 0.7907 (t0) REVERT: B 118 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.8098 (tt) REVERT: B 127 ASP cc_start: 0.8296 (m-30) cc_final: 0.7939 (m-30) REVERT: B 147 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.8038 (tp30) REVERT: C 24 MET cc_start: 0.9030 (mtm) cc_final: 0.8830 (mtp) REVERT: C 166 GLU cc_start: 0.8363 (tp30) cc_final: 0.7439 (mm-30) REVERT: D 13 TYR cc_start: 0.8492 (t80) cc_final: 0.8207 (t80) REVERT: D 41 GLU cc_start: 0.8231 (tm-30) cc_final: 0.7862 (tm-30) REVERT: D 112 ASP cc_start: 0.8543 (t0) cc_final: 0.8212 (t0) REVERT: D 137 LYS cc_start: 0.8780 (tppp) cc_final: 0.8465 (tppt) REVERT: E 4 PHE cc_start: 0.7766 (m-80) cc_final: 0.7443 (m-80) REVERT: E 11 LYS cc_start: 0.8351 (pptt) cc_final: 0.8133 (ptpp) REVERT: E 48 LYS cc_start: 0.8621 (tttp) cc_final: 0.8142 (tptt) REVERT: E 56 LEU cc_start: 0.8880 (mp) cc_final: 0.8664 (mt) REVERT: G 2 GLN cc_start: 0.7844 (tm-30) cc_final: 0.7534 (tm-30) REVERT: G 24 GLU cc_start: 0.8971 (mm-30) cc_final: 0.8487 (mm-30) REVERT: G 32 ASP cc_start: 0.8357 (m-30) cc_final: 0.8141 (m-30) REVERT: I 11 LYS cc_start: 0.8046 (pptt) cc_final: 0.7771 (pptt) REVERT: I 41 GLN cc_start: 0.7471 (OUTLIER) cc_final: 0.6652 (pm20) REVERT: L 51 GLU cc_start: 0.6529 (mp0) cc_final: 0.6043 (mp0) REVERT: L 64 GLU cc_start: 0.8530 (tm-30) cc_final: 0.7999 (tm-30) REVERT: M 14 ARG cc_start: 0.8028 (mtm110) cc_final: 0.7648 (ttp80) REVERT: N 11 TYR cc_start: 0.8435 (t80) cc_final: 0.8137 (t80) REVERT: N 14 ARG cc_start: 0.8243 (tpp80) cc_final: 0.7895 (tpp80) REVERT: N 86 ASP cc_start: 0.8344 (p0) cc_final: 0.8105 (p0) REVERT: O 95 TYR cc_start: 0.7964 (t80) cc_final: 0.6439 (t80) REVERT: P 6 ASP cc_start: 0.8166 (t0) cc_final: 0.7964 (t0) REVERT: P 95 TYR cc_start: 0.7017 (t80) cc_final: 0.6553 (t80) outliers start: 45 outliers final: 28 residues processed: 383 average time/residue: 0.2726 time to fit residues: 148.4006 Evaluate side-chains 370 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 338 time to evaluate : 1.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 GLU Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain J residue 54 ARG Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 138 CYS Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 24 MET Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 147 GLU Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 24 MET Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain G residue 9 THR Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain I residue 39 ASP Chi-restraints excluded: chain I residue 41 GLN Chi-restraints excluded: chain L residue 12 THR Chi-restraints excluded: chain L residue 39 ASP Chi-restraints excluded: chain M residue 82 VAL Chi-restraints excluded: chain N residue 82 VAL Chi-restraints excluded: chain N residue 90 SER Chi-restraints excluded: chain P residue 10 LYS Chi-restraints excluded: chain P residue 15 ASN Chi-restraints excluded: chain P residue 17 SER Chi-restraints excluded: chain P residue 55 LEU Chi-restraints excluded: chain P residue 88 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 135 optimal weight: 8.9990 chunk 92 optimal weight: 1.9990 chunk 2 optimal weight: 7.9990 chunk 120 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 chunk 138 optimal weight: 1.9990 chunk 112 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 82 optimal weight: 0.9990 chunk 145 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 49 GLN A 116 GLN M 21 ASN ** O 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14312 Z= 0.221 Angle : 0.593 7.582 19395 Z= 0.305 Chirality : 0.043 0.193 2255 Planarity : 0.004 0.049 2497 Dihedral : 4.701 47.655 1914 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.64 % Allowed : 20.19 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.21), residues: 1729 helix: 0.21 (0.17), residues: 1033 sheet: -1.39 (0.35), residues: 193 loop : 0.65 (0.30), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP O 56 HIS 0.007 0.001 HIS A 111 PHE 0.016 0.001 PHE C 107 TYR 0.038 0.001 TYR N 95 ARG 0.008 0.000 ARG O 52 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 376 time to evaluate : 1.788 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: H 1 MET cc_start: 0.7458 (ttp) cc_final: 0.7139 (ttm) REVERT: H 18 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.7767 (tm-30) REVERT: H 21 ASP cc_start: 0.8131 (m-30) cc_final: 0.7528 (m-30) REVERT: H 31 GLN cc_start: 0.8622 (tp40) cc_final: 0.8088 (tp40) REVERT: F 41 GLN cc_start: 0.7081 (mt0) cc_final: 0.6803 (mt0) REVERT: F 59 TYR cc_start: 0.8215 (m-80) cc_final: 0.7997 (m-80) REVERT: F 63 LYS cc_start: 0.9087 (ptpt) cc_final: 0.8825 (pttp) REVERT: F 65 SER cc_start: 0.8521 (m) cc_final: 0.8289 (m) REVERT: J 18 GLU cc_start: 0.8775 (mp0) cc_final: 0.8269 (mp0) REVERT: J 31 GLN cc_start: 0.8934 (tm-30) cc_final: 0.8583 (tp40) REVERT: J 54 ARG cc_start: 0.7463 (OUTLIER) cc_final: 0.6979 (mtt-85) REVERT: K 1 MET cc_start: 0.7550 (ttp) cc_final: 0.7109 (ttp) REVERT: B 8 ASP cc_start: 0.8005 (t70) cc_final: 0.7629 (t0) REVERT: B 23 LYS cc_start: 0.9027 (ptmt) cc_final: 0.8748 (ptpp) REVERT: B 95 MET cc_start: 0.8545 (OUTLIER) cc_final: 0.8274 (mmp) REVERT: B 101 ASP cc_start: 0.8324 (t0) cc_final: 0.7903 (t0) REVERT: B 118 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.7999 (tt) REVERT: B 127 ASP cc_start: 0.8255 (m-30) cc_final: 0.7887 (m-30) REVERT: B 147 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.8043 (tp30) REVERT: B 170 ARG cc_start: 0.7969 (mmt90) cc_final: 0.7732 (mmt90) REVERT: C 23 LYS cc_start: 0.8917 (ttpp) cc_final: 0.8607 (mtpp) REVERT: D 13 TYR cc_start: 0.8439 (t80) cc_final: 0.8203 (t80) REVERT: D 41 GLU cc_start: 0.8210 (tm-30) cc_final: 0.7843 (tm-30) REVERT: D 112 ASP cc_start: 0.8503 (t0) cc_final: 0.8162 (t0) REVERT: D 137 LYS cc_start: 0.8766 (tppp) cc_final: 0.8457 (tppt) REVERT: E 4 PHE cc_start: 0.7545 (m-80) cc_final: 0.7249 (m-80) REVERT: E 48 LYS cc_start: 0.8656 (tttp) cc_final: 0.8184 (tptt) REVERT: G 2 GLN cc_start: 0.7903 (tm-30) cc_final: 0.7265 (pp30) REVERT: G 24 GLU cc_start: 0.8987 (mm-30) cc_final: 0.8528 (mm-30) REVERT: G 72 ARG cc_start: 0.7771 (mtm110) cc_final: 0.7220 (mtp85) REVERT: I 41 GLN cc_start: 0.7565 (OUTLIER) cc_final: 0.6749 (pm20) REVERT: I 54 ARG cc_start: 0.7673 (ttm-80) cc_final: 0.7121 (tpp80) REVERT: L 24 GLU cc_start: 0.8068 (mp0) cc_final: 0.7725 (mp0) REVERT: L 51 GLU cc_start: 0.6396 (mp0) cc_final: 0.5895 (mp0) REVERT: L 64 GLU cc_start: 0.8500 (tm-30) cc_final: 0.7992 (tm-30) REVERT: M 14 ARG cc_start: 0.7991 (mtm110) cc_final: 0.7619 (ttp80) REVERT: M 63 GLN cc_start: 0.8722 (pp30) cc_final: 0.8517 (pp30) REVERT: N 1 MET cc_start: 0.5835 (tpp) cc_final: 0.5333 (tpp) REVERT: N 11 TYR cc_start: 0.8418 (t80) cc_final: 0.8132 (t80) REVERT: N 86 ASP cc_start: 0.8332 (p0) cc_final: 0.8093 (p0) REVERT: O 95 TYR cc_start: 0.8008 (t80) cc_final: 0.6413 (t80) REVERT: P 6 ASP cc_start: 0.8152 (t0) cc_final: 0.7920 (t0) REVERT: P 18 ASN cc_start: 0.9073 (m110) cc_final: 0.8871 (m110) REVERT: P 49 SER cc_start: 0.9137 (m) cc_final: 0.8556 (p) REVERT: P 95 TYR cc_start: 0.6906 (t80) cc_final: 0.6410 (t80) outliers start: 41 outliers final: 25 residues processed: 402 average time/residue: 0.2771 time to fit residues: 158.1180 Evaluate side-chains 387 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 356 time to evaluate : 1.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 GLU Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 61 ILE Chi-restraints excluded: chain J residue 54 ARG Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain A residue 138 CYS Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 24 MET Chi-restraints excluded: chain B residue 95 MET Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 147 GLU Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 24 MET Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain G residue 9 THR Chi-restraints excluded: chain I residue 39 ASP Chi-restraints excluded: chain I residue 41 GLN Chi-restraints excluded: chain L residue 12 THR Chi-restraints excluded: chain L residue 17 VAL Chi-restraints excluded: chain M residue 83 ASP Chi-restraints excluded: chain N residue 82 VAL Chi-restraints excluded: chain P residue 10 LYS Chi-restraints excluded: chain P residue 55 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 54 optimal weight: 2.9990 chunk 146 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 162 optimal weight: 8.9990 chunk 134 optimal weight: 0.0570 chunk 75 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 85 optimal weight: 0.7980 overall best weight: 0.7500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 2 GLN K 60 ASN A 187 GLN D 111 HIS ** E 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 2 GLN L 25 ASN M 21 ASN ** O 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14312 Z= 0.181 Angle : 0.572 9.621 19395 Z= 0.295 Chirality : 0.041 0.172 2255 Planarity : 0.004 0.047 2497 Dihedral : 4.599 48.384 1914 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.77 % Allowed : 21.09 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.21), residues: 1729 helix: 0.37 (0.17), residues: 1033 sheet: -1.33 (0.36), residues: 193 loop : 0.68 (0.30), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP O 56 HIS 0.007 0.001 HIS C 111 PHE 0.014 0.001 PHE C 107 TYR 0.031 0.001 TYR N 95 ARG 0.007 0.000 ARG O 52 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 382 time to evaluate : 1.653 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: H 1 MET cc_start: 0.7501 (ttp) cc_final: 0.7191 (ttm) REVERT: H 18 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.7636 (tm-30) REVERT: H 21 ASP cc_start: 0.8137 (m-30) cc_final: 0.7462 (m-30) REVERT: H 31 GLN cc_start: 0.8581 (tp40) cc_final: 0.8027 (tp40) REVERT: F 41 GLN cc_start: 0.7007 (mt0) cc_final: 0.6749 (mt0) REVERT: F 54 ARG cc_start: 0.7307 (mmt-90) cc_final: 0.7024 (mmt-90) REVERT: F 63 LYS cc_start: 0.9048 (ptpt) cc_final: 0.8773 (pttp) REVERT: F 65 SER cc_start: 0.8511 (m) cc_final: 0.8256 (m) REVERT: J 18 GLU cc_start: 0.8761 (mp0) cc_final: 0.8270 (mp0) REVERT: J 21 ASP cc_start: 0.7869 (m-30) cc_final: 0.6811 (m-30) REVERT: J 31 GLN cc_start: 0.8929 (tm-30) cc_final: 0.8592 (tp40) REVERT: A 138 CYS cc_start: 0.8901 (OUTLIER) cc_final: 0.8316 (m) REVERT: A 187 GLN cc_start: 0.8634 (OUTLIER) cc_final: 0.8282 (mt0) REVERT: B 8 ASP cc_start: 0.7933 (t70) cc_final: 0.7628 (t0) REVERT: B 23 LYS cc_start: 0.9038 (ptmt) cc_final: 0.8764 (ptpp) REVERT: B 95 MET cc_start: 0.8526 (OUTLIER) cc_final: 0.8320 (mmp) REVERT: B 101 ASP cc_start: 0.8327 (t0) cc_final: 0.7877 (t0) REVERT: B 118 LEU cc_start: 0.8295 (OUTLIER) cc_final: 0.7924 (tt) REVERT: B 127 ASP cc_start: 0.8241 (m-30) cc_final: 0.7911 (m-30) REVERT: B 147 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.8150 (tp30) REVERT: B 170 ARG cc_start: 0.7972 (mmt90) cc_final: 0.7741 (mmt90) REVERT: C 127 ASP cc_start: 0.8407 (t70) cc_final: 0.7599 (t0) REVERT: C 166 GLU cc_start: 0.8363 (mm-30) cc_final: 0.7833 (tp30) REVERT: D 13 TYR cc_start: 0.8423 (t80) cc_final: 0.8214 (t80) REVERT: D 41 GLU cc_start: 0.8181 (tm-30) cc_final: 0.7805 (tm-30) REVERT: D 112 ASP cc_start: 0.8467 (t0) cc_final: 0.8127 (t0) REVERT: E 4 PHE cc_start: 0.7472 (m-80) cc_final: 0.7180 (m-80) REVERT: E 48 LYS cc_start: 0.8676 (tttp) cc_final: 0.8208 (tptt) REVERT: E 51 GLU cc_start: 0.8150 (tp30) cc_final: 0.7875 (tp30) REVERT: G 2 GLN cc_start: 0.7843 (OUTLIER) cc_final: 0.7265 (pp30) REVERT: G 6 LYS cc_start: 0.8407 (mtpp) cc_final: 0.8155 (mtpp) REVERT: G 24 GLU cc_start: 0.8993 (mm-30) cc_final: 0.8550 (mm-30) REVERT: G 54 ARG cc_start: 0.8740 (mmm-85) cc_final: 0.8482 (mmm-85) REVERT: G 72 ARG cc_start: 0.7764 (mtm110) cc_final: 0.7282 (mtp-110) REVERT: I 1 MET cc_start: 0.7558 (tpt) cc_final: 0.7253 (tpt) REVERT: I 41 GLN cc_start: 0.7615 (OUTLIER) cc_final: 0.6818 (pm20) REVERT: I 54 ARG cc_start: 0.7663 (ttm-80) cc_final: 0.7041 (tpp80) REVERT: L 40 GLN cc_start: 0.8415 (mm-40) cc_final: 0.7800 (mp10) REVERT: L 51 GLU cc_start: 0.6407 (mp0) cc_final: 0.5838 (mp0) REVERT: L 64 GLU cc_start: 0.8484 (tm-30) cc_final: 0.7947 (tm-30) REVERT: M 14 ARG cc_start: 0.7956 (mtm110) cc_final: 0.7590 (ttp80) REVERT: N 1 MET cc_start: 0.5840 (tpp) cc_final: 0.5371 (tpp) REVERT: N 11 TYR cc_start: 0.8334 (t80) cc_final: 0.8049 (t80) REVERT: N 86 ASP cc_start: 0.8305 (p0) cc_final: 0.8076 (p0) REVERT: O 40 ASP cc_start: 0.8456 (m-30) cc_final: 0.8180 (m-30) REVERT: O 95 TYR cc_start: 0.7961 (t80) cc_final: 0.6727 (t80) REVERT: P 6 ASP cc_start: 0.8091 (t0) cc_final: 0.7859 (t0) REVERT: P 49 SER cc_start: 0.9136 (m) cc_final: 0.8570 (p) REVERT: P 95 TYR cc_start: 0.6983 (t80) cc_final: 0.6561 (t80) outliers start: 43 outliers final: 25 residues processed: 407 average time/residue: 0.2778 time to fit residues: 160.0708 Evaluate side-chains 391 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 358 time to evaluate : 1.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 GLU Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 61 ILE Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain A residue 138 CYS Chi-restraints excluded: chain A residue 187 GLN Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 24 MET Chi-restraints excluded: chain B residue 95 MET Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 147 GLU Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 24 MET Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain G residue 2 GLN Chi-restraints excluded: chain G residue 9 THR Chi-restraints excluded: chain I residue 39 ASP Chi-restraints excluded: chain I residue 41 GLN Chi-restraints excluded: chain L residue 12 THR Chi-restraints excluded: chain L residue 14 THR Chi-restraints excluded: chain M residue 83 ASP Chi-restraints excluded: chain P residue 10 LYS Chi-restraints excluded: chain P residue 17 SER Chi-restraints excluded: chain P residue 55 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 156 optimal weight: 5.9990 chunk 18 optimal weight: 0.9990 chunk 92 optimal weight: 5.9990 chunk 118 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 136 optimal weight: 5.9990 chunk 90 optimal weight: 0.9980 chunk 161 optimal weight: 0.4980 chunk 101 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 2 GLN ** E 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 2 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14312 Z= 0.204 Angle : 0.575 7.644 19395 Z= 0.296 Chirality : 0.042 0.165 2255 Planarity : 0.004 0.045 2497 Dihedral : 4.535 48.811 1914 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.70 % Allowed : 22.44 % Favored : 74.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.21), residues: 1729 helix: 0.48 (0.17), residues: 1030 sheet: -1.27 (0.36), residues: 193 loop : 0.66 (0.30), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP O 56 HIS 0.007 0.001 HIS C 111 PHE 0.015 0.001 PHE C 107 TYR 0.026 0.001 TYR N 95 ARG 0.007 0.000 ARG H 54 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 369 time to evaluate : 2.111 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: H 1 MET cc_start: 0.7577 (ttp) cc_final: 0.7360 (ttm) REVERT: H 18 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.7644 (tm-30) REVERT: H 21 ASP cc_start: 0.8144 (m-30) cc_final: 0.7471 (m-30) REVERT: F 41 GLN cc_start: 0.6986 (mt0) cc_final: 0.6751 (mt0) REVERT: F 54 ARG cc_start: 0.7248 (mmt-90) cc_final: 0.6965 (mmt-90) REVERT: F 63 LYS cc_start: 0.9030 (ptpt) cc_final: 0.8753 (pttp) REVERT: F 65 SER cc_start: 0.8514 (m) cc_final: 0.8294 (m) REVERT: J 18 GLU cc_start: 0.8783 (mp0) cc_final: 0.8163 (mp0) REVERT: J 21 ASP cc_start: 0.7860 (m-30) cc_final: 0.6714 (m-30) REVERT: J 31 GLN cc_start: 0.8937 (tm-30) cc_final: 0.8587 (tp40) REVERT: A 24 MET cc_start: 0.8876 (ptp) cc_final: 0.8578 (ptp) REVERT: A 138 CYS cc_start: 0.8899 (OUTLIER) cc_final: 0.8421 (m) REVERT: B 8 ASP cc_start: 0.7936 (t70) cc_final: 0.7653 (t0) REVERT: B 23 LYS cc_start: 0.9037 (ptmt) cc_final: 0.8763 (ptpp) REVERT: B 101 ASP cc_start: 0.8315 (t0) cc_final: 0.7858 (t0) REVERT: B 118 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.7899 (tt) REVERT: B 127 ASP cc_start: 0.8274 (m-30) cc_final: 0.7927 (m-30) REVERT: B 147 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.8185 (tp30) REVERT: B 170 ARG cc_start: 0.7978 (mmt90) cc_final: 0.7706 (mmt-90) REVERT: C 127 ASP cc_start: 0.8408 (t70) cc_final: 0.8036 (t0) REVERT: C 166 GLU cc_start: 0.8380 (mm-30) cc_final: 0.7797 (mm-30) REVERT: D 41 GLU cc_start: 0.8192 (tm-30) cc_final: 0.7810 (tm-30) REVERT: D 112 ASP cc_start: 0.8460 (t0) cc_final: 0.8143 (t0) REVERT: E 4 PHE cc_start: 0.7482 (m-80) cc_final: 0.7211 (m-80) REVERT: E 48 LYS cc_start: 0.8693 (tttp) cc_final: 0.8234 (tptt) REVERT: E 51 GLU cc_start: 0.8187 (tp30) cc_final: 0.7856 (tp30) REVERT: G 2 GLN cc_start: 0.8057 (OUTLIER) cc_final: 0.7831 (tm-30) REVERT: G 6 LYS cc_start: 0.8414 (mtpp) cc_final: 0.8143 (mtpp) REVERT: G 29 LYS cc_start: 0.8663 (mttp) cc_final: 0.8195 (mttp) REVERT: G 72 ARG cc_start: 0.7800 (mtm110) cc_final: 0.7321 (mtp-110) REVERT: I 1 MET cc_start: 0.7565 (tpt) cc_final: 0.7288 (tpt) REVERT: I 41 GLN cc_start: 0.7633 (OUTLIER) cc_final: 0.6849 (pm20) REVERT: I 54 ARG cc_start: 0.7723 (ttm-80) cc_final: 0.7050 (tpp80) REVERT: L 40 GLN cc_start: 0.8470 (mm-40) cc_final: 0.7954 (mp10) REVERT: L 51 GLU cc_start: 0.6435 (mp0) cc_final: 0.5827 (mp0) REVERT: L 62 GLN cc_start: 0.8398 (mp10) cc_final: 0.8046 (mp10) REVERT: L 64 GLU cc_start: 0.8464 (tm-30) cc_final: 0.7905 (tm-30) REVERT: M 14 ARG cc_start: 0.7951 (mtm110) cc_final: 0.7620 (ttp80) REVERT: N 11 TYR cc_start: 0.8330 (t80) cc_final: 0.8058 (t80) REVERT: N 86 ASP cc_start: 0.8297 (p0) cc_final: 0.8071 (p0) REVERT: O 40 ASP cc_start: 0.8456 (m-30) cc_final: 0.8177 (m-30) REVERT: P 49 SER cc_start: 0.9134 (m) cc_final: 0.8568 (p) REVERT: P 95 TYR cc_start: 0.6987 (t80) cc_final: 0.6532 (t80) outliers start: 42 outliers final: 24 residues processed: 395 average time/residue: 0.2692 time to fit residues: 151.5408 Evaluate side-chains 388 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 358 time to evaluate : 1.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 GLU Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 61 ILE Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain A residue 138 CYS Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 24 MET Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 147 GLU Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 24 MET Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain G residue 2 GLN Chi-restraints excluded: chain G residue 9 THR Chi-restraints excluded: chain I residue 39 ASP Chi-restraints excluded: chain I residue 41 GLN Chi-restraints excluded: chain L residue 12 THR Chi-restraints excluded: chain M residue 82 VAL Chi-restraints excluded: chain M residue 83 ASP Chi-restraints excluded: chain N residue 82 VAL Chi-restraints excluded: chain P residue 17 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 100 optimal weight: 10.0000 chunk 64 optimal weight: 0.7980 chunk 96 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 102 optimal weight: 0.3980 chunk 110 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 15 optimal weight: 8.9990 chunk 127 optimal weight: 3.9990 chunk 147 optimal weight: 4.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 2 GLN A 187 GLN ** E 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 2 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14312 Z= 0.229 Angle : 0.595 9.287 19395 Z= 0.303 Chirality : 0.042 0.170 2255 Planarity : 0.004 0.043 2497 Dihedral : 4.519 48.808 1914 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.64 % Allowed : 22.44 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.21), residues: 1729 helix: 0.50 (0.17), residues: 1031 sheet: -1.18 (0.36), residues: 193 loop : 0.61 (0.29), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP O 56 HIS 0.007 0.001 HIS A 111 PHE 0.016 0.001 PHE G 4 TYR 0.041 0.001 TYR N 95 ARG 0.007 0.000 ARG H 54 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 371 time to evaluate : 2.038 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: H 1 MET cc_start: 0.7587 (ttp) cc_final: 0.7382 (ttm) REVERT: H 18 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.7647 (tm-30) REVERT: H 21 ASP cc_start: 0.8159 (m-30) cc_final: 0.7480 (m-30) REVERT: F 41 GLN cc_start: 0.6945 (mt0) cc_final: 0.6719 (mt0) REVERT: F 54 ARG cc_start: 0.7266 (mmt-90) cc_final: 0.6652 (mmt-90) REVERT: F 63 LYS cc_start: 0.9022 (ptpt) cc_final: 0.8741 (pttp) REVERT: F 65 SER cc_start: 0.8508 (m) cc_final: 0.8275 (m) REVERT: J 18 GLU cc_start: 0.8796 (mp0) cc_final: 0.8167 (mp0) REVERT: J 21 ASP cc_start: 0.7874 (m-30) cc_final: 0.6586 (m-30) REVERT: J 31 GLN cc_start: 0.8941 (tm-30) cc_final: 0.8575 (tp40) REVERT: B 8 ASP cc_start: 0.7929 (t70) cc_final: 0.7640 (t0) REVERT: B 23 LYS cc_start: 0.9040 (ptmt) cc_final: 0.8781 (ptpp) REVERT: B 101 ASP cc_start: 0.8323 (t0) cc_final: 0.7857 (t0) REVERT: B 118 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.7903 (tt) REVERT: B 127 ASP cc_start: 0.8271 (m-30) cc_final: 0.7925 (m-30) REVERT: B 147 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.8208 (tp30) REVERT: B 170 ARG cc_start: 0.7960 (mmt90) cc_final: 0.7461 (mmt180) REVERT: C 127 ASP cc_start: 0.8401 (t70) cc_final: 0.8028 (t0) REVERT: C 166 GLU cc_start: 0.8423 (mm-30) cc_final: 0.7778 (tp30) REVERT: D 41 GLU cc_start: 0.8208 (tm-30) cc_final: 0.7824 (tm-30) REVERT: D 112 ASP cc_start: 0.8486 (t0) cc_final: 0.8171 (t0) REVERT: E 4 PHE cc_start: 0.7479 (m-80) cc_final: 0.7226 (m-80) REVERT: E 48 LYS cc_start: 0.8701 (tttp) cc_final: 0.8241 (tptt) REVERT: E 51 GLU cc_start: 0.8220 (tp30) cc_final: 0.7818 (tp30) REVERT: G 24 GLU cc_start: 0.8973 (mm-30) cc_final: 0.8600 (mm-30) REVERT: G 72 ARG cc_start: 0.7792 (mtm110) cc_final: 0.7313 (mtp-110) REVERT: I 1 MET cc_start: 0.7631 (tpt) cc_final: 0.7351 (tpt) REVERT: I 41 GLN cc_start: 0.7744 (OUTLIER) cc_final: 0.6852 (pm20) REVERT: I 54 ARG cc_start: 0.7691 (ttm-80) cc_final: 0.7053 (tpp80) REVERT: L 40 GLN cc_start: 0.8459 (mm-40) cc_final: 0.7957 (mp10) REVERT: L 51 GLU cc_start: 0.6439 (mp0) cc_final: 0.5809 (mp0) REVERT: L 62 GLN cc_start: 0.8368 (mp10) cc_final: 0.8029 (mp10) REVERT: L 64 GLU cc_start: 0.8456 (tm-30) cc_final: 0.7889 (tm-30) REVERT: M 14 ARG cc_start: 0.7960 (mtm110) cc_final: 0.7628 (ttp80) REVERT: N 1 MET cc_start: 0.5639 (tpp) cc_final: 0.5045 (tpp) REVERT: N 11 TYR cc_start: 0.8335 (t80) cc_final: 0.8054 (t80) REVERT: N 86 ASP cc_start: 0.8291 (p0) cc_final: 0.8072 (p0) REVERT: O 40 ASP cc_start: 0.8455 (m-30) cc_final: 0.8216 (m-30) REVERT: P 49 SER cc_start: 0.9130 (m) cc_final: 0.8559 (p) REVERT: P 95 TYR cc_start: 0.7034 (t80) cc_final: 0.6488 (t80) outliers start: 41 outliers final: 27 residues processed: 395 average time/residue: 0.2758 time to fit residues: 155.6941 Evaluate side-chains 392 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 361 time to evaluate : 1.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 GLU Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 61 ILE Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain A residue 138 CYS Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 24 MET Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 147 GLU Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 24 MET Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain G residue 9 THR Chi-restraints excluded: chain I residue 39 ASP Chi-restraints excluded: chain I residue 41 GLN Chi-restraints excluded: chain L residue 12 THR Chi-restraints excluded: chain M residue 82 VAL Chi-restraints excluded: chain M residue 83 ASP Chi-restraints excluded: chain N residue 82 VAL Chi-restraints excluded: chain P residue 17 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 155 optimal weight: 0.8980 chunk 141 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 chunk 90 optimal weight: 0.6980 chunk 65 optimal weight: 0.5980 chunk 118 optimal weight: 7.9990 chunk 46 optimal weight: 6.9990 chunk 136 optimal weight: 4.9990 chunk 142 optimal weight: 0.8980 chunk 99 optimal weight: 0.6980 chunk 159 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 2 GLN ** E 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.3127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14312 Z= 0.184 Angle : 0.587 8.902 19395 Z= 0.301 Chirality : 0.041 0.165 2255 Planarity : 0.004 0.042 2497 Dihedral : 4.470 49.296 1914 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.12 % Allowed : 23.34 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.21), residues: 1729 helix: 0.60 (0.17), residues: 1032 sheet: -1.09 (0.37), residues: 193 loop : 0.64 (0.30), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP M 56 HIS 0.006 0.001 HIS C 111 PHE 0.014 0.001 PHE C 107 TYR 0.040 0.001 TYR N 95 ARG 0.007 0.000 ARG O 41 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 380 time to evaluate : 1.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 18 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.7634 (tm-30) REVERT: H 21 ASP cc_start: 0.8054 (m-30) cc_final: 0.7291 (m-30) REVERT: F 41 GLN cc_start: 0.6908 (mt0) cc_final: 0.6693 (mt0) REVERT: F 54 ARG cc_start: 0.7277 (mmt-90) cc_final: 0.6976 (mmt-90) REVERT: F 63 LYS cc_start: 0.8981 (ptpt) cc_final: 0.8690 (pttp) REVERT: F 65 SER cc_start: 0.8465 (m) cc_final: 0.8261 (m) REVERT: J 18 GLU cc_start: 0.8809 (mp0) cc_final: 0.8155 (mp0) REVERT: J 21 ASP cc_start: 0.7862 (m-30) cc_final: 0.6562 (m-30) REVERT: J 31 GLN cc_start: 0.8943 (tm-30) cc_final: 0.8590 (tp40) REVERT: B 8 ASP cc_start: 0.7884 (t70) cc_final: 0.7615 (t0) REVERT: B 23 LYS cc_start: 0.9036 (ptmt) cc_final: 0.8769 (ptpp) REVERT: B 60 GLU cc_start: 0.8416 (tm-30) cc_final: 0.8186 (tm-30) REVERT: B 101 ASP cc_start: 0.8291 (t0) cc_final: 0.7825 (t0) REVERT: B 118 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.7884 (tt) REVERT: B 127 ASP cc_start: 0.8281 (m-30) cc_final: 0.7931 (m-30) REVERT: B 147 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.8216 (tp30) REVERT: B 170 ARG cc_start: 0.7988 (mmt90) cc_final: 0.7488 (mmt180) REVERT: C 127 ASP cc_start: 0.8367 (t70) cc_final: 0.7985 (t0) REVERT: C 147 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7503 (tp30) REVERT: D 41 GLU cc_start: 0.8195 (tm-30) cc_final: 0.7801 (tm-30) REVERT: D 112 ASP cc_start: 0.8458 (t0) cc_final: 0.8133 (t0) REVERT: E 4 PHE cc_start: 0.7414 (m-80) cc_final: 0.7133 (m-80) REVERT: E 48 LYS cc_start: 0.8717 (tttp) cc_final: 0.8253 (tptt) REVERT: E 51 GLU cc_start: 0.8225 (tp30) cc_final: 0.7776 (tp30) REVERT: E 57 SER cc_start: 0.8988 (OUTLIER) cc_final: 0.8617 (p) REVERT: G 18 GLU cc_start: 0.8350 (mp0) cc_final: 0.7441 (mp0) REVERT: G 51 GLU cc_start: 0.8304 (tt0) cc_final: 0.8103 (tt0) REVERT: G 72 ARG cc_start: 0.7774 (mtm110) cc_final: 0.7308 (mtp-110) REVERT: I 1 MET cc_start: 0.7468 (tpt) cc_final: 0.7090 (tpt) REVERT: I 41 GLN cc_start: 0.7739 (OUTLIER) cc_final: 0.6848 (pm20) REVERT: I 54 ARG cc_start: 0.7764 (ttm-80) cc_final: 0.7173 (tpp80) REVERT: L 40 GLN cc_start: 0.8342 (mm-40) cc_final: 0.7879 (mp10) REVERT: L 51 GLU cc_start: 0.6357 (mp0) cc_final: 0.5722 (mp0) REVERT: L 62 GLN cc_start: 0.8373 (mp10) cc_final: 0.8041 (mp10) REVERT: L 64 GLU cc_start: 0.8440 (tm-30) cc_final: 0.7849 (tm-30) REVERT: M 14 ARG cc_start: 0.7935 (mtm110) cc_final: 0.7605 (ttp80) REVERT: N 1 MET cc_start: 0.5728 (tpp) cc_final: 0.5165 (tpp) REVERT: N 11 TYR cc_start: 0.8316 (t80) cc_final: 0.8076 (t80) REVERT: N 86 ASP cc_start: 0.8314 (p0) cc_final: 0.8096 (p0) REVERT: O 40 ASP cc_start: 0.8472 (m-30) cc_final: 0.8218 (m-30) REVERT: P 49 SER cc_start: 0.9129 (m) cc_final: 0.8569 (p) REVERT: P 95 TYR cc_start: 0.6988 (t80) cc_final: 0.6513 (t80) outliers start: 33 outliers final: 21 residues processed: 400 average time/residue: 0.2692 time to fit residues: 154.0898 Evaluate side-chains 393 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 366 time to evaluate : 1.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 GLU Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain F residue 61 ILE Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain A residue 138 CYS Chi-restraints excluded: chain B residue 24 MET Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 147 GLU Chi-restraints excluded: chain C residue 24 MET Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 147 GLU Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain G residue 9 THR Chi-restraints excluded: chain I residue 39 ASP Chi-restraints excluded: chain I residue 41 GLN Chi-restraints excluded: chain L residue 12 THR Chi-restraints excluded: chain M residue 82 VAL Chi-restraints excluded: chain M residue 83 ASP Chi-restraints excluded: chain N residue 82 VAL Chi-restraints excluded: chain P residue 17 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 97 optimal weight: 1.9990 chunk 75 optimal weight: 0.2980 chunk 110 optimal weight: 0.8980 chunk 167 optimal weight: 3.9990 chunk 154 optimal weight: 3.9990 chunk 133 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 102 optimal weight: 0.7980 chunk 81 optimal weight: 9.9990 chunk 105 optimal weight: 0.8980 chunk 141 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 41 GLN K 2 GLN ** E 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 14312 Z= 0.200 Angle : 0.595 9.161 19395 Z= 0.305 Chirality : 0.042 0.303 2255 Planarity : 0.004 0.043 2497 Dihedral : 4.485 49.140 1914 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.25 % Allowed : 23.86 % Favored : 73.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.21), residues: 1729 helix: 0.66 (0.17), residues: 1032 sheet: -1.03 (0.37), residues: 194 loop : 0.63 (0.30), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP O 56 HIS 0.006 0.001 HIS C 111 PHE 0.014 0.001 PHE C 107 TYR 0.037 0.001 TYR N 95 ARG 0.007 0.000 ARG O 41 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 365 time to evaluate : 1.600 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: H 18 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.7673 (tm-30) REVERT: H 21 ASP cc_start: 0.8022 (m-30) cc_final: 0.7282 (m-30) REVERT: H 31 GLN cc_start: 0.8535 (tp40) cc_final: 0.7922 (tp40) REVERT: H 54 ARG cc_start: 0.8362 (mmt-90) cc_final: 0.7992 (mmt-90) REVERT: F 41 GLN cc_start: 0.6912 (mt0) cc_final: 0.6695 (mt0) REVERT: F 54 ARG cc_start: 0.7276 (mmt-90) cc_final: 0.6653 (mmt-90) REVERT: F 63 LYS cc_start: 0.8967 (ptpt) cc_final: 0.8674 (pttp) REVERT: F 65 SER cc_start: 0.8479 (m) cc_final: 0.8271 (m) REVERT: J 18 GLU cc_start: 0.8796 (mp0) cc_final: 0.8138 (mp0) REVERT: J 21 ASP cc_start: 0.7866 (m-30) cc_final: 0.6555 (m-30) REVERT: J 31 GLN cc_start: 0.8965 (tm-30) cc_final: 0.8587 (tp40) REVERT: J 51 GLU cc_start: 0.7312 (tt0) cc_final: 0.6926 (mm-30) REVERT: K 14 THR cc_start: 0.8333 (m) cc_final: 0.8002 (t) REVERT: K 41 GLN cc_start: 0.7848 (OUTLIER) cc_final: 0.7620 (mp10) REVERT: B 8 ASP cc_start: 0.7880 (t70) cc_final: 0.7623 (t0) REVERT: B 23 LYS cc_start: 0.9018 (ptmt) cc_final: 0.8744 (ptpp) REVERT: B 60 GLU cc_start: 0.8478 (tm-30) cc_final: 0.8232 (tm-30) REVERT: B 101 ASP cc_start: 0.8290 (t0) cc_final: 0.7819 (t0) REVERT: B 118 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.7881 (tt) REVERT: B 127 ASP cc_start: 0.8245 (m-30) cc_final: 0.7908 (m-30) REVERT: B 147 GLU cc_start: 0.8602 (OUTLIER) cc_final: 0.8247 (tp30) REVERT: B 170 ARG cc_start: 0.7987 (mmt90) cc_final: 0.7513 (mmt180) REVERT: C 127 ASP cc_start: 0.8363 (t70) cc_final: 0.7984 (t0) REVERT: C 147 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7486 (tp30) REVERT: D 41 GLU cc_start: 0.8201 (tm-30) cc_final: 0.7803 (tm-30) REVERT: D 56 MET cc_start: 0.7726 (OUTLIER) cc_final: 0.7500 (mtp) REVERT: D 112 ASP cc_start: 0.8457 (t0) cc_final: 0.8146 (t0) REVERT: E 4 PHE cc_start: 0.7409 (m-80) cc_final: 0.7118 (m-80) REVERT: E 33 LYS cc_start: 0.7437 (ptpt) cc_final: 0.6933 (pttm) REVERT: E 48 LYS cc_start: 0.8717 (tttp) cc_final: 0.8256 (tptt) REVERT: E 51 GLU cc_start: 0.8247 (tp30) cc_final: 0.7750 (tp30) REVERT: E 57 SER cc_start: 0.8942 (OUTLIER) cc_final: 0.8546 (p) REVERT: G 51 GLU cc_start: 0.8330 (tt0) cc_final: 0.8127 (tt0) REVERT: G 72 ARG cc_start: 0.7781 (mtm110) cc_final: 0.7067 (mtp-110) REVERT: I 1 MET cc_start: 0.7504 (tpt) cc_final: 0.7203 (tpt) REVERT: I 41 GLN cc_start: 0.7745 (OUTLIER) cc_final: 0.6855 (pm20) REVERT: I 54 ARG cc_start: 0.7781 (ttm-80) cc_final: 0.7176 (tpp80) REVERT: L 40 GLN cc_start: 0.8341 (mm-40) cc_final: 0.7897 (mp10) REVERT: L 51 GLU cc_start: 0.6325 (mp0) cc_final: 0.5662 (mp0) REVERT: L 62 GLN cc_start: 0.8371 (mp10) cc_final: 0.8046 (mp10) REVERT: L 64 GLU cc_start: 0.8416 (tm-30) cc_final: 0.7796 (tm-30) REVERT: M 14 ARG cc_start: 0.7938 (mtm110) cc_final: 0.7606 (ttp80) REVERT: N 11 TYR cc_start: 0.8311 (t80) cc_final: 0.8034 (t80) REVERT: N 86 ASP cc_start: 0.8307 (p0) cc_final: 0.8099 (p0) REVERT: O 40 ASP cc_start: 0.8466 (m-30) cc_final: 0.8210 (m-30) REVERT: P 49 SER cc_start: 0.9138 (m) cc_final: 0.8589 (p) REVERT: P 95 TYR cc_start: 0.6984 (t80) cc_final: 0.6519 (t80) outliers start: 35 outliers final: 21 residues processed: 386 average time/residue: 0.2808 time to fit residues: 156.1656 Evaluate side-chains 389 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 360 time to evaluate : 2.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 GLU Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain K residue 41 GLN Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain A residue 138 CYS Chi-restraints excluded: chain B residue 24 MET Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 147 GLU Chi-restraints excluded: chain C residue 24 MET Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 147 GLU Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 56 MET Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain G residue 9 THR Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain I residue 39 ASP Chi-restraints excluded: chain I residue 41 GLN Chi-restraints excluded: chain L residue 12 THR Chi-restraints excluded: chain M residue 82 VAL Chi-restraints excluded: chain M residue 83 ASP Chi-restraints excluded: chain N residue 82 VAL Chi-restraints excluded: chain P residue 17 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 40 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 19 optimal weight: 6.9990 chunk 37 optimal weight: 5.9990 chunk 133 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 137 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 117 optimal weight: 6.9990 chunk 7 optimal weight: 10.0000 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 41 GLN K 2 GLN A 187 GLN ** G 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.094338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.074505 restraints weight = 29995.111| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 2.63 r_work: 0.2928 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2935 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2935 r_free = 0.2935 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2925 r_free = 0.2925 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2925 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 14312 Z= 0.302 Angle : 0.629 9.143 19395 Z= 0.320 Chirality : 0.044 0.204 2255 Planarity : 0.004 0.043 2497 Dihedral : 4.559 48.627 1914 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.51 % Allowed : 24.12 % Favored : 73.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.21), residues: 1729 helix: 0.60 (0.17), residues: 1035 sheet: -1.10 (0.37), residues: 196 loop : 0.68 (0.30), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 177 HIS 0.007 0.001 HIS A 111 PHE 0.015 0.001 PHE C 107 TYR 0.037 0.001 TYR N 95 ARG 0.007 0.000 ARG O 41 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3500.51 seconds wall clock time: 64 minutes 2.06 seconds (3842.06 seconds total)